
R version 3.2.0 Patched (2015-04-29 r68279) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin14.3.0 (64-bit)

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[Previously saved workspace restored]

> 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 object is masked from ‘package:stats’:

    xtabs

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

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

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: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
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')
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
> library(digest)
> 
> Mset.illumina <- preprocessIllumina(RGsetEx)
> digest_preprocessIllumina <- list(Meth = minfi:::.digestMatrix(getMeth(Mset.illumina)),
+                                       Unmeth = minfi:::.digestMatrix(getUnmeth(Mset.illumina)))
> save(digest_preprocessIllumina, file = "../unitTests/digest_preprocessIllumina.rda")
> 
> sessionInfo()                         
R version 3.2.0 Patched (2015-04-29 r68279)
Platform: x86_64-apple-darwin14.3.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

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_0.6.8                                      
 [2] minfiData_0.10.0                                  
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [4] IlluminaHumanMethylation450kmanifest_0.4.0        
 [5] minfi_1.15.2                                      
 [6] bumphunter_1.8.0                                  
 [7] locfit_1.5-9.1                                    
 [8] iterators_1.0.7                                   
 [9] foreach_1.4.2                                     
[10] Biostrings_2.36.1                                 
[11] XVector_0.8.0                                     
[12] GenomicRanges_1.20.3                              
[13] GenomeInfoDb_1.4.0                                
[14] IRanges_2.2.1                                     
[15] S4Vectors_0.6.0                                   
[16] lattice_0.20-31                                   
[17] Biobase_2.28.0                                    
[18] BiocGenerics_0.14.0                               

loaded via a namespace (and not attached):
 [1] mclust_5.0.1            rgl_0.95.1247           base64_1.1             
 [4] Rcpp_0.11.6             Rsamtools_1.20.1        plyr_1.8.2             
 [7] futile.options_1.0.0    RSQLite_1.0.0           zlibbioc_1.14.0        
[10] GenomicFeatures_1.20.1  annotate_1.46.0         preprocessCore_1.30.0  
[13] splines_3.2.0           BiocParallel_1.2.1      stringr_1.0.0          
[16] igraph_0.7.1            pheatmap_1.0.2          RCurl_1.95-4.6         
[19] biomaRt_2.24.0          munsell_0.4.2           RGCCA_2.0              
[22] rtracklayer_1.28.2      multtest_2.24.0         pkgmaker_0.22          
[25] GEOquery_2.34.0         quadprog_1.5-5          codetools_0.2-11       
[28] matrixStats_0.14.0      XML_3.98-1.1            reshape_0.8.5          
[31] GenomicAlignments_1.4.1 MASS_7.3-40             bitops_1.0-6           
[34] grid_3.2.0              nlme_3.1-120            xtable_1.7-4           
[37] gtable_0.1.2            registry_0.2            DBI_0.3.1              
[40] magrittr_1.5            scales_0.2.4            stringi_0.4-1          
[43] genefilter_1.50.0       doRNG_1.6               limma_3.24.3           
[46] futile.logger_1.4.1     nor1mix_1.2-0           lambda.r_1.1.7         
[49] RColorBrewer_1.1-2      mixOmics_5.0-4          siggenes_1.42.0        
[52] tools_3.2.0             illuminaio_0.10.0       rngtools_1.2.4         
[55] survival_2.38-1         colorspace_1.2-6        AnnotationDbi_1.30.1   
[58] beanplot_1.2           
> rm(list = ls())
> 
> proc.time()
   user  system elapsed 
 22.789   1.130  24.262 
