Running ‘callAllelicBalanceByBAFs.PairedPSCBS.R’ [1s/1s]
  Running ‘cnr.R’ [1s/2s]
Running the tests in ‘tests/cnr.R’ failed.
Complete output:
  > library("aroma.cn")
  Loading required package: R.utils
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.21.0 (2016-10-30) successfully loaded. See ?R.oo for help.
  
  Attaching package: 'R.oo'
  
  The following objects are masked from 'package:methods':
  
      getClasses, getMethods
  
  The following objects are masked from 'package:base':
  
      attach, detach, gc, load, save
  
  R.utils v2.6.0 (2017-11-04) successfully loaded. See ?R.utils for help.
  
  Attaching package: 'R.utils'
  
  The following object is masked from 'package:utils':
  
      timestamp
  
  The following objects are masked from 'package:base':
  
      cat, commandArgs, getOption, inherits, isOpen, parse, warnings
  
  Loading required package: aroma.core
  Loading required package: R.filesets
  R.filesets v2.12.1 successfully loaded. See ?R.filesets for help.
  
  Attaching package: 'R.filesets'
  
  The following objects are masked from 'package:R.utils':
  
      extract, validate
  
  The following objects are masked from 'package:base':
  
      append, readLines
  
  Loading required package: R.devices
  R.devices v2.15.1 (2016-11-09) successfully loaded. See ?R.devices for help.
  aroma.core v3.1.1 (2017-09-12) successfully loaded. See ?aroma.core for help.
  
  Attaching package: 'aroma.core'
  
  The following objects are masked from 'package:base':
  
      .Machine, colMeans, colSums, library, require, write
  
  Loading required package: aroma.light
  aroma.light v3.9.1 (2017-12-19) successfully loaded. See ?aroma.light for help.
  
  Attaching package: 'aroma.light'
  
  The following objects are masked from 'package:aroma.core':
  
      callNaiveGenotypes, normalizeTumorBoost
  
  aroma.cn v1.6.1 (2015-10-27) successfully loaded. See ?aroma.cn for help.
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  > # Build up a tumor CN profile
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  > pT <- cnr(1,1000, 2) +
  +      cnr(400,500) +
  +      cnr(600,800) +
  +      cnr(600,700) +
  +      cnr(100,200) - cnr(850,900)
  *** S3 method lookup problem ***
  [1] "$<-"
  <environment: namespace:base>
  <environment: namespace:R.oo>
  Error in UseMethod("$<-") : 
    no applicable method for '$<-' applied to an object of class "c('CopyNumberRegions', 'Object')"
  Calls: +.CopyNumberRegions -> [[<- -> [[<-.Object
  Execution halted