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

[Martin Maechler]

>>>>> 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.

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 Windows is special, but that might be outdated...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
    >>>>> 
    >>>> 
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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

    > _______________________________________________
    > Bioc-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/bioc-devel