******************************************************* Rscript /share/data/umw_biocore/dnext_data/genome_data_other/tRAX/tRAX/checkRmodules.R DESeq2 Loading required package: S4Vectors Loading required package: stats4 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, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, 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.max, which.min Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars 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")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Warning messages: 1: package ‘DESeq2’ was built under R version 4.0.3 2: package ‘S4Vectors’ was built under R version 4.0.3 3: package ‘BiocGenerics’ was built under R version 4.0.3 4: package ‘IRanges’ was built under R version 4.0.3 5: package ‘GenomicRanges’ was built under R version 4.0.3 6: package ‘GenomeInfoDb’ was built under R version 4.0.3 7: package ‘SummarizedExperiment’ was built under R version 4.0.3 8: package ‘MatrixGenerics’ was built under R version 4.0.3 9: package ‘matrixStats’ was built under R version 4.0.5 10: package ‘Biobase’ was built under R version 4.0.3 Warning message: package ‘reshape2’ was built under R version 4.0.5 Warning message: package ‘scales’ was built under R version 4.0.5 Attaching package: ‘plyr’ The following object is masked from ‘package:matrixStats’: count The following object is masked from ‘package:IRanges’: desc The following object is masked from ‘package:S4Vectors’: rename Warning message: package ‘plyr’ was built under R version 4.0.5 Attaching package: ‘gridExtra’ The following object is masked from ‘package:Biobase’: combine The following object is masked from ‘package:BiocGenerics’: combine Warning message: package ‘gridExtra’ was built under R version 4.0.5 Warning message: package ‘getopt’ was built under R version 4.0.5