Running examples in 'gbutils-Ex.R' failed
The error most likely occurred in:

> ### Name: adjacencyOfClasses
> ### Title: Adjacency graph of classes in packages
> ### Aliases: adjacencyOfClasses
> ### Keywords: programming S4classes
> 
> ### ** Examples
> 
> adjacencyOfClasses("gbutils")
$vertices
[1] "objectPad" "list"     

$edges
[1] "list -> objectPad"

> adjacencyOfClasses("gbutils", TRUE)
$vertices
[1] "objectPad" "list"      "vector"   

$edges
[1] "list -> objectPad" "vector -> list"   

> 
> adjacencyOfClasses("gbutils", FALSE, "matrixOfPairs")
$vertices
[1] "objectPad" "list"     

$edges
     [,1]   [,2]       
[1,] "list" "objectPad"

> adjacencyOfClasses("gbutils", TRUE,  "matrixOfPairs")
$vertices
[1] "objectPad" "list"      "vector"   

$edges
     [,1]     [,2]       
[1,] "list"   "objectPad"
[2,] "vector" "list"     

> 
> adjacencyOfClasses("gbutils", FALSE, "adjacencyMatrix")
$vertices
[1] "objectPad" "list"     

$AM
          objectPad list
objectPad         0    1
list              0    0

> adjacencyOfClasses("gbutils", TRUE,  "adjacencyMatrix")
$vertices
[1] "objectPad" "list"      "vector"   

$AM
          objectPad list vector
objectPad         0    1      0
list              0    0      1
vector            0    0      0

> 
> ## as above, also represent the graph using the edges
> adjacencyOfClasses("gbutils", Wolfram = TRUE)
Graph[{objectPad,list}, {list -> objectPad}, VertexLabels -> Automatic] 

$vertices
[1] "objectPad" "list"     

$edges
[1] "list -> objectPad"

> adjacencyOfClasses("gbutils", TRUE, Wolfram = TRUE)
Graph[{objectPad,list,vector}, {list -> objectPad, vector -> list}, VertexLabels -> Automatic] 

$vertices
[1] "objectPad" "list"      "vector"   

$edges
[1] "list -> objectPad" "vector -> list"   

> 
> ## here the graph is represented by the adjacency matrix: 
> adjacencyOfClasses("gbutils", FALSE, "adjacencyMatrix", Wolfram = TRUE)
AdjacencyGraph[{objectPad,list}, {{0, 0},
{1, 0} }
, VertexLabels -> Automatic] 

$vertices
[1] "objectPad" "list"     

$AM
          objectPad list
objectPad         0    1
list              0    0

> adjacencyOfClasses("gbutils", TRUE,  "adjacencyMatrix", Wolfram = TRUE)
AdjacencyGraph[{objectPad,list,vector}, {{0, 0, 0},
{1, 0, 0},
{0, 1, 0} }
, VertexLabels -> Automatic] 

$vertices
[1] "objectPad" "list"      "vector"   

$AM
          objectPad list vector
objectPad         0    1      0
list              0    0      1
vector            0    0      0

> 
> if(requireNamespace("graph") && requireNamespace("Rgraphviz")) withAutoprint({
+     ## another package
+     adjacencyOfClasses("graph")
+     ac1 <- adjacencyOfClasses("graph", FALSE, "adjacencyMatrix")
+     gr_ac1 <- graph::graphAM(adjMat = ac1$AM, edgemode = "directed")
+     if(require("Rgraphviz"))
+         plot(gr_ac1)
+     ## more than one package
+     ac2 <- adjacencyOfClasses(c("graph", "Rgraphviz"), FALSE, "adjacencyMatrix")
+     gr_ac2 <- graph::graphAM(adjMat = ac2$AM, edgemode = "directed")
+     if(require("Rgraphviz"))
+         plot(gr_ac2)
+ })
Loading required namespace: graph
Loading required namespace: Rgraphviz
Warning: multiple methods tables found for 'plot'
> adjacencyOfClasses("graph")
$vertices
 [1] "attrPos"      "edgeSet"      "graphBase"    "renderInfo"   "MGEdgeSet"   
 [6] "MultiGraph"   "UEdgeSet"     "simpleEdge"   "graphAM"      "graphBAM"    
[11] "clusterGraph" "attrData"     "multiGraph"   "distGraph"    "edgeSetAM"   
[16] "DiEdgeSet"    "edgeSetNEL"   "graphNEL"     "graph"       

$edges
 [1] "edgeSet -> edgeSetNEL"   "edgeSet -> edgeSetAM"   
 [3] "graphBase -> graph"      "graphBase -> MultiGraph"
 [5] "graph -> graphNEL"       "graph -> graphAM"       
 [7] "graph -> distGraph"      "graph -> clusterGraph"  
 [9] "graph -> graphBAM"       "MGEdgeSet -> DiEdgeSet" 
[11] "MGEdgeSet -> UEdgeSet"  

> ac1 <- adjacencyOfClasses("graph", FALSE, "adjacencyMatrix")
> gr_ac1 <- graph::graphAM(adjMat = ac1$AM, edgemode = "directed")
> if (require("Rgraphviz")) plot(gr_ac1)
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: grid
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: withAutoprint ... eval -> eval -> plot -> plot -> plot.default -> xy.coords
Execution halted