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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eventTimingOverList
> ### Title: eventTiming for multiple samples and regions
> ### Aliases: eventTimingOverList getPi0Summary
> 
> ### ** Examples
> 
> if(require(GenomicRanges)){
+ 	#fix up mutation data to right format
+ 	data(mutData)
+ 	colnames(mutData)[1]<-c("chr")
+ 	colnames(mutData)[grep("t_alt_count",colnames(mutData))]<-"nMutAllele"
+ 	colnames(mutData)[grep("t_ref_count",colnames(mutData))]<-"nRefAllele"
+ 	mutData$nReads<-mutData$nMutAllele+mutData$nRefAllele
+ 	mutData$mutationId<-1:nrow(mutData)
+ 	
+ 	#add segmentation annotation -- second region is bogus, only for illustration
+ 	segs<-data.frame(chr=c(17,17),start=c(1,1.8e7+100),end=c(1.8e7,81195210),
+ 		normCont=0.22,segId=c("Seg1","Seg2"),type=c("CNLOH","SingleGain"))
+ 	##Create Trivial segmentation annotation for example
+ 	mutId<-mut2Seg(mutData,segs)
+ 	eventOut<-eventTimingOverList(dfList=list(Sample1=mutId),normCont=0.22)
+ 	getPi0Summary(eventOut)
+ }
Loading required package: GenomicRanges
Loading required package: stats4
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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Error in ..Internal(is.unsorted(x, FALSE)) : 
  2 arguments passed to .Internal(is.unsorted) which requires 3
Calls: mut2Seg ... .local -> <Anonymous> -> .splitAsList_by_Rle -> <Anonymous>
Execution halted