Running 'examplewithLprobit.R' [11s]
  Running 'examplewithNAvalues.R' [10s]
  Running 'examplewithRNAseq.R' [12s]
  Running 'examplewithanchoringdata.R' [12s]
  Running 'examplewithmetabolomic.R' [14s]
  Running 'examplewithmicroarray.R' [13s]
  Running 'examplewithnoreplicate.R' [12s]
  Running 'testAIC.R' [13s]
  Running 'testbmdcalc.R' [13s]
  Running 'testresidualtests.R' [14s]
  Running 'testthat.R' [11s]
Running the tests in 'tests/examplewithRNAseq.R' failed.
Complete output:
  > library(DRomics)
  Loading required package: limma
  Loading required package: 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 object is masked from 'package:limma':
  
      plotMA
  
  The following objects are masked from 'package:stats':
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which.max, which.min
  
  
  Attaching package: 'S4Vectors'
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  Loading required package: IRanges
  
  Attaching package: 'IRanges'
  
  The following object is masked from 'package:grDevices':
  
      windows
  
  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
  
  > visualize <- FALSE # put to TRUE for a manual check of plots
  > doboot <- FALSE
  > 
  > # importation and check of RNAseq data and normalization
  > # with respect to library size and transformation 
  > # options to put in shiny : transfo.method (2 methods, rlog or vst)
  > datafilename <- system.file("extdata", "RNAseq_sample.txt", package="DRomics")
  > # small data set 'less than 1000 items (999)
  > (o.vst <- RNAseqdata(datafilename, check = TRUE, transfo.method = "vst"))
  Error in ..Internal(is.unsorted(x, FALSE)) : 
    2 arguments passed to .Internal(is.unsorted) which requires 3
  Calls: RNAseqdata ... asMethod -> PartitioningByEnd -> .numeric2end -> <Anonymous>
  Execution halted