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  1.  
  2. R version 3.4.0 Patched (2017-05-05 r72662) -- "You Stupid Darkness"
  3. Copyright (C) 2017 The R Foundation for Statistical Computing
  4. Platform: x86_64-w64-mingw32/x64 (64-bit)
  5.  
  6. R is free software and comes with ABSOLUTELY NO WARRANTY.
  7. You are welcome to redistribute it under certain conditions.
  8. Type 'license()' or 'licence()' for distribution details.
  9.  
  10. R is a collaborative project with many contributors.
  11. Type 'contributors()' for more information and
  12. 'citation()' on how to cite R or R packages in publications.
  13.  
  14. Type 'demo()' for some demos, 'help()' for on-line help, or
  15. 'help.start()' for an HTML browser interface to help.
  16. Type 'q()' to quit R.
  17.  
  18. > remove.packages("minfi")
  19. Removing package from ‘C:/Program Files/R/R-3.4.0patched/library’
  20. (as ‘lib’ is unspecified)
  21. > install.packages("C:/Users/mac/Desktop/minfi_1.20.2.tar.gz", repos = NULL, type = "source")
  22. * installing *source* package 'minfi' ...
  23. ** R
  24. ** inst
  25. ** preparing package for lazy loading
  26. ** help
  27. *** installing help indices
  28. ** building package indices
  29. ** installing vignettes
  30. ** testing if installed package can be loaded
  31. * DONE (minfi)
  32. > library("ChAMP")
  33. Loading required package: minfi
  34. Loading required package: BiocGenerics
  35. Loading required package: parallel
  36.  
  37. Attaching package: ‘BiocGenerics’
  38.  
  39. The following objects are masked from ‘package:parallel’:
  40.  
  41.     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
  42.  
  43. The following objects are masked from ‘package:stats’:
  44.  
  45.     IQR, mad, sd, var, xtabs
  46.  
  47. The following objects are masked from ‘package:base’:
  48.  
  49.     anyDuplicated, append, as.data.frame, cbind, colMeans, colnames, colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
  50.     lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
  51.     tapply, union, unique, unsplit, which, which.max, which.min
  52.  
  53. Loading required package: Biobase
  54. Welcome to Bioconductor
  55.  
  56.     Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
  57.  
  58. Loading required package: GenomicRanges
  59. Loading required package: stats4
  60. Loading required package: S4Vectors
  61.  
  62. Attaching package: ‘S4Vectors’
  63.  
  64. The following object is masked from ‘package:base’:
  65.  
  66.     expand.grid
  67.  
  68. Loading required package: IRanges
  69. Loading required package: GenomeInfoDb
  70. Loading required package: SummarizedExperiment
  71. Loading required package: DelayedArray
  72. Loading required package: matrixStats
  73.  
  74. Attaching package: ‘matrixStats’
  75.  
  76. The following objects are masked from ‘package:Biobase’:
  77.  
  78.     anyMissing, rowMedians
  79.  
  80.  
  81. Attaching package: ‘DelayedArray’
  82.  
  83. The following objects are masked from ‘package:matrixStats’:
  84.  
  85.     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
  86.  
  87. The following object is masked from ‘package:base’:
  88.  
  89.     apply
  90.  
  91. Loading required package: Biostrings
  92. Loading required package: XVector
  93.  
  94. Attaching package: ‘Biostrings’
  95.  
  96. The following object is masked from ‘package:DelayedArray’:
  97.  
  98.     type
  99.  
  100. The following object is masked from ‘package:base’:
  101.  
  102.     strsplit
  103.  
  104. Loading required package: bumphunter
  105. Loading required package: foreach
  106. foreach: simple, scalable parallel programming from Revolution Analytics
  107. Use Revolution R for scalability, fault tolerance and more.
  108. http://www.revolutionanalytics.com
  109. Loading required package: iterators
  110. Loading required package: locfit
  111. locfit 1.5-9.1   2013-03-22
  112. Setting options('download.file.method.GEOquery'='auto')
  113. Setting options('GEOquery.inmemory.gpl'=FALSE)
  114. Loading required package: ChAMPdata
  115. Loading required package: FEM
  116. Loading required package: AnnotationDbi
  117. Loading required package: Matrix
  118.  
  119. Attaching package: ‘Matrix’
  120.  
  121. The following object is masked from ‘package:S4Vectors’:
  122.  
  123.     expand
  124.  
  125. Loading required package: marray
  126. Loading required package: limma
  127.  
  128. Attaching package: ‘limma’
  129.  
  130. The following object is masked from ‘package:BiocGenerics’:
  131.  
  132.     plotMA
  133.  
  134. Loading required package: corrplot
  135. Loading required package: igraph
  136.  
  137. Attaching package: ‘igraph’
  138.  
  139. The following object is masked from ‘package:Biostrings’:
  140.  
  141.     union
  142.  
  143. The following object is masked from ‘package:GenomicRanges’:
  144.  
  145.     union
  146.  
  147. The following object is masked from ‘package:IRanges’:
  148.  
  149.     union
  150.  
  151. The following object is masked from ‘package:S4Vectors’:
  152.  
  153.     union
  154.  
  155. The following objects are masked from ‘package:BiocGenerics’:
  156.  
  157.     normalize, union
  158.  
  159. The following objects are masked from ‘package:stats’:
  160.  
  161.     decompose, spectrum
  162.  
  163. The following object is masked from ‘package:base’:
  164.  
  165.     union
  166.  
  167. Loading required package: impute
  168. Loading required package: org.Hs.eg.db
  169.  
  170. Loading required package: graph
  171.  
  172. Attaching package: ‘graph’
  173.  
  174. The following objects are masked from ‘package:igraph’:
  175.  
  176.     degree, edges, intersection
  177.  
  178. The following object is masked from ‘package:Biostrings’:
  179.  
  180.     complement
  181.  
  182. Loading required package: DMRcate
  183. Loading required package: DSS
  184. Loading required package: bsseq
  185.  
  186. Attaching package: ‘bsseq’
  187.  
  188. The following object is masked from ‘package:minfi’:
  189.  
  190.     getMeth
  191.  
  192. Loading required package: splines
  193. Loading required package: DMRcatedata
  194.  
  195. Loading required package: Illumina450ProbeVariants.db
  196. Loading required package: IlluminaHumanMethylationEPICmanifest
  197. Package loaded
  198.        ___ _      _   __  __ ___
  199.       / __| |_   /_\ |  \/  | _ \
  200.      | (__| ' \ / _ \| |\/| |  _/
  201.      \___|_||_/_/ \_\_|  |_|_|  
  202.      ------------------------------
  203. ChAMP provides comprehensive integrated analysis pipeline for DNA methylation HumanMethylation Beadchip.
  204.  
  205. You may use vignette("ChAMP") to view html version guildbook.
  206.  
  207. If you have any question or suggestion about ChAMP, please email to champ450k@gmail.com.
  208. There were 15 warnings (use warnings() to see them)
  209.  
  210.  
  211.  
  212.  
  213.  
  214.  
  215.  
  216.  
  217.  
  218. > testDir=system.file("extdata",package="ChAMPdata")
  219. > myLoad <- champ.load(testDir,arraytype="450K")
  220. [===========================]
  221. [<<<< ChAMP.LOAD START >>>>>]
  222. -----------------------------
  223. Loading data from C:/Program Files/R/R-3.4.0patched/library/ChAMPdata/extdata
  224. [read.metharray.sheet] Found the following CSV files:
  225.  
  226. [1] "C:/Program Files/R/R-3.4.0patched/library/ChAMPdata/extdata/lung_test_set.csv"
  227. Loading required package: IlluminaHumanMethylation450kmanifest
  228. << Read DataSet Success. >>
  229.  
  230. The fraction of failed positions per sample
  231.  
  232.            (You may need to delete samples with high proportion of failed probes
  233. ):
  234.   Failed CpG Fraction.
  235. C1         0.0013429122
  236. C2         0.0022162171
  237. C3         0.0003563249
  238. C4         0.0002842360
  239. T1         0.0003831007
  240. T2         0.0011946152
  241. T3         0.0014953286
  242. T4         0.0015447610
  243. Filtering probes with a detection p-value above 0.01 in one or more samples has removed 2728 probes from the analysis. If a large number of probes have been removed, ChAMP suggests you to identify potentially bad samples.
  244. << Filter DetP Done. >>
  245.  
  246. Error in bc_temp[TypeII.Name, ] <- nbcg[getProbeInfo(x, type = "II")$Address,  :
  247.  replacement has length zero
  248.  
  249.  
  250.  
  251.  
  252.  
  253.  
  254.  
  255.  
  256.  
  257.  
  258.  
  259.  
  260.  
  261. > sessionInfo()
  262. R version 3.4.0 Patched (2017-05-05 r72662)
  263. Platform: x86_64-w64-mingw32/x64 (64-bit)
  264. Running under: Windows >= 8 x64 (build 9200)
  265.  
  266. Matrix products: default
  267.  
  268. locale:
  269. [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                          
  270. [5] LC_TIME=English_United Kingdom.1252    
  271.  
  272. attached base packages:
  273. [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base    
  274.  
  275. other attached packages:
  276. [1] IlluminaHumanMethylation450kmanifest_0.4.0 ChAMP_2.8.0                                IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.12.0        
  277. [5] DMRcate_1.12.0                             DMRcatedata_1.12.0                         DSS_2.16.0                                 bsseq_1.12.1                              
  278. [9] FEM_3.4.0                                  graph_1.54.0                               org.Hs.eg.db_3.4.1                         impute_1.50.1                            
  279. [13] igraph_1.0.1                               corrplot_0.77                              marray_1.54.0                              limma_3.32.2                              
  280. [17] Matrix_1.2-10                              AnnotationDbi_1.38.0                       ChAMPdata_2.8.0                            minfi_1.20.2                              
  281. [21] bumphunter_1.16.0                          locfit_1.5-9.1                             iterators_1.0.8                            foreach_1.4.3                            
  282. [25] Biostrings_2.44.0                          XVector_0.16.0                             SummarizedExperiment_1.6.1                 DelayedArray_0.2.2                        
  283. [29] matrixStats_0.52.2                         GenomicRanges_1.28.1                       GenomeInfoDb_1.12.0                        IRanges_2.10.0                            
  284. [33] S4Vectors_0.14.0                           Biobase_2.36.2                             BiocGenerics_0.22.0                      
  285.  
  286. loaded via a namespace (and not attached):
  287.  [1] R.utils_2.5.0                                       IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 RSQLite_1.1-2                                      
  288.  [4] htmlwidgets_0.8                                     trimcluster_0.1-2                                   grid_3.4.0                                        
  289.  [7] BiocParallel_1.10.1                                 munsell_0.4.3                                       codetools_0.2-15                                  
  290. [10] preprocessCore_1.38.1                               statmod_1.4.29                                      colorspace_1.3-2                                  
  291. [13] fastICA_1.2-0                                       BiocInstaller_1.26.0                                knitr_1.15.1                                      
  292. [16] robustbase_0.92-7                                   JADE_2.0-0                                          isva_1.9                                          
  293. [19] GenomeInfoDbData_0.99.0                             biovizBase_1.24.0                                   diptest_0.75-7                                    
  294. [22] R6_2.2.0                                            doParallel_1.0.10                                   illuminaio_0.18.0                                  
  295. [25] clue_0.3-53                                         AnnotationFilter_1.0.0                              flexmix_2.3-14                                    
  296. [28] bitops_1.0-6                                        reshape_0.8.6                                       assertthat_0.2.0                                  
  297. [31] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0  scales_0.4.1                                        nnet_7.3-12                                        
  298. [34] gtable_0.2.0                                        methylumi_2.22.0                                    sva_3.24.0                                        
  299. [37] ensembldb_2.0.1                                     genefilter_1.58.1                                   rtracklayer_1.36.0                                
  300. [40] lazyeval_0.2.0                                      acepack_1.4.1                                       GEOquery_2.42.0                                    
  301. [43] dichromat_2.0-0                                     checkmate_1.8.2                                     yaml_2.1.14                                        
  302. [46] reshape2_1.4.2                                      GenomicFeatures_1.28.0                              backports_1.0.5                                    
  303. [49] httpuv_1.3.3                                        qvalue_2.8.0                                        Hmisc_4.0-3                                        
  304. [52] tools_3.4.0                                         nor1mix_1.2-2                                       ggplot2_2.2.1                                      
  305. [55] RColorBrewer_1.1-2                                  DNAcopy_1.50.1                                      siggenes_1.50.0                                    
  306. [58] Rcpp_0.12.10                                        plyr_1.8.4                                          base64enc_0.1-3                                    
  307. [61] zlibbioc_1.22.0                                     purrr_0.2.2                                         RCurl_1.95-4.8                                    
  308. [64] BiasedUrn_1.07                                      rpart_4.1-11                                        openssl_0.9.6                                      
  309. [67] viridis_0.4.0                                       cluster_2.0.6                                       magrittr_1.5                                      
  310. [70] data.table_1.10.4                                   goseq_1.28.0                                        mvtnorm_1.0-6                                      
  311. [73] wateRmelon_1.20.0                                   whisker_0.3-2                                       ProtGenerics_1.8.0                                
  312. [76] missMethyl_1.10.0                                   RPMM_1.25                                           mime_0.5                                          
  313. [79] xtable_1.8-2                                        XML_3.98-1.7                                        mclust_5.2.3                                      
  314. [82] gridExtra_2.2.1                                     compiler_3.4.0                                      biomaRt_2.32.0                                    
  315. [85] tibble_1.3.0                                        R.oo_1.21.0                                         htmltools_0.3.6                                    
  316. [88] mgcv_1.8-17                                         Formula_1.2-1                                       tidyr_0.6.2                                        
  317. [91] DBI_0.6-1                                           geneLenDataBase_1.12.0                              MASS_7.3-47                                        
  318. [94] fpc_2.1-10                                          permute_0.9-4                                       quadprog_1.5-5                                    
  319. [97] R.methodsS3_1.7.1                                   Gviz_1.20.0                                         RefFreeEWAS_2.1                                    
  320. [100] GenomicAlignments_1.12.0                            registry_0.3                                        foreign_0.8-68                                    
  321. [103] plotly_4.6.0                                        annotate_1.54.0                                     rngtools_1.2.4                                    
  322. [106] pkgmaker_0.22                                       multtest_2.32.0                                     beanplot_1.2                                      
  323. [109] ruv_0.9.6                                           doRNG_1.6.6                                         stringr_1.2.0                                      
  324. [112] VariantAnnotation_1.22.0                            digest_0.6.12                                       base64_2.0                                        
  325. [115] htmlTable_1.9                                       dendextend_1.5.2                                    kernlab_0.9-25                                    
  326. [118] shiny_1.0.3                                         Rsamtools_1.28.0                                    gtools_3.5.0                                      
  327. [121] modeltools_0.2-21                                   nlme_3.1-131                                        jsonlite_1.4                                      
  328. [124] viridisLite_0.2.0                                   BSgenome_1.44.0                                     lattice_0.20-35                                    
  329. [127] DEoptimR_1.0-8                                      httr_1.2.1                                          survival_2.41-3                                    
  330. [130] GO.db_3.4.1                                         interactiveDisplayBase_1.14.0                       shinythemes_1.1.1                                  
  331. [133] prabclus_2.2-6                                      class_7.3-14                                        stringi_1.1.5                                      
  332. [136] AnnotationHub_2.8.1                                 latticeExtra_0.6-28                                 memoise_1.1.0                                      
  333. [139] dplyr_0.5.0
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