[BioC] aCGH telling me to run find.hmm.states before merge hmm.states even though I have.

[Cian Murphy]

I have run find.hmm.states by:

aCGH.hmm <- find.hmm.states(aCGH) on an aCGH object. That seems to run 
fine as it displays its processing of each chromosome for every sample. 
I follow it with

hmm.merged(aCGH.hmm) <-  mergeHmmStates(aCGH.hmm) as per the manual. 
This nomenclature looks strange so I tried the more normal
aCGH.hmm.merged <-  mergeHmmStates(aCGH.hmm)

However both commands give the error

Error in mergeHmmStates(aCGH.hmm) :
   compute the hmm states first using find.hmm.states


What's going on? Why is it asking me to do something that I have just done?

Thanks,


Cian