Errors in running code in vignettes:
when running code in 'clValid.Rnw'

> options(prompt = "R> ")

> library("clValid")
Loading required package: cluster

> data(mouse)

> express <- mouse[, c("M1", "M2", "M3", "NC1", "NC2", 
+     "NC3")]

> rownames(express) <- mouse$ID

> intern <- clValid(express, 2:6, clMethods = c("hierarchical", 
+     "kmeans", "pam"), validation = "internal")

> summary(intern)

Clustering Methods:
 hierarchical kmeans pam 

Cluster sizes:
 2 3 4 5 6 

Validation Measures:
                                 2       3       4       5       6
                                                                  
hierarchical Connectivity   5.3270 14.2528 20.7520 27.0726 30.6194
             Dunn           0.1291  0.0788  0.0857  0.0899  0.0899
             Silhouette     0.5133  0.4195  0.3700  0.3343  0.3233
kmeans       Connectivity  13.2548 17.6651 37.3980 43.2655 50.6095
             Dunn           0.0464  0.0873  0.0777  0.0815  0.0703
             Silhouette     0.4571  0.4182  0.3615  0.3367  0.3207
pam          Connectivity  18.7917 27.9651 30.9302 44.9671 32.9667
             Dunn           0.0391  0.0597  0.0510  0.0761  0.0816
             Silhouette     0.4271  0.3489  0.3563  0.3530  0.4152

Optimal Scores:

             Score  Method       Clusters
Connectivity 5.3270 hierarchical 2       
Dunn         0.1291 hierarchical 2       
Silhouette   0.5133 hierarchical 2       


> op <- par(no.readonly = TRUE)

> par(mfrow = c(2, 2), mar = c(4, 4, 3, 1))

> plot(intern, legend = FALSE)

> plot(nClusters(intern), measures(intern, "Dunn")[, 
+     , 1], type = "n", axes = F, xlab = "", ylab = "")

> legend("center", clusterMethods(intern), col = 1:9, 
+     lty = 1:9, pch = paste(1:9))

> par(op)

> op <- par(no.readonly = TRUE)

> par(mfrow = c(2, 2), mar = c(4, 4, 3, 1))

> plot(intern, legend = FALSE)

> plot(nClusters(intern), measures(intern, "Dunn")[, 
+     , 1], type = "n", axes = F, xlab = "", ylab = "")

> legend("center", clusterMethods(intern), col = 1:9, 
+     lty = 1:9, pch = paste(1:9))

> par(op)

> stab <- clValid(express, 2:6, clMethods = c("hierarchical", 
+     "kmeans", "pam"), validation = "stability")

> optimalScores(stab)
        Score       Method Clusters
APN 0.0478101 hierarchical        2
AD  1.5271789          pam        6
ADM 0.1400795          pam        6
FOM 0.5158032          pam        6

> par(mfrow = c(2, 2), mar = c(4, 4, 3, 1))

> plot(stab, measure = c("APN", "AD", "ADM"), legend = FALSE)

> plot(nClusters(stab), measures(stab, "APN")[, , 1], 
+     type = "n", axes = F, xlab = "", ylab = "")

> legend("center", clusterMethods(stab), col = 1:9, 
+     lty = 1:9, pch = paste(1:9))

> par(op)

> par(mfrow = c(2, 2), mar = c(4, 4, 3, 1))

> plot(stab, measure = c("APN", "AD", "ADM"), legend = FALSE)

> plot(nClusters(stab), measures(stab, "APN")[, , 1], 
+     type = "n", axes = F, xlab = "", ylab = "")

> legend("center", clusterMethods(stab), col = 1:9, 
+     lty = 1:9, pch = paste(1:9))

> par(op)

> fc <- tapply(rownames(express), mouse$FC, c)

> fc <- fc[!names(fc) %in% c("EST", "Unknown")]

> bio <- clValid(express, 2:6, clMethods = c("hierarchical", 
+     "kmeans", "pam"), validation = "biological", annotation = fc)

> fc2 <- readAnnotationFile("fc.csv")
Read 7 items

> optimalScores(bio)
        Score       Method Clusters
BHI 0.2025793       kmeans        5
BSI 0.6755826 hierarchical        2

> plot(bio, measure = "BHI", legendLoc = "topleft")

> plot(bio, measure = "BSI")

> plot(bio, measure = "BHI", legendLoc = "topleft")

> plot(bio, measure = "BSI")

> if (require("Biobase", quietly = TRUE) && require("annotate", 
+     quietly = TRUE) && require("GO.db", quietly = TRUE) && require("moe430a.db", 
+ .... [TRUNCATED] 

> if (exists("bio2")) optimalScores(bio2)

> result <- clValid(express, 4:6, clMethods = c("hierarchical", 
+     "kmeans", "pam"), validation = c("internal", "stability"))

> res <- getRanksWeights(result)

> print(res$ranks[, 1:3], quote = FALSE)
             1              2              3             
APN          pam-6          hierarchical-6 hierarchical-5
AD           pam-6          kmeans-6       hierarchical-6
ADM          pam-6          hierarchical-6 hierarchical-5
FOM          pam-6          kmeans-6       hierarchical-6
Connectivity hierarchical-4 hierarchical-5 hierarchical-6
Dunn         hierarchical-5 hierarchical-6 hierarchical-4
Silhouette   pam-6          hierarchical-4 kmeans-4      

> if (require("RankAggreg")) {
+     CEWS <- RankAggreg(x = res$ranks, k = 5, weights = res$weights, 
+         seed = 123, verbose = FALSE)
+     CEW .... [TRUNCATED] 
Loading required package: RankAggreg
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'RankAggreg'

> plot(CEWS)

  When sourcing 'clValid.R':
Error: error in evaluating the argument 'x' in selecting a method for function 'plot': object 'CEWS' not found
Execution halted

  'clValid.Rnw'... failed