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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: simPATHy
> ### Title: Simulate data from a graphical model
> ### Aliases: simPATHy
> 
> ### ** Examples
> 
> if(require(gRbase) & require(graph)){
+ 
+   ## Directed graph
+   ## sub-graph Acute Myel... Leukemia
+   graph<-gRbase::dag(~867:25+867:613+5295:867+5294:867+
+                        + 207:5295+207:5294+4193:207+3551:207+
+                        + 4792:3551+7157:4193+3265:6654+
+                        + 3845:6654+6654:2885+2885:25+2885:613)
+   genes<-graph::nodes(graph)
+ 
+   # covariance matrix of the reference condition
+   data<-t(chimera[genes,colnames(chimera)==1])
+   S<-cov(data)
+   S<-fitSgraph(graph,S)
+ 
+   # select path to dysregulate
+   path<-list(c("613","867"),c("867","5295"),c("5295","207"),
+              c("207","4193"),c("4193","7157"))
+   ## ..or select the path in an interactive plot
+   # path<-getPathShiny(graph)
+ 
+   # select parameters of the dysregulation
+   min<-c(2,8,2,0.1,0.5)
+   max<-c(2,10,2,4,0.5)
+   prob<-c(1,0,0,0.5,1)
+ 
+   # activation, switch, switch, random, deactivation
+   dys<-cbind(min,max,prob)
+   rownames(dys)<-sapply(path,paste,collapse = "~")
+   dys
+ 
+   set.seed(123)
+   # main function
+   Result<-simPATHy(graph,path,S,min,max,prob)
+   class(Result)
+   names(Result)
+ 
+   # simulated data from two conditions
+   round(Result$dataset[c(1:3,501:503),1:5],3)
+ 
+   # Summary
+   easyLookDys(Result)
+   # ..or interactive summary
+   # easyLookShiny(resObj=Result,graph=graph)
+ 
+ 
+   # Visualization
+   plotCorGraph(S1=Result$S1,S2 = Result$S2,graph = graph,path = path,colLim = c(-0.3,0.3))
+   plotGraphNELD3(S1=Result$S1,S2 = Result$S2,graph = graph,colLim = c(-0.3,0.3))
+   rm(list=ls())
+ 
+ 
+   ## Undirected graph
+   graph <- gRbase::ug(~a:b, ~a:c, ~c:d, ~b:d, ~b:c)
+   # when reference condition covariance matrix is not supplied simPATHy generate a random one
+   Result_ug<-simPATHy(graph)
+   easyLookDys(Result_ug)
+   plotGraphNELD3(S1=Result_ug$S1,S2 = Result_ug$S2,graph = graph,colLim = c(-0.5,0.5))
+ 
+ }
Loading required package: gRbase
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: rownames<- -> rownames<-
Execution halted