Dear mailing list, I'm developping a bioconductor package. I 'm using a method called "combine". This method is already defined in Biobase Thus, to avoid an overwriting of my method, I import the "combine" method from Biobase. However, I get some difficulties to add new parameters to this method. > library(Biobase) setMethod("combine", signature(x="numeric", y="numeric"), function(x, y, test=TRUE,...) { return(sum(x,y)) }) > combine(1,2) [1] 3 #OK > combine(1,2, test=TRUE) Error in do.call(callGeneric, list(y, ...)) : element 1 is empty; the part of the args list of 'list' being evaluated was: (y, ...) Error in combine(x, do.call(callGeneric, list(y, ...))) : error in evaluating the argument 'y' in selecting a method for function 'combine' Error in combine(x, do.call(callGeneric, list(y, ...))) : error in evaluating the argument 'y' in selecting a method for function 'combine' This is due to the definition of the method by Biobase : > library(Biobase) >combine nonstandardGenericFunction for "combine" defined from package "Biobase" function (x, y, ...) { if (length(list(...)) > 0) { #HERE IS MY PROBLEM callGeneric(x, do.call(callGeneric, list(y, ...))) } else { standardGeneric("combine") } } <environment: 0x102ddea00=""> Methods may be defined for arguments: x, y Use showMethods("combine") for currently available ones. The function's looking for futher arguments and calls different functions depending of that. I'm not able to enter inside the "else" if I add any arguments. Is there any way to avoid that ? Thanks. ------------------------------------------ Eloi Mercier Computational Biology, IRCM 110 av. Des Pins O. Montreal Canada, QC

On 05/20/2010 10:22 AM, Mercier Eloi wrote: > > Dear mailing list, > > I'm developping a bioconductor package. I 'm using a method called "combine". This method is already defined in Biobase > Thus, to avoid an overwriting of my method, I import the "combine" method from Biobase. > > However, I get some difficulties to add new parameters to this method. > >> library(Biobase) > > setMethod("combine", > signature(x="numeric", y="numeric"), > function(x, y, test=TRUE,...) > { > return(sum(x,y)) > }) > >> combine(1,2) > [1] 3 #OK >> combine(1,2, test=TRUE) > Error in do.call(callGeneric, list(y, ...)) : > element 1 is empty; > the part of the args list of 'list' being evaluated was: > (y, ...) > Error in combine(x, do.call(callGeneric, list(y, ...))) : > error in evaluating the argument 'y' in selecting a method for function 'combine' > Error in combine(x, do.call(callGeneric, list(y, ...))) : > error in evaluating the argument 'y' in selecting a method for function 'combine' > > > This is due to the definition of the method by Biobase : > >> library(Biobase) >> combine > nonstandardGenericFunction for "combine" defined from package "Biobase" > > function (x, y, ...) > { > if (length(list(...)) > 0) { #HERE IS MY PROBLEM > callGeneric(x, do.call(callGeneric, list(y, ...))) > } > else { > standardGeneric("combine") > } > } > <environment: 0x102ddea00=""> > Methods may be defined for arguments: x, y > Use showMethods("combine") for currently available ones. > > The function's looking for futher arguments and calls different functions depending of that. > I'm not able to enter inside the "else" if I add any arguments. > > Is there any way to avoid that ? Hi -- I don't know that there is a way to avoid this, short of revising the 'combine' function, and since 'combine' is not elegant I'm open to doing that. I was wondering whether your method is in the spirit of the 'combine' generic, which is to say, from ?combine, 'given an arbitrary number of arguments of the same class... combine them into a single instance in a a sensible way', Martin > > Thanks. > > ------------------------------------------ > Eloi Mercier > Computational Biology, IRCM > 110 av. Des Pins O. > Montreal > Canada, QC > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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