Package check result: OK

Changes to worse in reverse depends:

Package: BCSub
Check: examples
New result: ERROR
  Running examples in ‘BCSub-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: BCSub
  > ### Title: A Bayesian semiparametric factor analysis model for subtype
  > ###   identification (Clustering).
  > ### Aliases: BCSub
  > 
  > ### ** Examples
  > 
  > set.seed(1)
  > n = 100 ## number of subjects
  > G = 200 ## number of genes
  > SNR = 0 ## ratio of noise genes
  > ## loading matrix with four factors
  > lam = matrix(0,G,4)
  > lam[1:(G/4),1] = runif(G/4,-3,3)
  > lam[(G/4+1):(G/2),2] = runif(G/4,-3,3)
  > lam[(G/2+1):(3*G/4),3] = runif(G/4,-3,3)
  > lam[(3*G/4+1):(G),4] = runif(G/4,-3,3)
  > ## generate low-rank covariance matrix
  > sigma <- lam%*%t(lam) + diag(rep(1,G))
  > sigma <- cov2cor(sigma)
  > ## true cluster structure ##
  > e.true = c(rep(1,n/2),rep(2,n/2))
  > 
  > ## generate data matrix ##
  > mu1 = rep(1,G)
  > mu1[sample(1:G,SNR*G)] = 0
  > mu2 <- rep(0,G)
  > A = rbind(mvrnorm(n/2,mu1,sigma),mvrnorm(n/2,mu2,sigma))
  > 
  > ## factor analysis to decide the number of factors
  > ## Not run: 
  > ##D ev = eigen(cor(A))
  > ##D ap = parallel(subject=nrow(A),var=ncol(A),rep=100,cent=.05)
  > ##D nS = nScree(x=ev$values, aparallel=ap$eigen$qevpea)
  > ##D M = nS$Components[1,3] ## number of factors
  > ## End(Not run)
  > M = 4
  > ## run BCSub for clustering
  > iters = 1000 ## total number of iterations
  > seq = 600:1000 ## posterior samples used for inference
  > system.time(res <- BCSub(A,iter=iters,seq=seq,M=M))
     user  system elapsed 
    3.178   0.011   3.190 
  > res$CL ## inferred cluster structure
    [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
   [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
   [75] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
  > 
  > ## calculate and plot similarity matrix
  > sim = calSim(t(res$E[,seq]))
  > 
  > ## plot similarity matrix
  > x <- rep(1:n,times=n)
  > y <- rep(1:n,each=n)
  > z <- as.vector(sim)
  > levelplot(z~x*y,col.regions=rev(gray.colors(n^2)), xlab = "Subject ID",ylab = "Subject ID")
  Error in levelplot(z ~ x * y, col.regions = rev(gray.colors(n^2)), xlab = "Subject ID",  : 
    could not find function "levelplot"
  Execution halted