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

Ramon Diaz-Uriarte rdiaz02 at gmail.com
Mon Apr 16 17:36:56 CEST 2018


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, 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")
>
> 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 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
>     >>>>> 
>     >>>> 
>     >>>> [[alternative HTML version deleted]]
>     >>>> 
>     >>>> _______________________________________________
>     >>>> Bioc-devel at r-project.org mailing list
>     >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>     >>>> 
>     >>> 
>     >>> [[alternative HTML version deleted]]
>     >>> 
>     >>> _______________________________________________
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>     >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>     >>> 
>     >> 
>     >> 
>     >> This email message may contain legally privileged
>     >> and/or...{{dropped:2}}
>     >> 
>     >> _______________________________________________
>     >> 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 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


-- 
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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