
R Under development (unstable) (2016-11-14 r71659) -- "Unsuffered Consequences"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.1.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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, sd, var, xtabs

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

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, 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, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

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

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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: 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.quantile <- preprocessQuantile(MsetEx)
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing.
> digest_preprocessQuantile <- list(M = minfi:::.digestMatrix(getM(GRset.quantile)),
+                                   CN = minfi:::.digestMatrix(getCN(GRset.quantile)))
> save(digest_preprocessQuantile, file = "../unitTests/digest_preprocessQuantile.rda")
> 
> sessionInfo()                         
R Under development (unstable) (2016-11-14 r71659)
Platform: x86_64-apple-darwin16.1.0 (64-bit)
Running under: macOS Sierra 10.12.1

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_0.6.10                                     
 [2] minfiData_0.21.1                                  
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
 [4] IlluminaHumanMethylation450kmanifest_0.4.0        
 [5] minfi_1.21.3                                      
 [6] bumphunter_1.15.0                                 
 [7] locfit_1.5-9.1                                    
 [8] iterators_1.0.8                                   
 [9] foreach_1.4.3                                     
[10] Biostrings_2.43.1                                 
[11] XVector_0.15.0                                    
[12] SummarizedExperiment_1.5.3                        
[13] Biobase_2.35.0                                    
[14] GenomicRanges_1.27.16                             
[15] GenomeInfoDb_1.11.6                               
[16] IRanges_2.9.14                                    
[17] S4Vectors_0.13.5                                  
[18] BiocGenerics_0.21.1                               

loaded via a namespace (and not attached):
 [1] mclust_5.2               base64_2.0               Rcpp_0.12.8             
 [4] lattice_0.20-34          Rsamtools_1.27.5         R6_2.2.0                
 [7] plyr_1.8.4               RSQLite_1.1              httr_1.2.1              
[10] zlibbioc_1.21.0          GenomicFeatures_1.27.4   data.table_1.10.0       
[13] annotate_1.53.0          Matrix_1.2-7.1           preprocessCore_1.37.0   
[16] splines_3.4.0            BiocParallel_1.9.2       stringr_1.1.0           
[19] RCurl_1.95-4.8           biomaRt_2.31.3           compiler_3.4.0          
[22] rtracklayer_1.35.1       multtest_2.31.0          pkgmaker_0.22           
[25] openssl_0.9.5            GEOquery_2.41.0          quadprog_1.5-5          
[28] codetools_0.2-15         matrixStats_0.51.0       XML_3.98-1.5            
[31] reshape_0.8.6            GenomicAlignments_1.11.6 MASS_7.3-45             
[34] bitops_1.0-6             grid_3.4.0               nlme_3.1-128            
[37] xtable_1.8-2             registry_0.3             DBI_0.5-1               
[40] magrittr_1.5             stringi_1.1.2            genefilter_1.57.0       
[43] doRNG_1.6                limma_3.31.6             nor1mix_1.2-2           
[46] RColorBrewer_1.1-2       siggenes_1.49.0          tools_3.4.0             
[49] illuminaio_0.17.0        rngtools_1.2.4           survival_2.40-1         
[52] AnnotationDbi_1.37.0     beanplot_1.2             memoise_1.0.0           
> rm(list = ls())
> 
> proc.time()
   user  system elapsed 
 35.815   2.237  38.703 
