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

Mon Apr 9 17:23:22 CEST 2018

On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote:
> 
> 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.

yeah, this is a pretty good one. If you look at

   https://github.com/wch/r-source/tree/trunk/src/library/parallel/man

you'll see that there are different man pages for different operating 
systems. On windows there is mcdummies, on unix mclapply & friends. This 
seems like a bad idea (users comparing notes to work through a problem 
get different help pages!). I don't really know how to link explicitly 
to these in a conditional manner.

And in general it seems highly fragile to link to the name of the help 
page, rather than to the alias. I'd treat the 'warning' as (maybe bad) 
advice, rather than a requirement.

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

it does (but on windows there is no mclapply.html). But also on windows 
the '...treated as a topic' part of the warning actually indicates that 
R has figured out where it should link, so you get the warning but also 
a working link.

> 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")

yes the first pass should also be the simplest -- no fancy markup unless 
necessary.

Martin

> 
> 
>> 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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>>>
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>>
>>
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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
> 

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