And I have now asked this in R-pkg-devel
(https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html), as
suggested by Martin Maechler
(https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013169.html) in the
thread linked by Lori.
But if you can use \link{foo} (instead of \link[pkg]{foo} and
\link[pkg:bar]{foo}), as also suggested by Håkon Tjeldnes, then you should
have no problems.
Best,
R.
On Mon, 16-April-2018, at 13:16:54, Shepherd, Lori
<lori.sheph...@roswellpark.org> wrote:
> This was also discussed in this thread a few weeks ago
>
> https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
>
>
>
> 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-boun...@r-project.org> on behalf of Mike Smith
> <grimbo...@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.rai...@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 <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
>> >
>>
>>
>
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--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
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