Martin Morgan
2012-Dec-08 23:05 UTC
[Rd] namespace S3 and S4 generic imports cannot both be satisfied:
PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods indicates that one should setGeneric("unique") setClass("A") unique.A <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "A", unique.A) Both S3 and S4 methods need to be exported in the NAMESPACE import(methods) S3method(unique, A) exportMethods(unique) PkgB introduces a new class and method setClass("B") unique.B <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "B", unique.B) and in the NAMESPACE has import(methods) importFrom(PkgA, unique) S3method(unique, B) exportMethods(unique) Unfortuantely, R CMD check says that * checking whether package 'PkgB' can be installed ... WARNING Found the following significant warnings: Warning: found an S4 version of 'unique' so it has not been imported correctly See '/home/mtmorgan/tmp/PkgB.Rcheck/00install.out' for details. This is from (svn r61253) R-devel/src/library/base/R/namespace.R:1339, where the code finds the S4 generic, but not the S3 generic. Obviously the namespace cannot have both the S3 and S4 symbols defined, but this seems to be required? A workaround might extend the check to include getGeneric(genname)@default. This scenario is reproducible in the attached tarball tar xzf PkgAB.tar.gz R CMD INSTALL PkgA R CMD check PkgB Martin Morgan -- 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: PkgAB.tar.gz Type: application/x-gzip Size: 973 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-devel/attachments/20121208/df47c96a/attachment.gz>
John Chambers
2012-Dec-09 19:27 UTC
[Rd] namespace S3 and S4 generic imports cannot both be satisfied:
Yes, you are right. Mixing S3 and S4 methods for a generic is fine, although in subtle cases one is safer promoting the S3 method to an S4 method, as you did in your example. Usually, the default method for the S4 generic is the S3 generic. But, in general, it's not possible to check algorithmically whether the S3 methods will be dispatched. For example, an S4 method on "vector" could dispatch S3 methods on subclasses "numeric", etc. (don't ask why ...), for a generic that had no default method. That the trouble with this check isn't found right away is likely because one is typically working with a primitive where no generic function is created. Should be fixed in rev. 61263. Please check on your real example; it seems fine on the test you submitted. Thanks for the catch. John On 12/8/12 3:05 PM, Martin Morgan wrote:> PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods > indicates that one should > > setGeneric("unique") > > setClass("A") > unique.A <- function(x, incomparables=FALSE, ...) {} > setMethod(unique, "A", unique.A) > > Both S3 and S4 methods need to be exported in the NAMESPACE > > import(methods) > S3method(unique, A) > exportMethods(unique) > > PkgB introduces a new class and method > > setClass("B") > unique.B <- function(x, incomparables=FALSE, ...) {} > setMethod(unique, "B", unique.B) > > and in the NAMESPACE has > > import(methods) > importFrom(PkgA, unique) > S3method(unique, B) > exportMethods(unique) > > Unfortuantely, R CMD check says that > > * checking whether package 'PkgB' can be installed ... WARNING > Found the following significant warnings: > Warning: found an S4 version of 'unique' so it has not been imported > correctly > See '/home/mtmorgan/tmp/PkgB.Rcheck/00install.out' for details. > > This is from (svn r61253) R-devel/src/library/base/R/namespace.R:1339, > where the code finds the S4 generic, but not the S3 generic. Obviously > the namespace cannot have both the S3 and S4 symbols defined, but this > seems to be required? A workaround might extend the check to include > getGeneric(genname)@default. > > This scenario is reproducible in the attached tarball > > tar xzf PkgAB.tar.gz > R CMD INSTALL PkgA > R CMD check PkgB > > Martin Morgan > > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
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