Dear Martin,
On Mon, 09-April-2018, at 17:35:47, Martin Maechler <maech...@stat.math.ethz.ch> wrote: >>>>>> Ramon Diaz-Uriarte <rdia...@gmail.com> >>>>>> on Mon, 9 Apr 2018 16:51:38 +0200 writes: > > > 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") > > Only on Windows, indeed, > mclapply() is just a dummy function, calling lapply() IIRC. > > It is unfortunate that given the above you would be lead to use > different \link{}s if you are on Windows than on non-Win... > > This would be a good question on the R-package-devel mailing > list. > Done (https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html). Thanks, R. > 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 Windows is special, but that might be outdated...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 > >> > >> 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 -- 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