import bumphunter, foldChange => log2FoldChange

note: I only passed check with --no-examples. otherwise I saw the following error:

pltCls> plotCluster(idx=1, regions=regsWithP$regions, annotation=annotation, coverageInfo=covInfo$coverage, groupInfo=group, txdb=TxDb.Hsapiens.UCSC.hg19.knownGene)
Error in initialize(value, ...) : 
  cannot use object of class “gg” in new():  class “Ideogram” does not extend that class
Calls: example ... plotIdeogram -> Ideogram -> new -> initialize -> initialize
In addition: Warning message:
In sampleDepth(list(genomeData$coverage), prob = 0.5, nonzero = TRUE,  :
  Sample column(s) 24, 25, 26, 28, 29, 30, 31 have sample depth coverage (nonzero=TRUE) as NA. Setting them to 0 (before centering if center=TRUE). Check for possible issues with this sample!
Calls: example ... source -> withVisible -> eval -> eval -> sampleDepth

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin12.5.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
 [2] GenomicFeatures_1.14.0                  
 [3] AnnotationDbi_1.24.0                    
 [4] Biobase_2.22.0                          
 [5] bumphunter_1.2.0                        
 [6] locfit_1.5-9.1                          
 [7] iterators_1.0.6                         
 [8] foreach_1.4.1                           
 [9] GenomicRanges_1.14.3                    
[10] XVector_0.2.0                           
[11] IRanges_1.20.5                          
[12] BiocGenerics_0.8.0                      
[13] derfinder_0.0.32                        
[14] RcppArmadillo_0.3.920.1                 
[15] Rcpp_0.10.6                             
[16] devtools_1.3                            
[17] BiocInstaller_1.12.0                    
[18] Defaults_1.1-1                          

loaded via a namespace (and not attached):
 [1] biomaRt_2.18.0          Biostrings_2.30.1       biovizBase_1.10.3      
 [4] bitops_1.0-6            BSgenome_1.30.0         cluster_1.14.4         
 [7] codetools_0.2-8         colorspace_1.2-4        DBI_0.2-7              
[10] dichromat_2.0-0         digest_0.6.3            doRNG_1.5.5            
[13] evaluate_0.5.1          ggbio_1.10.6            ggplot2_0.9.3.1        
[16] grid_3.0.2              gridExtra_0.9.1         gtable_0.1.2           
[19] Hmisc_3.12-2            httr_0.2                itertools_0.1-1        
[22] labeling_0.2            lattice_0.20-24         MASS_7.3-29            
[25] matrixStats_0.8.12      memoise_0.1             munsell_0.4.2          
[28] pkgmaker_0.17.4         plyr_1.8                proto_0.3-10           
[31] qvalue_1.36.0           R.methodsS3_1.5.2       RColorBrewer_1.0-5     
[34] RCurl_1.95-4.1          registry_0.2            reshape2_1.2.2         
[37] rngtools_1.2.3          rpart_4.1-3             Rsamtools_1.14.1       
[40] RSQLite_0.11.4          rtracklayer_1.22.0      scales_0.2.3           
[43] stats4_3.0.2            stringr_0.6.2           tcltk_3.0.2            
[46] tools_3.0.2             VariantAnnotation_1.8.5 whisker_0.3-2          
[49] XML_3.98-1.1            xtable_1.7-1            zlibbioc_1.8.0