[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 Windows is special, but that might be outdated...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]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> 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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