Dear Martin name masking is a separate issue, which I do not want to explore here.
If one accepts the notion that unrelated generics of the same name may exist in different namespaces (user confusion aside, I don't see a technical reason why one shouldn't), then I find the behaviour of R in the below case puzzling: the value of "showMethods(something)" called from the global environment depends on whether or not the expression "package::something" has previously been evaluated. The value of isGeneric(something) is different when called from top-level and when called within showMethods. Best wishes Wolfgang PS1: I do apologize if this behaviour is intentional, and documented somewhere. I would then be puzzled even more though. PS2: My code example used ":::", and there are some vague warnings in its man page that ":::" is "dangerous". The problem also occurs with "::". ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 28/02/2009 11:34 Martin Maechler scripsit >>>>>> "Wolfi" == Wolfgang Huber <hu...@ebi.ac.uk> >>>>>> on Wed, 25 Feb 2009 18:15:03 +0000 writes: > > Wolfi> Hi, > Wolfi> when running the following on a fresh R, > > > Wolfi> library("IRanges") > Wolfi> annotation > Wolfi> showMethods("annotation") > Wolfi> Biobase:::annotation > Wolfi> showMethods("annotation") > > > Wolfi> I get (see the "^^^^^" marked output at the bottom): > > > >> library("IRanges") > > Wolfi> Carico il pacchetto richiesto: 'IRanges' > > Wolfi> The following object(s) are masked from package:base : > > Wolfi> cbind, > Wolfi> order, > Wolfi> pmax, > Wolfi> pmax.int, > Wolfi> pmin, > Wolfi> pmin.int, > Wolfi> rbind, > Wolfi> rep.int, > Wolfi> table > > >> annotation > Wolfi> standardGeneric for "annotation" defined from package "IRanges" > > Wolfi> function (x, ...) > Wolfi> standardGeneric("annotation") > Wolfi> <environment: 0x1a302b0> > Wolfi> Methods may be defined for arguments: x > Wolfi> Use showMethods("annotation") for currently available ones. > > >> showMethods("annotation") > Wolfi> Function: annotation (package IRanges) > Wolfi> x="AnnotatedList" > > >> Biobase:::annotation > Wolfi> standardGeneric for "annotation" defined from package "Biobase" > > Wolfi> function (object) > Wolfi> standardGeneric("annotation") > Wolfi> <environment: 0x205cee0> > Wolfi> Methods may be defined for arguments: object > Wolfi> Use showMethods("annotation") for currently available ones. > > >> showMethods("annotation") > > Wolfi> Function "annotation": > Wolfi> <not a generic function> > Wolfi> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > > Wolfi> It seems that the value of isGeneric("annotation"), when it is > called > Wolfi> within showMethods, is FALSE, while it is TRUE when called outside. > > Hi Wolfgang, > > I have looked at the NAMESPACE files of the two packages > Biobase and IRanges, (the Bioconductor development version in SVN), > and I think the problem might result from the fact > that IRanges does export the annotation generic, does not > exportMethods( ... annotation ...). > > OTOH, Biobase exportMethods( annotation ) only [but not the generic]. > and then both packages do not at all mention each other, > neither in DESCRIPTION nor NAMESPACE. > > Either you are talking about conceptually the same generic > annotation(); in that case one package needs to import*() it > from the other, > or then you have two completely different animals, but then > (masking) problems are unavoidable > -- in spite of the fact that I vaguely remember that some > Bioconductor developers repeatedly emphasize that these > problems are not problems for them > > Martin > > >> sessionInfo() > Wolfi> R version 2.9.0 Under development (unstable) (2009-02-25 r48007) > Wolfi> x86_64-unknown-linux-gnu > > Wolfi> locale: > Wolfi> > LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C > > Wolfi> attached base packages: > Wolfi> [1] stats graphics grDevices utils datasets methods > base > > Wolfi> other attached packages: > Wolfi> [1] IRanges_1.1.40 > > Wolfi> loaded via a namespace (and not attached): > Wolfi> [1] Biobase_2.3.10 > > > > Wolfi> Best wishes > Wolfi> Wolfgang > > Wolfi> ------------------------------------------------------------------ > Wolfi> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > Wolfi> ______________________________________________ > Wolfi> R-devel@r-project.org mailing list > Wolfi> https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
