Thanks for the update Ramon,
I believe that in my case \link{foo} will not work, because e.g. the pickPeaks
method is defined in ProtGenerics, but I want to link to the implementation in
MSnbase.
I'm with Martin proposing this should be a NOTE rather than a WARNING
(https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002622.html)
jo
> On 16 Apr 2018, at 17:41, Ramon Diaz-Uriarte <rdia...@gmail.com> wrote:
>
>
> 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
>
> Email: rdia...@gmail.com
> ramon.d...@iib.uam.es
>
> http://ligarto.org/rdiaz
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