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

[Ramon Diaz-Uriarte]

Dear Martin,

On Fri, 06-April-2018, at 18:59:00, Martin Morgan <martin.morgan at roswellpark.org> wrote:
> 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

I am confused here: as far as I can tell, there is an mclapply.html file:

http://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mclapply.html

In addition, when I use the \link[parallel:mcdummies] I get a warning when
testing under Linux.

On rereading section 2.5, I think \link[pkg]{foo} should work too (if there
is a foo.html file.)

Nevertheless, section 2.5 indicates that \link[pkg]{foo} and
\link[pkg:bar]{foo} are rarely needed, so I'll try to remove them (except
in those cases, covered in section 2.5, where "more than one package offers
help on a topic")



> 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 special, but that might be outdated...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...])
>

I am only getting the warnings under Windows (which lead me to think it was
windows misbehaving).


> - 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...).

OK, thanks.

Best,


R.


>
> 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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--
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