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

> ### Name: plot_manhattanRuns
> ### Title: Plot the proportion of times SNPs are inside runs - MANHATTAN
> ###   PLOT
> ### Aliases: plot_manhattanRuns
> 
> ### ** Examples
> 
> # getting map and ped paths
> genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
> mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")
> 
> # calculating runs of Homozygosity
> ## Not run: 
> ##D # skipping runs calculation
> ##D runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1,  minSNP = 15,
> ##D ROHet = FALSE,  maxOppositeGenotype = 1, maxMiss = 1,  minLengthBps = 100000,  minDensity = 1/10000)
> ## End(Not run)
> # loading pre-calculated data
> runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
> runsDF <- readExternalRuns(inputFile = runsFile, program = 'detectRUNS')
Loading file from detectRUNS
> 
> # plot runs per animal (interactive)
> plot_manhattanRuns(runs = runsDF, genotypeFile = genotypeFile, mapFile = mapFile,
+ savePlots = FALSE, plotTitle = "ROHom")
[1] "Calculation % SNP in ROH"
[1] "Chromosome founds:  2"

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[1] "Calculation % SNP in ROH finish"
[1] "Manhattan plot: START"
[1] "Processing Groups: Jacobs"
[1] "Creating Manhattan plot for  Jacobs"
[1] "Manhattan plot created for  Jacobs"
[1] "Processing Groups: Navajo-Churro"
[1] "Creating Manhattan plot for  Navajo-Churro"
[1] "Manhattan plot created for  Navajo-Churro"
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	gsub("[,\\; \t]", "\t", readLines(inputFile)) (textConnection)
Execution halted