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

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> wrote:

On 04/06/2018 10:44 AM, Llu?s 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.

yeah, this is a pretty good one. If you look at

  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.

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/cbd7ca1b1aedf0405e11e
e2440fbde891cba524e

    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.INSTALL2
3343f935731/

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 Aut?noma 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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--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Aut?noma 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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