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

Wed Apr 18 20:45:11 CEST 2018

On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

>
>
> 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.
>

Does this mean that to cross-reference to MArrayLM-class, I need to find
limma source and
determine that the topic is covered in marraylm.Rd and use
\link[limma:marraylm]{MArrayLM-class} for
the cross-reference?  I don't see how this is good -- are the page names
programmatically accessible
to developers who want to cross-reference?  here's the grep result:

marraylm.Rd:\alias{MArrayLM-class}

>
> 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/cbd7ca1b1aedf0405e11e
>>> e2440fbde891cba524e
>>>
>>>     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.INSTALL2
>>>>>> 3343f935731/
>>>>>>
>>>>> 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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>>>>>
>>>>> _______________________________________________
>>>>> 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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>>>
>>> _______________________________________________
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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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