> sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base =========================================================== installed.packages() Version Priority akima "0.5-10" NA annotate "1.36.0" NA AnnotationDbi "1.20.6" NA base "2.15.2" "base" Biobase "2.18.0" NA BiocGenerics "0.4.0" NA BiocInstaller "1.8.3" NA biomaRt "2.14.0" NA bitops "1.0-5" NA boot "1.3-7" "recommended" class "7.3-5" "recommended" cluster "1.14.3" "recommended" codetools "0.2-8" "recommended" compiler "2.15.2" "base" datasets "2.15.2" "base" DBI "0.2-5" NA DESeq "1.10.1" NA DEXSeq "1.4.0" NA foreign "0.8-52" "recommended" genefilter "1.40.0" NA geneplotter "1.36.0" NA graphics "2.15.2" "base" grDevices "2.15.2" "base" grid "2.15.2" "base" hwriter "1.3" NA IRanges "1.16.6" NA KernSmooth "2.23-9" "recommended" lattice "0.20-13" "recommended" locfit "1.5-8" NA MASS "7.3-23" "recommended" Matrix "1.0-11" "recommended" methods "2.15.2" "base" mgcv "1.7-22" "recommended" nlme "3.1-108" "recommended" nnet "7.3-5" "recommended" parallel "2.15.2" "base" pasilla "0.2.15" NA plyr "1.8" NA RColorBrewer "1.0-5" NA RCurl "1.95-4.1" NA rpart "4.1-0" "recommended" RSQLite "0.11.2" NA spatial "7.3-5" "recommended" splines "2.15.2" "base" statmod "1.4.17" NA stats "2.15.2" "base" stats4 "2.15.2" "base" stringr "0.6.2" NA survival "2.37-4" "recommended" tcltk "2.15.2" "base" tools "2.15.2" "base" utils "2.15.2" "base" XML "3.95-0.2" NA xtable "1.7-1" NA Depends akima "R (>= 2.0.0)" annotate "R (>= 2.10), AnnotationDbi (>= 0.1.15)" AnnotationDbi "R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.1.13),\nBiobase (>= 1.17.0)" base NA Biobase "R (>= 2.10), BiocGenerics (>= 0.3.2), utils" BiocGenerics "methods, graphics, stats" BiocInstaller "R (>= 2.15.0)" biomaRt "methods" bitops NA boot "R (>= 2.14.0), graphics, stats" class "R (>= 2.5.0), stats, utils" cluster "R (>= 2.10.0), stats, graphics, utils" codetools "R (>= 2.1)" compiler NA datasets NA DBI "R (>= 2.3.0), methods" DESeq "Biobase (>= 2.13.11), locfit, lattice" DEXSeq "Biobase (>= 2.13.11)" foreign "R (>= 2.14.0), stats" genefilter NA geneplotter "R (>= 2.10),Biobase (>= 2.5.5), annotate, lattice" graphics NA grDevices NA grid NA hwriter "R (>= 2.6.0)" IRanges "R (>= 2.8.0), methods, utils, stats, BiocGenerics (>= 0.1.4)" KernSmooth "R (>= 2.5.0), stats" lattice "R (>= 2.15.1)" locfit "R (>= 2.0.1)" MASS "R (>= 2.14.0), grDevices, graphics, stats, utils" Matrix "R (>= 2.15.0), stats, methods, utils, lattice" methods NA mgcv "R (>= 2.14.0), stats, graphics" nlme "graphics, stats, R (>= 2.14.0), R (< 3.0.0)" nnet "R (>= 2.5.0), stats, utils" parallel NA pasilla "DEXSeq, DESeq" plyr "R (>= 2.11.0)" RColorBrewer "R (>= 2.0.0)" RCurl "R (>= 2.7.0), methods, bitops" rpart "R (>= 2.14.0), graphics, stats, grDevices" RSQLite "R (>= 2.10.0), methods, DBI (>= 0.2-5)" spatial "R (>= 2.5.0), graphics, stats, utils" splines NA statmod "R (>= 1.6.1)" stats NA stats4 "methods, graphics, stats" stringr "R (>= 2.14)" survival "stats, utils, graphics, splines, R (>= 2.13.0)" tcltk NA tools NA utils NA XML "R (>= 1.2.0), methods, utils" xtable "R (>= 2.10.0)" Imports akima NA annotate "Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats,\nmethods, XML (>= 0.92-2), BiocGenerics (>= 0.1.13)" AnnotationDbi "methods, utils, DBI, RSQLite, BiocGenerics, Biobase, IRanges" base NA Biobase "methods, BiocGenerics" BiocGenerics "methods, graphics, stats" BiocInstaller NA biomaRt "utils, XML, RCurl" bitops NA boot NA class "MASS" cluster NA codetools NA compiler NA datasets NA DBI "methods" DESeq "genefilter, geneplotter, methods, MASS, RColorBrewer" DEXSeq "biomaRt, hwriter, methods, stringr, statmod (>= 1.4.15)" foreign "methods, utils" genefilter "AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10),\ngraphics, methods, stats, survival" geneplotter "annotate, AnnotationDbi, Biobase (>= 2.5.5), graphics,\ngrDevices, grid, methods, RColorBrewer, stats, utils" graphics "grDevices" grDevices NA grid "grDevices" hwriter NA IRanges "methods, utils, stats, BiocGenerics, stats4" KernSmooth NA lattice "grid, grDevices, graphics, stats, utils" locfit "akima, lattice" MASS NA Matrix "graphics, grid" methods "utils" mgcv "nlme, methods, Matrix" nlme "lattice" nnet NA parallel NA pasilla NA plyr NA RColorBrewer NA RCurl "methods" rpart NA RSQLite "methods, DBI (>= 0.2-3)" spatial NA splines "graphics, stats" statmod NA stats NA stats4 NA stringr NA survival NA tcltk NA tools NA utils NA XML "methods" xtable NA LinkingTo akima NA annotate NA AnnotationDbi NA base NA Biobase NA BiocGenerics NA BiocInstaller NA biomaRt NA bitops NA boot NA class NA cluster NA codetools NA compiler NA datasets NA DBI NA DESeq NA DEXSeq NA foreign NA genefilter NA geneplotter NA graphics NA grDevices NA grid NA hwriter NA IRanges NA KernSmooth NA lattice NA locfit NA MASS NA Matrix NA methods NA mgcv NA nlme NA nnet NA parallel NA pasilla NA plyr NA RColorBrewer NA RCurl NA rpart NA RSQLite NA spatial NA splines NA statmod NA stats NA stats4 NA stringr NA survival NA tcltk NA tools NA utils NA XML NA xtable NA Suggests akima NA annotate "Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.25.10),\nrae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, XML\n(>= 0.92-2), org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC,\nRgraphviz, RUnit," AnnotationDbi "DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db,\norg.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit,\nTxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db,\nseqnames.db, reactome.db, AnnotationForge" base NA Biobase "tools, tkWidgets, ALL" BiocGenerics "Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses,\noligo, affyPLM, RUnit" BiocInstaller "RUnit, BiocGenerics" biomaRt "annotate" bitops NA boot "MASS, survival" class NA cluster "MASS" codetools NA compiler NA datasets NA DBI NA DESeq "pasilla (>= 0.2.10), vsn, gplots" DEXSeq "pasilla (>= 0.2.13)" foreign NA genefilter "Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets,\nALL, ROC" geneplotter "Biobase (>= 2.5.5), Rgraphviz, annotate, fibroEset,\nhgu95av2.db, hu6800.db, hgu133a.db" graphics NA grDevices NA grid "lattice" hwriter NA IRanges "GenomicRanges, RUnit" KernSmooth "MASS" lattice "grid, KernSmooth, MASS" locfit "gam" MASS "lattice, nlme, nnet, survival" Matrix "expm, MASS" methods NA mgcv "nlme (>= 3.1-64), splines, Matrix, parallel" nlme "Hmisc, MASS" nnet "MASS" parallel NA pasilla "locfit, edgeR, xtable" plyr "abind, testthat (>= 0.2), tcltk, foreach, doMC, itertools,\niterators" RColorBrewer NA RCurl "Rcompression, XML" rpart "survival" RSQLite "RUnit (>= 0.4.22)" spatial "MASS" splines NA statmod "MASS, tweedie" stats NA stats4 NA stringr "testthat (>= 0.3)" survival NA tcltk NA tools NA utils NA XML "bitops, RCurl" xtable NA Enhances OS_type akima NA NA annotate NA NA AnnotationDbi NA NA base NA NA Biobase NA NA BiocGenerics NA NA BiocInstaller NA NA biomaRt NA NA bitops NA NA boot NA NA class NA NA cluster NA NA codetools NA NA compiler NA NA datasets NA NA DBI NA NA DESeq NA NA DEXSeq "parallel" NA foreign NA NA genefilter NA NA geneplotter NA NA graphics NA NA grDevices NA NA grid NA NA hwriter NA NA IRanges NA NA KernSmooth NA NA lattice "chron" NA locfit NA NA MASS NA NA Matrix "MatrixModels, graph, SparseM, sfsmisc" NA methods NA NA mgcv NA NA nlme NA NA nnet NA NA parallel "snow" NA pasilla NA NA plyr NA NA RColorBrewer NA NA RCurl NA NA rpart NA NA RSQLite NA NA spatial NA NA splines NA NA statmod NA NA stats NA NA stats4 NA NA stringr NA NA survival NA NA tcltk NA NA tools NA NA utils NA NA XML NA NA xtable NA NA License Built akima "file LICENSE" "2.15.2" annotate "Artistic-2.0" "2.15.2" AnnotationDbi "Artistic-2.0" "2.15.2" base "Part of R 2.15.2" "2.15.2" Biobase "Artistic-2.0" "2.15.2" BiocGenerics "Artistic-2.0" "2.15.2" BiocInstaller "Artistic-2.0" "2.15.2" biomaRt "Artistic-2.0" "2.15.2" bitops "GPL (>= 2)" "2.15.2" boot "Unlimited" "2.15.2" class "GPL-2 | GPL-3" "2.15.2" cluster "GPL (>= 2)" "2.15.2" codetools "GPL" "2.15.2" compiler "Part of R 2.15.2" "2.15.2" datasets "Part of R 2.15.2" "2.15.2" DBI "LGPL (>= 2)" "2.15.2" DESeq "GPL (>= 3)" "2.15.2" DEXSeq "GPL (>= 3)" "2.15.2" foreign "GPL (>= 2)" "2.15.2" genefilter "Artistic-2.0" "2.15.2" geneplotter "Artistic-2.0" "2.15.2" graphics "Part of R 2.15.2" "2.15.2" grDevices "Part of R 2.15.2" "2.15.2" grid "Part of R 2.15.2" "2.15.2" hwriter "LGPL-2.1" "2.15.2" IRanges "Artistic-2.0" "2.15.2" KernSmooth "Unlimited" "2.15.2" lattice "GPL (>= 2)" "2.15.2" locfit "GPL (>= 2)" "2.15.2" MASS "GPL-2 | GPL-3" "2.15.2" Matrix "GPL (>= 2)" "2.15.2" methods "Part of R 2.15.2" "2.15.2" mgcv "GPL (>=2)" "2.15.2" nlme "GPL (>= 2)" "2.15.2" nnet "GPL-2 | GPL-3" "2.15.2" parallel "Part of R 2.15.2" "2.15.2" pasilla "LGPL" "2.15.2" plyr "MIT" "2.15.2" RColorBrewer "Apache License 2.0" "2.15.2" RCurl "BSD" "2.15.2" rpart "GPL-2 | GPL-3" "2.15.2" RSQLite "LGPL (>= 2)" "2.15.2" spatial "GPL-2 | GPL-3" "2.15.2" splines "Part of R 2.15.2" "2.15.2" statmod "GPL (>= 2)" "2.15.2" stats "Part of R 2.15.2" "2.15.2" stats4 "Part of R 2.15.2" "2.15.2" stringr "GPL-2" "2.15.2" survival "LGPL (>= 2)" "2.15.2" tcltk "Part of R 2.15.2" "2.15.2" tools "Part of R 2.15.2" "2.15.2" utils "Part of R 2.15.2" "2.15.2" XML "BSD" "2.15.2" xtable "GPL (>= 2)" "2.15.2"