On Wed, 18-April-2018, at 21:09:32, Martin Morgan <martin.mor...@roswellpark.org> wrote: > 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. >
Martin, thanks for the detailed explanation (and the choice of sanity over perfection :-) ). Best, R. > 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 >> >> _______________________________________________ >> Bioc-devel@r-project.org >> <mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org >> <mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org >> <mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >> >> >> >> This email message may contain legally privileged >> and/or...{{dropped:2}} >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> <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 <mailto:rdia...@gmail.com> >> ramon.d...@iib.uam.es <mailto:ramon.d...@iib.uam.es> >> >> http://ligarto.org/rdiaz >> >> >> >> This email message may contain legally privileged and/or >> confidential information. If you are not the intended recipient(s), >> or the employee or agent responsible for the delivery of this >> message to the intended recipient(s), you are hereby notified that >> any disclosure, copying, distribution, or use of this email message >> is prohibited. If you have received this message in error, please >> notify the sender immediately by e-mail and delete this email >> message from your computer. Thank you. >> >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. -- 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
