[BioC] "GOHyperGResult" is not a defined class

Paul Shannon ptshannon at speakeasy.net
Mon Feb 4 05:05:20 CET 2008

Hi all,

I have encountered a puzzling problem with the ever-reliable  
hyperGTest function.  It
runs the usual amount of time (30 or more seconds) and then fails  
with the message
that 'GOHyperGResult' is not defined.    Here is the whole of my  
session, with sessionInfo

Any ideas?  Thanks!

  - Paul

 > library (Category)
 > library (org.Hs.eg.db)
 > library (GO)
 > genes = c ("8038", "259", "51529", "164", "335", "336", "338", "341")
 > params = new ("GOHyperGParams", geneIds=genes,  
annotation='org.Hs.eg.db', ontology='BP')
 > hgr.bp = hyperGTest (params)
Error in getClass(Class, where = topenv(parent.frame())) :
   c("\"GOHyperGResult\" is not a defined class", "\"BPHyperGResult\"  
is not a defined class")
 > sessionInfo ()
R version 2.6.1 (2007-11-26)


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

other attached packages:
  [1] GO_1.17.0           org.Hs.eg.db_2.0.2  Category_2.4.0       
genefilter_1.16.0   survival_2.34       annotate_1.16.0     xtable_1.5-1
  [8] AnnotationDbi_1.0.6 RSQLite_0.6-2       DBI_0.2-3            
graph_1.15.17       Biobase_1.16.0

loaded via a namespace (and not attached):
[1] RBGL_1.13.6    cluster_1.11.9

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