[BioC] error in plotKEGGGraph

[Robert M. Flight]

Hi All,

I'm playing around with KEGGGraph to examine some pathways, and I am
running into some errors.

When I try to plot some pathways, I get the error: "Error in
.subtypeDisplay(object) :  Given subtype 'missing interaction' is not
found!"

Here is an example with one pathway that gives the error and another
that does not:

library(KEGGgraph)

# this one gives the error
keggID <- "05213"
tmpXML <- "testKGML1.xml"
retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, method="wget")
tmpGraph1 <- parseKGML2Graph(tmpXML, genesOnly=FALSE)
plotKEGGgraph(tmpGraph1)

# this one does not give an error, and spits out a very complicated graph
keggID <- "04810"
tmpXML <- "testKGML2.xml"
retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, method="wget")
tmpGraph2 <- parseKGML2Graph(tmpXML, genesOnly=FALSE)
plotKEGGgraph(tmpGraph2)

Any help on why this error is cropping up would be appreciated.

R version 2.11.1 (2010-05-31)
i386-pc-mingw32

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

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

other attached packages:
[1] KEGGgraph_1.4.0  Rgraphviz_1.26.0 graph_1.26.0     XML_3.1-0

loaded via a namespace (and not attached):
[1] tools_2.11.1

Thanks in advance,

-Robert

Robert M. Flight, Ph.D.
Bioinformatics and Biomedical Computing Laboratory
University of Louisville
Louisville, KY

PH 502-852-0467
EM robert.flight at louisville.edu
EM rflight79 at gmail.com

Williams and Holland's Law:
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