[BioC] slow insertions in to graphNEL object (24 hours for 16k nodes)

[Paul Shannon]

It took nearly 24 hours (!) to create a 16k node graph using two  
different techniques:

    g = fromGXL (file ('someFile.gxl'))

and

   g = new ('graphNEL', edgemode='undirected')
   edgeDataDefaults (g, attr='edgeType') = 'edge'
   edgeDataDefaults (g, attr='source') = 'unknown'

   ...

   for (r in 1:max) {
     ...
     g = addNode (a, g)
     g = addNode (b, g)
     g = addEdge (a, b, g)
     edgeData (g, a, b, 'source') = source
     edgeData (g, a, b, 'edgeType') = method
     }

The 16k nodes and their edges are from a suitably parsed version of  
all of the reactions
reported by KEGG.

Is this user error, user misconception, ... or maybe an inefficiency  
that future versions
of the graph package could improve upon?

sessionInfo ()
R version 2.5.1 (2007-06-27)
i386-apple-darwin8.9.1

locale:
C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"   
"methods"   "base"

other attached packages:
    graph    RUnit
"1.14.0" "0.4.15"