Sorry, I just want to clarify some more on this.(maybe useful for others as well) What you actually mean is callNextMethod() used to drop both |...| and the other arguments explicitly supplied from the parent call (in my case, |parameters| argument). And now after your fix, both gets passed on and that’s why I should explicitly select the argument for callNextMethod?
Thanks. Mike On 01/23/2015 11:30 AM, Michael Lawrence wrote: > The bug has existed forever. The commit log may be confusing. The > actual bug (or at least a very undesirable behavior) was in > match.call(), not callNextMethod(). > > I think it's still true that callNextMethod() is the natural > invocation. When adding arguments to initialize that you do not want > to pass on (and thus set as slots), it's necessary to use explicit > args. There are other cases where callNextMethod() is exactly what you > want. Like the case in rtracklayer that motivated this fix. > > > On Fri, Jan 23, 2015 at 11:23 AM, Mike <wjia...@fhcrc.org> wrote: >> Michael, >> >> Thanks for the confirmation of the issue. I see you were trying to tackle it >> in the latest commits r67467:67472 which apparently haven’t fixed the bug >> yet (instead it triggers the error of the existing legacy code in other R >> packages like flowCore). I can certainly change the code to explicitly pass >> on all the arguments to callNextMethod as you and Martin suggested. I just >> wonder if the documentation should drop the sentence of Calling with no >> arguments is often the natural way to use callNextMethod and change the >> example code (at least before the bug is eventually fixed.) so that users >> won’t be misusing it. >> >> >> >> Mike >> >> On 01/23/2015 10:55 AM, Martin Morgan wrote: >> >> On 01/23/2015 10:52 AM, Michael Lawrence wrote: >> >> First let me apologize for my failure to read emails. There was a >> long-standing bug in the methods package where arguments passed as >> "..." to a method would be dropped by callNextMethod(). It turns out >> that in all known cases this affects calls to initialize(), probably >> because there are many initialize() methods, and new() calls >> initialize with "...". >> >> This case is a very typical one, and Martin's fix is the right one, >> according to the (unchanged) documentation of callNextMethod(). >> >> It's in general impossible to detect these cases from static analysis, >> since we do not know how the user is calling a method. But catching >> them in initialize() should be easy, with some false positives. Just >> look for callNextMethod(). >> >> Is it OK for me to checkout all of Bioconductor so that I can perform >> that analysis, or will that stress the servers too much? I have a >> package that embeds GNU Global to index and search >> CRAN/Bioconductor-size repositories for these cases. >> >> >> Hi Michael -- there is no problem checking out all >> (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks presumably) of >> Bioc. >> >> Thanks! Martin >> >> >> Michael >> >> On Thu, Jan 22, 2015 at 6:15 AM, Martin Morgan <mtmor...@fredhutch.org> >> wrote: >> >> On 01/22/2015 12:26 AM, Martin Maechler wrote: >> >> >> Mike <wjia...@fhcrc.org> >> on Tue, 20 Jan 2015 17:16:37 -0800 writes: >> >> >> >> > I don't think it has been addressed yet in the later commits of >> R-devel. >> > And that piece of code in flowCore package was written long time >> ago and >> > there is nothing wrong with it as far as I can see. >> >> You are right. >> >> I thought Michael Lawrence (member of R Core since last summer!) >> was also reading Bioc-devel, so wonder why he has not yet >> replied --> CC'ing him >> >> The changes to R-devel also did break the Matrix package in >> exactly the same way. You said >> >> Here is the |initialize|method for |parameterFilter| which causes the >> various errors from flow package vignettes. >> >> |setMethod("initialize", >> signature=signature(.Object="parameterFilter"), >> definition=function(.Object, parameters,...) >> { >> if (!missing(parameters)) >> parameters(.Object) <- parameters >> callNextMethod() >> }) >> | >> >> >> >> and I also had a _no argument_ call >> callNextMethod() >> inside an initialize method. >> >> I'm pretty sure that if you change (the same as I) >> >> callNextMethod() >> to >> callNextMethod(.Object, ...) >> >> you'll have a version of the code that works both in current R 3.1.2 >> (and older versions) *and* in the R-devel version. >> >> >> I also pinged Michael?? >> >> What's a precise statement of the problem -- no-argument callNextMethod() >> inside initialize? Any suggestions on ways to discover these without relying >> on package break during build / check / install? >> >> Martin Morgan >> >> Michael L and I were not sure how many other packages or R code this >> would influence and he was expecting very very few. >> >> Best regards, >> >> Martin Maechler, ETH Zurich >> >> >> > On 01/20/2015 05:06 PM, Dan Tenenbaum wrote: >> >> I'm not sure if you were implying that this has already been fixed >> in R-devel. Note that the devel build machines currently have r67501 >> installed, which is later than all the commits you cite above, yet the flow >> packages are still broken. >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> >> >> >> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
