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. 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") > 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 special, but that might be outdated...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 <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.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 >>>> 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel