
R version 3.3.1 RC (2016-06-14 r70789) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.5.0 (64-bit)

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> library(minfiData)
Loading required package: minfi
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, xtabs

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

    anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
    Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
> library(digest)
> 
> GRset.funnorm <- preprocessFunnorm(RGsetEx)
[preprocessFunnorm] Background and dye bias correction with noob 

[preprocessNoob] Applying R/G ratio flip to fix dye bias...
[preprocessFunnorm] Mapping to genome

[preprocessFunnorm] Quantile extraction

[preprocessFunnorm] Normalization

> digest_preprocessFunnorm <- list(M = minfi:::.digestMatrix(getM(GRset.funnorm)),
+                                  CN = minfi:::.digestMatrix(getCN(GRset.funnorm)))
> save(digest_preprocessFunnorm, file = "../unitTests/digest_preprocessFunnorm.rda")
> 
> sessionInfo()                         
R version 3.3.1 RC (2016-06-14 r70789)
Platform: x86_64-apple-darwin15.5.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] digest_0.6.9                                      
 [2] minfiData_0.16.0                                  
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.5.1
 [4] IlluminaHumanMethylation450kmanifest_0.5.0        
 [5] minfi_1.19.10                                     
 [6] bumphunter_1.13.1                                 
 [7] locfit_1.5-9.1                                    
 [8] iterators_1.0.8                                   
 [9] foreach_1.4.3                                     
[10] Biostrings_2.41.4                                 
[11] XVector_0.13.6                                    
[12] SummarizedExperiment_1.3.7                        
[13] GenomicRanges_1.25.9                              
[14] GenomeInfoDb_1.9.4                                
[15] IRanges_2.7.11                                    
[16] S4Vectors_0.11.9                                  
[17] lattice_0.20-33                                   
[18] Biobase_2.33.0                                    
[19] BiocGenerics_0.19.2                               

loaded via a namespace (and not attached):
 [1] genefilter_1.55.2       splines_3.3.1           beanplot_1.2           
 [4] rtracklayer_1.33.10     GenomicFeatures_1.25.15 chron_2.3-47           
 [7] XML_3.98-1.4            survival_2.39-4         DBI_0.4-1              
[10] BiocParallel_1.7.4      RColorBrewer_1.1-2      registry_0.3           
[13] rngtools_1.2.4          doRNG_1.6               matrixStats_0.50.2     
[16] plyr_1.8.4              pkgmaker_0.22           stringr_1.0.0          
[19] zlibbioc_1.19.0         codetools_0.2-14        biomaRt_2.29.2         
[22] AnnotationDbi_1.35.4    illuminaio_0.15.0       preprocessCore_1.35.0  
[25] Rcpp_0.12.6             xtable_1.8-2            openssl_0.9.4          
[28] limma_3.29.14           base64_2.0              annotate_1.51.0        
[31] Rsamtools_1.25.0        stringi_1.1.1           nor1mix_1.2-1          
[34] grid_3.3.1              GEOquery_2.39.3         quadprog_1.5-5         
[37] tools_3.3.1             bitops_1.0-6            magrittr_1.5           
[40] siggenes_1.47.0         RCurl_1.95-4.8          RSQLite_1.0.0          
[43] MASS_7.3-45             Matrix_1.2-6            data.table_1.9.6       
[46] httr_1.2.1              reshape_0.8.5           R6_2.1.2               
[49] mclust_5.2              GenomicAlignments_1.9.6 multtest_2.29.0        
[52] nlme_3.1-128           
> rm(list = ls())
> 
> proc.time()
   user  system elapsed 
 52.123   4.689  57.390 
