[Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "
Dear Martin,
On Mon, 09-April-2018, at 17:35:47, Martin Maechler <maechler at stat.math.ethz.ch> wrote:
Ramon Diaz-Uriarte <rdiaz02 at gmail.com>
on Mon, 9 Apr 2018 16:51:38 +0200 writes:
> 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, Llu?s 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:
> 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")
Only on Windows, indeed,
mclapply() is just a dummy function, calling lapply() IIRC.
It is unfortunate that given the above you would be lead to use
different \link{}s if you are on Windows than on non-Win...
This would be a good question on the R-package-devel mailing
list.
Done (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html). Thanks, R.
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 Windows is special, but that might be outdated...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 Aut?noma 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 Aut?noma de Madrid
> Arzobispo Morcillo, 4 28029 Madrid Spain
> Phone: +34-91-497-2412
> Email: rdiaz02 at gmail.com ramon.diaz at iib.uam.es
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Aut?noma 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