[BioC] Error when calculating coverageMat in ontoTools 1.2.1

[Rohan BH Williams]

Hi,

I am obtaining an error when using coverageMat to compute the coverage matrix 
of the mouse LocusLink to GOCC mappings

The error I obtain is:
Error in mat(x) %*% mat(y) : matrices not conformable for multiplication

I'm running ontoTools v1.2.1 on R 1.9.0 Dev for Windows. GO version is 1.5 and 
MouseLLMappings is 1.1.1

Code used to generate mappings was:
mu.ll.tags <- ls(env=mouseLLMappingsLL2GO)
mu.ll2goCC.Env <- new.env(hash=TRUE)
mu.kvmap.CC <- list()

#do ll-goid extractions for mu-LL and CC
cat(length(mu.ll.tags ))
for (i in 1:length(mu.ll.tags )) {
	if (i%%200 == 0)
		cat(i)
	tmp <- get(mu.ll.tags[i], env = mouseLLMappingsLL2GO) #extract GO-ids 
for current LL id
	tmp <- tmp[tmp %in% GOCCtags] #find those GO-ids that occur in 
Molecular Function only
	if (length(tmp) > 0) {
		mu.kvmap.CC[[mu.ll.tags[i]]] <- tmp
		assign(mu.ll.tags[i], tmp, env = mu.ll2goCC.Env)
	}
}

#unique LL and GO id's are species and sub-ontology specific, so use the 
following
gotargs.mu.CC <- sort(unique(unlist(mu.kvmap.CC)))
llused.mu.CC <- names(mu.kvmap.CC)
#generate mapping object
mu.LL2GOCC.ooMap.1.5 <- otkvEnv2namedSparse(llused.mu.CC, gotargs.mu.CC , 
mu.ll2goCC.Env)
#generate object-ontology complex
mu.LL2GOCC.ooc1.5 <- new("OOC", ontology=GOCC1.5, OOmap=mu.LL2GOCC.ooMap.1.5)

covMat.mu.LL2GOCC.ooc1.5 <- coverageMat(mu.LL2GOCC.ooc1.5)
25050075010001250Error in mat(x) %*% mat(y) : matrices not conformable for 
multiplication

The error is always occuring after the 1250 LocusLink block count

Any help in solving this would be most appreciated.

Best,

Rohan Williams