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

> ### Name: RSeed-class
> ### Title: Class "RSeed"
> ### Aliases: RSeed RSeed-class buildGraph,RSeed-method
> ###   confidenceLevel,RSeed-method connectedComponentCutOff,RSeed-method
> ###   connectedComponentCutOff<-,RSeed-method
> ###   currencyMetabolites,RSeed-method currencyMetabolites<-,RSeed-method
> ###   getSourceMetabolites,RSeed-method graph_network,RSeed-method
> ###   graph_network<-,RSeed-method graph_scc,RSeed-method
> ###   graph_scc<-,RSeed-method initialize,RSeed-method list_sc,RSeed-method
> ###   list_sc<-,RSeed-method makeExperiment,RSeed-method
> ###   model_changes,RSeed-method model_changes<-,RSeed-method
> ###   model_edited,RSeed-method model_edited<-,RSeed-method
> ###   model_original,RSeed-method model_original<-,RSeed-method
> ###   plot,RSeed,missing-method scc_sizes,RSeed-method
> ###   scc_sizes<-,RSeed-method scc,RSeed-method scc<-,RSeed-method
> ###   sourceCompounds,RSeed-method show,RSeed-method buildGraph
> ###   combined_nodes combined_nodes<- confidenceLevel
> ###   connectedComponentCutOff connectedComponentCutOff<-
> ###   currencyMetabolites currencyMetabolites<- getSourceMetabolites
> ###   graph_network graph_network<- graph_scc graph_scc<- initialize
> ###   list_sc list_sc<- makeExperiment model_changes model_changes<-
> ###   model_edited model_edited<- model_original model_original<-
> ###   plot,RSeed,missing-method scc_sizes scc_sizes<- scc scc<-
> ###   sourceCompounds show
> ### Keywords: classes
> 
> ### ** Examples
> 
> 	data(Ec_core)
> 	ec <- new("RSeed", Ec_core)
> 	
> 	# run the experiment
> 	# calls of
> 	# buildGraph(ec)
> 	# sourceCompounds(ec)
> 	# would do the same in two steps.
> 	makeExperiment(ec)
building graph
preprocessing: checking if graph is connected
graph is connected
==Original Model:
model name:             Ecoli_core_model 
number of compartments  2 
                        C_c 
                        C_e 
number of reactions:    95 
number of metabolites:  72 
number of unique genes: 137 
objective function:     +1 Biomass_Ecoli_core_w_GAM 
==Connected Component Cut Off:
[1] 10
==currencyMetabolites:
NULL

==Edited Model:
NULL

==Model Changes:
  rmMet rmReact 
      0       0 

==Graph of the Network:
A graphNEL graph with directed edges
Number of Nodes = 72 
Number of Edges = 455 

==List of the Strong Connected Components:
[1] 7
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    1.00    1.00   10.29    1.50   65.00 

==Graph of the Strong Connected Components:
A graphAM graph with directed edges
Number of Nodes = 7 
Number of Edges = 6 

==List of the Source Compounds:
[1] 6
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   1.000   1.167   1.000   2.000 
> 	
> 	# look which nodes aggregate
> 	scc(ec)
$c1
 [1] "n1"  "n2"  "n3"  "n4"  "n5"  "n6"  "n7"  "n8"  "n9"  "n10" "n11" "n12"
[13] "n13" "n14" "n15" "n16" "n17" "n18" "n19" "n20" "n21" "n22" "n23" "n24"
[25] "n25" "n26" "n27" "n28" "n29" "n31" "n33" "n34" "n36" "n38" "n39" "n40"
[37] "n41" "n42" "n43" "n44" "n45" "n46" "n47" "n48" "n50" "n51" "n52" "n53"
[49] "n54" "n55" "n58" "n59" "n60" "n61" "n62" "n63" "n64" "n65" "n66" "n67"
[61] "n68" "n69" "n70" "n71" "n72"

$n30
[1] "n30"

$n32
[1] "n32"

$n35
[1] "n35"

$n37
[1] "n37"

$n49
[1] "n49"

$c7
[1] "n56" "n57"

> 	
> 	# look at source metabolites
> 	# (every list entry is a source compound)
> 	getSourceMetabolites(ec)
$n30
[1] "fru[e]"

$n32
[1] "fum[e]"

$n35
[1] "glc_D[e]"

$n37
[1] "gln_L[e]"

$n49
[1] "mal_L[e]"

$c7
[1] "o2[c]" "o2[e]"

> 	
> 	# plot the graph
> 	plot(ec)
Loading required namespace: Rgraphviz
Warning: multiple methods tables found for 'plot'
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted