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> library(WayFindR)
> ## input directly from file
> xmlfile <- system.file("pathways/WP3850.gpml", package = "WayFindR")
> nodes <- collectNodes(xmlfile)
> class(nodes)
[1] "matrix" "array" 
> dim(nodes)
[1] 52  3
> head(nodes)
      GraphId label    Type         
a169c "a169c" "GSK3B"  "GeneProduct"
a2d31 "a2d31" "PI3K"   "GeneProduct"
a4cc9 "a4cc9" "SMAD3"  "GeneProduct"
a531f "a531f" "4EPB"   "GeneProduct"
a5550 "a5550" "EIF2B2" "GeneProduct"
a8bb6 "a8bb6" "N-WASP" "GeneProduct"
> tail(nodes)
      GraphId label               Type         
b3910 "b3910" "Protein synthesis" "Pathway"    
c2a5c "c2a5c" "MTOR"              "GeneProduct"
f5051 "f5051" "MLST8"             "GeneProduct"
e1ccf "e1ccf" "MAPKAP1"           "GeneProduct"
c6e5f "c6e5f" "RICTOR"            "GeneProduct"
a3b41 "a3b41" "MTOR"              "GeneProduct"
> ## Alternative: input first, then look for nodes
> doc <- XML::xmlParseDoc(xmlfile)
> wnodes <- collectNodes(doc)
> all( wnodes == nodes )
[1] TRUE
> ## Obvious failure modes
> try( collectNodes() )
Error in collectNodes() : argument "xmldoc" is missing, with no default
> try( collectNodes("bogus") )
Error in collectNodes("bogus") : Cannot locate file 'bogus'!
> badfile <- system.file("perl/nodeTypes.txt", package = "WayFindR")
> try( collectNodes(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 
   0.39    0.14    0.48