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

> ### Name: labelSeg
> ### Title: Helper functions for plotting
> ### Aliases: labelSeg numChromosome divideGenome
> 
> ### ** Examples
> 
> data(mutData)
> segData<-data.frame(chromosome="17",start=c(0,1.8e7+1),
+     end=c(1.8e7,max(mutData$position)),totalCpy=c(2,NA),
+     markRegion=c(FALSE,TRUE))
> if(require(GenomicRanges) & require(IRanges)) labelSeg(chr=segData$chromosome,
+     start=segData$start,end=segData$end)
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, colMeans, colSums, colnames,
    dirname, 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

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] "p" "q"
> chr<-c("1","4","10","23","X")
> chr[order(chr)]
[1] "1"  "10" "23" "4"  "X" 
> chr[order(numChromosome(chr))]
Error in .makeSortEnum(decreasing, na.last) : 
  could not find function ".makeSortEnum"
Calls: order -> standardGeneric -> eval -> eval -> eval -> order
Execution halted