Running 'examplewithLprobit.R' [37s/41s]
  Running 'examplewithRNAseq.R' [16s/18s]
  Running 'examplewithmetabolomic.R' [34s/36s]
  Running 'examplewithmicroarray.R' [124s/133s]
  Running 'testthat.R' [15s/16s]
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, 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: 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: DelayedArray
  Loading required package: matrixStats
  
  Attaching package: 'matrixStats'
  
  The following objects are masked from 'package:Biobase':
  
      anyMissing, rowMedians
  
  Loading required package: BiocParallel
  
  Attaching package: 'DelayedArray'
  
  The following objects are masked from 'package:matrixStats':
  
      colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
  
  The following objects are masked from 'package:base':
  
      aperm, apply, rowsum
  
  > # 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")
  > (o <- RNAseqdata(datafilename, check = TRUE, transfo.method = "rlog"))
  Just wait, the transformation using regularized logarithm (rlog)
          may take a few minutes.
  converting counts to integer mode
  Error in `assays<-`(`*tmp*`, value = `*vtmp*`) : 
    please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
    withDimnames=FALSE)) <- value' when the dimnames on the supplied
    assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
  Calls: RNAseqdata ... rlog -> estimateDispersionsGeneEst -> assays<- -> assays<-
  Execution halted