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Hi, Tony, I suspect "nodes" as parameter name is in conflict w/ function "nodes"... I tried and tested some new codes... and checked in methods- Hypergraph.R Let me know what you think. Li > According to the man pages for Hypergraph-class, the following example of > a > very trivial hypergraph should still work though it does not: > > #######Code Starts######### > library(hypergraph) > namedList = vector("list") > namedList$n = "a" > id = names(namedList) > he <- mapply(function(x,y) Hyperedge(x,y), namedList, id) > >> he > $n > A Hyperedge containing 1 nodes. > >> hg = new("Hypergraph", nodes = unique(unlist(namedList)), he) > Error in get(as.character(FUN), mode = "function", envir = envir) : > variable "a" of mode "function" was not found > In addition: Warning message: > In all(goodHyperedges) : coercing argument of type 'list' to logical > ########Code Ends######### > > > If the hypergraph has more than 1 node, however, it seems to work: > > #######Code Starts######### > namedList1 = vector("list") > namedList1$n = letters[1:2] > id1 = names(namedList1) > he1 <- mapply(function(x,y) Hyperedge(x,y), namedList1, id1) > >> he1 > $n > A Hyperedge containing 2 nodes. > >> hg1 = new("Hypergraph", nodes = unique(unlist(namedList1)), he1) > Warning message: > In all(goodHyperedges) : coercing argument of type 'list' to logical > >> hg1 > An object of class "Hypergraph" > Slot "nodes": > [1] "a" "b" > > Slot "hyperedges": > $n > A Hyperedge containing 2 nodes. > ########Code Ends########## > > It would appear that this boundary case breaks something in the code; > using > traceback(), I find that: > >> traceback() > 9: get(as.character(FUN), mode = "function", envir = envir) > 8: match.fun(FUN) > 7: lapply(hyperedges, nodes) > 6: unlist(lapply(hyperedges, nodes)) > 5: hypergraph:::checkValidHyperedges(hyperedges, nodes) > 4: .local(.Object, ...) > 3: initialize(value, ...) > 2: initialize(value, ...) > 1: new("Hypergraph", nodes = unique(unlist(namedList)), he) > > The checkValidHyperedges() method does not like to call the nodes() > methods > on the hyperedge list. I am at a loss as to how to patch this problem. > > Tony > >> sessionInfo() > R version 2.7.0 Under development (unstable) (2008-02-10 r44415) > i386-apple-darwin8.11.1 > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hypergraph_1.11.0 graph_1.17.14 > > loaded via a namespace (and not attached): > [1] cluster_1.11.9 tools_2.7.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >