[BioC] edge-less pathways in graphite

[Hamid Bolouri]

hi; I am finding that some KEGG pathway graphNELs generated by graphite have zero edges, even though the KGML description includes edges, e.g.

  > kegg[["ErbB signaling pathway"]]
  "ErbB signaling pathway" pathway from KEGG
  Number of nodes     = 87
  Number of edges     = 0
  Type of identifiers = native
  Retrieved on        = 2011-05-05

Whereas the KGML for the same pathway includes statements such as:

    <relation entry1="75" entry2="46" type="PPrel">
        <subtype name="activation" value="-->"/>
        <subtype name="phosphorylation" value="+p"/>
    </relation>

Am I missing something?

Thanks for a great package, BTW! 

Hamid Bolouri 
PS Of the 46 apparently edge-less graphite graphNELs, several have zero edges in KEGG also, e.g. kegg[["Spliceosome"]]. I am _not_ talking about those.

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] graphite_1.2.0       AnnotationDbi_1.18.0 Biobase_2.16.0      
[4] BiocGenerics_0.2.0   RSQLite_0.11.1       DBI_0.2-5           
[7] graph_1.34.0        

loaded via a namespace (and not attached):
[1] IRanges_1.14.2     org.Hs.eg.db_2.7.1 stats4_2.15.0      tools_2.15.0