On 04/18/2018 02:45 PM, Vincent Carey wrote:
On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan
<martin.mor...@roswellpark.org <mailto:martin.mor...@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.mor...@roswellpark.org
<mailto:martin.mor...@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
<st...@channing.harvard.edu
<mailto:st...@channing.harvard.edu>> wrote:
ive seen this too apropos bigrquery on windows
On Fri, Apr 6, 2018 at 10:22 AM Ramon Diaz-Uriarte
<rdia...@gmail.com <mailto:rdia...@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: rdia...@gmail.com <mailto:rdia...@gmail.com>
ramon.d...@iib.uam.es <mailto:ramon.d...@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: rdia...@gmail.com <mailto:rdia...@gmail.com>
ramon.d...@iib.uam.es <mailto:ramon.d...@iib.uam.es>
http://ligarto.org/rdiaz
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