during the Model tuning step I get the following error:

In mclapply(1:nrow(ud), FUN = function(x) iClusterPlus(dt1, dt2,  :
  144 function calls resulted in an error

Also if I simply try the

allrownameshn.cn)==rownames(hn.mut))
[1] TRUE

fit.single=iClusterPlus(dt1=hn.cn,dt2=hn.mut,type=c("gaussian","binomial"),
                        lambda=c(0.04,0.61),K=2,maxiter=20)

I also get Error in sort.list(y) : 'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?