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

> ### Name: plotCorGraph
> ### Title: Plot correlation or partial correlation matrix
> ### Aliases: plotCorGraph
> 
> ### ** Examples
> 
> if( require(gRbase) & require(graph)){
+  graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
+ 
+  S <- matrix(c(2,  0.8,0.5,-0.3,
+               0.8,1.5,0.6,-0.7,
+               0.5,0.6,1,  0.7,
+               -0.3,-0.7,0.7,3), ncol=4,nrow=4)
+  colnames(S) <- rownames(S) <- graph::nodes(graph)
+ 
+  # Plot the correlation matrix of S
+  plotCorGraph(S)
+ 
+ 
+  S<-fitSgraph(graph = graph,S = S)
+  # Change the color range
+  plotCorGraph(S, colLim=c(-0.5,0.5))
+ 
+  # Visualize the adjacency matrix
+  plotCorGraph(S, type="cor", graph = graph)
+ 
+  # Show the partial correlation matrix
+  plotCorGraph(S, type="pcor", graph = graph)
+ 
+  # Plot the difference between two matrices
+  S2 <- S
+  # Change the element c~a
+  S2["a","c"] <- S2["c","a"]<- -0.1
+  plotCorGraph(S1=S, S2=S2)
+  plotCorGraph(S1=S, S2=S2, type="pcor")
+ 
+  S2<-fitSgraph(graph = graph,S = S2)
+  # Highlight the graphical structure
+  plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph)
+  # Highlight the element c~a
+  plotCorGraph(S1=S, S2=S2, type="pcor",graph = graph,path = list(c("a","c")))
+ 
+ }
Loading required package: gRbase
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min


Attaching package: ‘graph’

The following objects are masked from ‘package:gRbase’:

    addEdge, adj, connComp, edges, nodes, removeEdge, subGraph

Error: unable to find an inherited method for function ‘nodes’ for signature ‘object = "igraph"’
Execution halted