[Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "
Martin Morgan
martin.morgan at roswellpark.org
Wed Apr 18 21:09:32 CEST 2018
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.
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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