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

[Rainer Johannes]

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 <rdiaz02 at 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.Shepherd at 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-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
>>>> 
>>>> _______________________________________________
>>>> Bioc-devel at 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: rdiaz02 at gmail.com
>       ramon.diaz at iib.uam.es
> 
> http://ligarto.org/rdiaz