R version 3.0.1 Patched (2013-06-03 r62859) -- "Good Sport"
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Platform: x86_64-apple-darwin12.3.0 (64-bit)

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> library(bumphunter)
Loading required package: IRanges
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 object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    duplicated, eval, Filter, Find, get, intersect, lapply, Map,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unlist

Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22

Attaching package: ‘locfit’

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

    left, right

>   
> ## Generate dummy data
> set.seed(123)
> dat <- dummyData()
> 
> ## loessByCluster      
> loessSmoothed <- loessByCluster(cluster=dat$cluster, y=dat$mat[,1],
+                               bpSpan = 1000, minNum=7, minInSpan=5, maxSpan=1)
> save(loessSmoothed, file="../unitTests/loessSmoothed.rda")
> 
> ## runmedByCluster
> runmedSmoothed <- runmedByCluster(cluster=dat$cluster, y=dat$mat[,1],  k=5, endrule="constant")
> save(runmedSmoothed, file="../unitTests/runmedSmoothed.rda")
> 
> ## bumphunter test 1
> set.seed(123)
> bumpsTest1 <- bumphunter (dat$mat, design=dat$design, chr=dat$chr, pos=dat$pos, cluster=dat$cluster,
+                           coef=2, cutoff=0.28, smooth=TRUE, B=500,
+                           verbose=TRUE, smoothFunction=loessByCluster)
bumphunterEngine: Using a single core (backend: doSEQ, version: 1.4.1)
bumphunterEngine: Computing coefficients.
bumphunterEngine: Smoothing coefficients.
Loading required package: pkgmaker
Loading required package: registry

Attaching package: ‘pkgmaker’

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

    new2

bumphunterEngine: Performing 500 permutations.
bumphunterEngine: Computing marginal permutation p-values.
bumphunterEngine: Smoothing permutation coefficients.
bumphunterEngine: cutoff: 0.28
bumphunterEngine: Finding regions.
bumphunterEngine: Computing regions for each permutation.
bumphunterEngine: Estimating p-values and FWER.
> save(bumpsTest1, file="../unitTests/bumpsTest1.rda")
> 
> ## bumphunter test 2: chr unspecified
> set.seed(123)
> bumpsTest2 <- bumphunter (dat$mat, design=dat$design, pos=dat$pos, cluster=dat$cluster,
+                           coef=2, cutoff=0.28, maxGap=500, smooth=TRUE, B=500,
+                           verbose=TRUE, smoothFunction=loessByCluster)
bumphunterEngine: Using a single core (backend: doSEQ, version: 1.4.1)
bumphunterEngine: Computing coefficients.
bumphunterEngine: Smoothing coefficients.
bumphunterEngine: Performing 500 permutations.
bumphunterEngine: Computing marginal permutation p-values.
bumphunterEngine: Smoothing permutation coefficients.
bumphunterEngine: cutoff: 0.28
bumphunterEngine: Finding regions.
bumphunterEngine: Computing regions for each permutation.
bumphunterEngine: Estimating p-values and FWER.
> save(bumpsTest2, file="../unitTests/bumpsTest2.rda")
> 
> 
> 
> proc.time()
   user  system elapsed 
  9.171   0.123   9.283