[Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

[Martin Morgan]

On 04/06/2018 10:44 AM, Lluís Revilla wrote:
> I have recently faced a similar warning.
> This is when a link to a help page of another package is broken (there is
> not such help page). Although those could be false positives:
> mclapply help page does exists in parallel package.
> as.MAList does exists in devel limma

when \link-ing to another package, from RShowDoc("R-exts") section 2.5 
the [] has to name the html help page, not the name of the function. For 
instance, `mclapply` is documented on a man page called mcdummies.Rd 
(!), so '\link[parallel:mcdummies]{nearest} would presumably not 
generate the warning. Similarly \link[limma:asmalist]{as.MAList}.

There are several things that still need exploration.

- platform-specific (I have a vague understanding that Windows is 
special, but that might be outdated... [at least in this context...])

- recent. I have to admit to changing the text of the warning with this 
commit

 
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e

   but what I was intending to do was to change what it says, from the 
warning in release ('missing file link') to what it says, correctly, in 
devel 'file link ... does not exist and so has been treated as a topic'. 
The old text appears in release, and the new in devel, as anticipated. 
If I messed up somehow please let me know...

- even with the warning, the link isn't broken in the dynamic help 
system (it might have been broken prior to my commit...).

Martin

> 
> HTH
> 
> On 6 April 2018 at 16:35, Vincent Carey <stvjc at channing.harvard.edu> wrote:
> 
>> ive seen this too apropos bigrquery on windows
>>
>> On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte <rdiaz02 at gmail.com>
>> wrote:
>>
>>>
>>> Dear All,
>>>
>>> Two packages I maintain are showing, in Windows, a warning during check
>>> with messages like
>>>
>>> Rd warning:
>>> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp21WlQD/R.INSTALL23343f935731/
>> OncoSimulR/man/oncoSimulIndiv.Rd:570:
>>> file link 'mclapply' in package 'parallel' does not exist and so has been
>>> treated as a topic
>>>
>>> or
>>>
>>> Rd warning:
>>> C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQfQaA1/R.
>> INSTALL1ec81d5b6233/ADaCGH2/man/inputToADaCGH.Rd:45:
>>> file link 'as.MAList' in package 'limma' does not exist and so has been
>>> treated as a topic
>>>
>>>
>>>
>>> that I cannot reproduce under Linux and that I think are false
>>> positives. Is there a way to avoid this warning? As far as I can tell,
>>> those links really exist.
>>>
>>> Best,
>>>
>>>
>>> R.
>>>
>>> --
>>> 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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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>>
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