On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan < 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> 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. >> > > 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. > 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} > > 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 <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> >>>>> 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 Autónoma de Madrid >>>>>> Arzobispo Morcillo, 4 >>>>>> 28029 Madrid >>>>>> Spain >>>>>> >>>>>> Phone: +34-91-497-2412 >>>>>> >>>>>> Email: rdia...@gmail.com >>>>>> ramon.d...@iib.uam.es >>>>>> >>>>>> http://ligarto.org/rdiaz >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-devel@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>>> >>>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@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@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: rdia...@gmail.com >> ramon.d...@iib.uam.es >> >> http://ligarto.org/rdiaz >> >> > > This email message may contain legally privileged and/or confidential > information. 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