Running examples in ‘GMD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: heatmap.3
> ### Title: Enhanced Heatmap Representation with Dendrogram and Partition
> ### Aliases: heatmap.3
> 
> ### ** Examples
> 
> ## ------------------------------------------------------------------------
> ## Example1: mtcars
> ## ------------------------------------------------------------------------
> ## load library
> require("GMD")
> 
> ## load data
> data(mtcars)
> 
> ## heatmap on raw data
> x  <- as.matrix(mtcars)
> 
> dev.new(width=10,height=8)
dev.new(): using pdf(file="Rplots4.pdf")
> heatmap.3(x)                               # default, with reordering and dendrogram
Warning in heatmap.3(x) :
  Discrepancy: row dendrogram is asked;  Rowv is set to `TRUE'.
Warning in heatmap.3(x) :
  Discrepancy: col dendrogram is asked;  Colv is set to `TRUE'.
Warning in heatmap.3(x) :
  Discrepancy: row dendrogram is asked; cluster.by.row is set to `TRUE'.
Warning in heatmap.3(x) :
  Discrepancy: col dendrogram is asked; cluster.by.col is set to `TRUE'.
1.dim(x): 32 11 
Preparing `hclust'... The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Preparing `dendrogram'... Reordering ... 2.dim(x): 32 11 
Scaling ... 3.dim(x): 32 11 
Making color breaks ... 4.dim(x): 32 11 
[1] "kr=2,kc=2"
5.dim(x): 32 11 
Plotting ... revC: FALSE , revR: FALSE 
5b.dim(x): 32 11 
5c.dim(x): 32 11 
scale: none 
5d.dim(x): 11 32 
6.dim(x): 11 32 
7.dim(x): 11 32 
8.dim(x): 11 32 
DONE!

> ## Not run: 
> ##D heatmap.3(x, Rowv=FALSE, Colv=FALSE)       # no reordering and no dendrogram
> ##D heatmap.3(x, dendrogram="none")            # reordering without dendrogram
> ##D heatmap.3(x, dendrogram="row")        # row dendrogram with row (and col) reordering
> ##D heatmap.3(x, dendrogram="row", Colv=FALSE) # row dendrogram with only row reordering
> ##D heatmap.3(x, dendrogram="col")             # col dendrogram
> ##D heatmap.3(x, dendrogram="col", Rowv=FALSE) # col dendrogram with only col reordering
> ##D heatmapOut <-
> ##D   heatmap.3(x, scale="column")             # sacled by column
> ##D names(heatmapOut)                          # view the list that is returned
> ##D heatmap.3(x, scale="column", x.center=0)   # colors centered around 0
> ##D heatmap.3(x, scale="column",trace="column")  # trun "trace" on
> ## End(Not run)
> 
> ## coloring cars (row observations) by brand
> brands <- sapply(rownames(x), function(e) strsplit(e," ")[[1]][1])
> names(brands) <- c()
> brands.index <- as.numeric(as.factor(brands))
> RowIndividualColors <- rainbow(max(brands.index))[brands.index]
> heatmap.3(x, scale="column", RowIndividualColors=RowIndividualColors)
Warning in heatmap.3(x, scale = "column", RowIndividualColors = RowIndividualColors) :
  Discrepancy: row dendrogram is asked;  Rowv is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", RowIndividualColors = RowIndividualColors) :
  Discrepancy: col dendrogram is asked;  Colv is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", RowIndividualColors = RowIndividualColors) :
  Discrepancy: row dendrogram is asked; cluster.by.row is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", RowIndividualColors = RowIndividualColors) :
  Discrepancy: col dendrogram is asked; cluster.by.col is set to `TRUE'.
1.dim(x): 32 11 
Preparing `hclust'... The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Preparing `dendrogram'... Reordering ... 2.dim(x): 32 11 
Scaling ... 3.dim(x): 32 11 
Making color breaks ... 4.dim(x): 32 11 
[1] "kr=2,kc=2"
5.dim(x): 32 11 
Plotting ... revC: FALSE , revR: FALSE 
5b.dim(x): 32 11 
5c.dim(x): 32 11 
scale: column 
5d.dim(x): 11 32 
6.dim(x): 11 32 
7.dim(x): 11 32 
8.dim(x): 11 32 
DONE!

> 
> ## coloring attributes (column features) randomly (just for a test :)
> heatmap.3(x, scale="column", ColIndividualColors=rainbow(ncol(x)))
Warning in heatmap.3(x, scale = "column", ColIndividualColors = rainbow(ncol(x))) :
  Discrepancy: row dendrogram is asked;  Rowv is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", ColIndividualColors = rainbow(ncol(x))) :
  Discrepancy: col dendrogram is asked;  Colv is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", ColIndividualColors = rainbow(ncol(x))) :
  Discrepancy: row dendrogram is asked; cluster.by.row is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", ColIndividualColors = rainbow(ncol(x))) :
  Discrepancy: col dendrogram is asked; cluster.by.col is set to `TRUE'.
1.dim(x): 32 11 
Preparing `hclust'... The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Preparing `dendrogram'... Reordering ... 2.dim(x): 32 11 
Scaling ... 3.dim(x): 32 11 
Making color breaks ... 4.dim(x): 32 11 
[1] "kr=2,kc=2"
5.dim(x): 32 11 
Plotting ... revC: FALSE , revR: FALSE 
5b.dim(x): 32 11 
5c.dim(x): 32 11 
scale: column 
5d.dim(x): 11 32 
6.dim(x): 11 32 
7.dim(x): 11 32 
8.dim(x): 11 32 
DONE!

> 
> ## add a single plot for all row individuals
> dev.new(width=12,height=8)
dev.new(): using pdf(file="Rplots5.pdf")
> expr1 <- list(quote(plot(row.data[rowInd,"hp"],1:nrow(row.data),
+ xlab="hp",ylab="",yaxt="n",main="Gross horsepower")),
+ quote(axis(2,1:nrow(row.data),rownames(row.data)[rowInd],las=2)))
> heatmap.3(x, scale="column", plot.row.individuals=TRUE, row.data=x,
+           plot.row.individuals.list=list(expr1))
Warning in heatmap.3(x, scale = "column", plot.row.individuals = TRUE, row.data = x,  :
  Discrepancy: row dendrogram is asked;  Rowv is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", plot.row.individuals = TRUE, row.data = x,  :
  Discrepancy: col dendrogram is asked;  Colv is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", plot.row.individuals = TRUE, row.data = x,  :
  Discrepancy: row dendrogram is asked; cluster.by.row is set to `TRUE'.
Warning in heatmap.3(x, scale = "column", plot.row.individuals = TRUE, row.data = x,  :
  Discrepancy: col dendrogram is asked; cluster.by.col is set to `TRUE'.
1.dim(x): 32 11 
Preparing `hclust'... The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Preparing `dendrogram'... Reordering ... 2.dim(x): 32 11 
Scaling ... 3.dim(x): 32 11 
Making color breaks ... 4.dim(x): 32 11 
[1] "kr=2,kc=2"
5.dim(x): 32 11 
Plotting ... revC: FALSE , revR: FALSE 
5b.dim(x): 32 11 
5c.dim(x): 32 11 
scale: column 
5d.dim(x): 11 32 
6.dim(x): 11 32 
7.dim(x): 11 32 
8.dim(x): 11 32 
DONE!

> 
> 
> ## ------------------------------------------------------------------------
> ## Example2: ruspini
> ## ------------------------------------------------------------------------
> ## load library
> require("GMD")
> require(cluster)
Loading required package: cluster
> 
> ## load data
> data(ruspini)
Warning in data(ruspini) : data set ‘ruspini’ not found
> 
> ## heatmap on a `dist' object
> x <- gdist(ruspini)
Error in as.matrix(x) : 
  cannot open file '/tmp/RtmpzDACWZ/RLIBS_66727d8bb5d/cluster/data/Rdata.rdb': Transport endpoint is not connected
Calls: gdist -> dist -> as.matrix
Execution halted