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

> ### Name: segmentByNonPairedPSCBS
> ### Title: Segment total copy numbers and allele B fractions using the
> ###   Non-paired PSCBS method
> ### Aliases: segmentByNonPairedPSCBS.default segmentByNonPairedPSCBS
> ###   segmentByNonPairedPSCBS.data.frame
> ###   segmentByNonPairedPSCBS.PairedPSCBS segmentByNonPairedPSCBS
> ### Keywords: IO
> 
> ### ** Examples
> 
> verbose <- R.utils::Arguments$getVerbose(-10*interactive(), timestamp=TRUE)
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Load SNP microarray data
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> data <- PSCBS::exampleData("paired.chr01")
> str(data)
'data.frame':	73346 obs. of  6 variables:
 $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
 $ x         : int  1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ...
 $ CT        : num  1.625 1.071 1.406 1.18 0.856 ...
 $ betaT     : num  0.757 0.771 0.834 0.778 0.229 ...
 $ CN        : num  2.36 2.13 2.59 1.93 1.71 ...
 $ betaN     : num  0.827 0.875 0.887 0.884 0.103 ...
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Paired PSCBS segmentation
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Drop single-locus outliers
> dataS <- dropSegmentationOutliers(data)
> 
> # Speed up example by segmenting fewer loci
> dataS <- dataS[seq(from=1, to=nrow(data), by=20),]
> 
> str(dataS)
'data.frame':	3668 obs. of  6 variables:
 $ chromosome: int  1 1 1 1 1 1 1 1 1 1 ...
 $ x         : int  1145994 4276892 5034491 6266412 8418532 11211748 13928296 14370144 15014887 16589707 ...
 $ CT        : num  1.63 1.16 1.35 1.39 1.55 ...
 $ betaT     : num  0.7574 0.0576 0.8391 0.7917 0.8141 ...
 $ CN        : num  2.36 2.32 2.33 2.97 2.31 ...
 $ betaN     : num  0.8274 0.0421 0.9406 0.869 0.6045 ...
> 
> R.oo::attachLocally(dataS)
> 
> # Non-Paired PSCBS segmentation
> fit <- segmentByNonPairedPSCBS(CT, betaT=betaT,
+                             chromosome=chromosome, x=x,
+                             seed=0xBEEF, verbose=verbose)
Warning in parseRepos(sets = repos, where = where, fallback = fallback,  :
  Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’
[2017-04-21 00:23:01] Exception: Package 'aroma.light' is not available from any of the repositories: ‘http://cran.r-project.org’

  at #06. installPkg(pkg, version = version, repos = repos, ..., quietly = quietly, 
              verbose = verbose)
          - installPkg() is local of the calling function

  at #05. use.default(package, ..., how = "load")
          - use.default() is in environment 'R.utils'

  at #04. use(package, ..., how = "load")
          - use() is in environment 'R.utils'

  at #03. .use("findPeaksAndValleys", package = "aroma.light")
          - .use() is in environment 'PSCBS'

  at #02. segmentByNonPairedPSCBS.default(CT, betaT = betaT, chromosome = chromosome, 
              x = x, seed = 48879, verbose = verbose)
          - segmentByNonPairedPSCBS.default() is in environment 'PSCBS'

  at #01. segmentByNonPairedPSCBS(CT, betaT = betaT, chromosome = chromosome, 
              x = x, seed = 48879, verbose = verbose)
          - segmentByNonPairedPSCBS() is in environment 'PSCBS'

Error: Package 'aroma.light' is not available from any of the repositories: ‘http://cran.r-project.org’
Execution halted