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> library(WayFindR)
> ## input directly from file
> xmlfile <- system.file("pathways/WP3850.gpml", package = "WayFindR")
> edges <- collectEdges(xmlfile)
> class(edges)
[1] "matrix" "array" 
> dim(edges)
[1] 46  3
> head(edges)
           Source  Target  MIM             
id2257fd8  "c0520" "b2305" "mim-inhibition"
id25882942 "a531f" "b3910" "Arrow"         
id25c739ca "f5259" "ceb96" "Arrow"         
id2848101a "cc7e6" "fea9d" "Arrow"         
id295ae5fe "a8bb6" "b687e" "Arrow"         
id2e105012 "fea9d" "cd260" "Arrow"         
> tail(edges)
           Source  Target  MIM             
idf7bb43f7 "f2f0d" "a2d31" "mim-inhibition"
idfc5a5200 "f58ce" "d3cde" "Arrow"         
idfea9f3db "ceb96" "a2d31" "Arrow"         
idfed646d2 "ba0fb" "fca28" "Arrow"         
id2d5bc3d8 "b0088" "b2d78" "mim-inhibition"
id70c7e487 "b62b2" "b3356" "mim-inhibition"
> ## Alternative: input first, then look for edges
> doc <- XML::xmlParseDoc(xmlfile)
> wedges <- collectEdges(doc)
> all( wedges == edges)
[1] TRUE
> ## Obvious failure modes
> try( collectEdges() )
Error in collectEdges() : argument "xmldoc" is missing, with no default
> try( collectEdges("bogus") )
Error in collectEdges("bogus") : Cannot locate file 'bogus'!
> badfile <- system.file("perl/nodeTypes.txt", package = "WayFindR")
> try( collectEdges(badfile) )
D:/RCompile/CRANincoming/R-devel/lib/WayFindR/perl/nodeTypes.txt:1: parser error : Start tag expected, '<' not found
CellularComponent	1
^
Error in UseMethod("xmlNamespace") : 
  no applicable method for 'xmlNamespace' applied to an object of class "NULL"
In addition: Warning message:
In xmlRoot.XMLInternalDocument(mydoc) : empty XML document
> 
> proc.time()
   user  system elapsed 
   0.50    0.04    0.51