[Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "
Ramon Diaz-Uriarte
rdiaz02 at gmail.com
Thu Apr 19 11:28:25 CEST 2018
On Wed, 18-April-2018, at 21:09:32, Martin Morgan <martin.morgan at roswellpark.org> wrote:
> On 04/18/2018 02:45 PM, Vincent Carey wrote:
>>
>>
>> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan
>> <martin.morgan at roswellpark.org <mailto: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
>> <mailto: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
>> <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
>> <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}
>
> I agree that this is a bad idea.
>
> I think the first solution is not to use \link[pkg]{foo} when it is not
> needed, which Writing R Extensions
> (https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences)
> says
>
> "These are rarely needed, perhaps to refer to not-yet-installed
> packages (but there the HTML help system will resolve the link at run
> time) or in the normally undesirable event that more than one package
> offers help on a topic"
>
> Packages you depend / import and even suggest will be installed by the
> build system, so the only need is when two or more packages define the
> same topic.
>
> But even then, when faced with a WARNING, and even Bioc core team
> members or reviewers for new packages hassling you about correcting
> WARNINGs, I personally would trade off sanity for perfection and stick
> with \link[limma]{MArrayLM-class} -- there is a WARNING, but the warning
> says that it's going to treat MArrayLM-class as a topic (alias) and
> it'll get resolved correctly.
>
Martin, thanks for the detailed explanation (and the choice of sanity over
perfection :-) ).
Best,
R.
> Also, for what it's worth, the opinion expressed in
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences
> is that the fact that these WARNINGs are often Windows-specific is more
> likely that the linux check is wrong (i.e., the WARNING should also be
> generated there). I will try to investigate that further.
>
> Martin
>
>
>>
>>
>> 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
>> <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
>> <mailto: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 <mailto: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 <mailto:rdiaz02 at gmail.com>
>> ramon.diaz at iib.uam.es <mailto:ramon.diaz at iib.uam.es>
>>
>> http://ligarto.org/rdiaz
>>
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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 <mailto:rdiaz02 at gmail.com>
>> ramon.diaz at iib.uam.es <mailto:ramon.diaz at iib.uam.es>
>>
>> http://ligarto.org/rdiaz
>>
>>
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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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