Running 'examplewithLprobit.R' [37s]
  Running 'examplewithRNAseq.R' [21s]
  Running 'examplewithmetabolomic.R' [30s]
  Running 'examplewithmicroarray.R' [128s]
  Running 'testthat.R' [13s]
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
  
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      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'
  
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      expand.grid
  
  Loading required package: IRanges
  
  Attaching package: 'IRanges'
  
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      windows
  
  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'
  
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      anyMissing, rowMedians
  
  Loading required package: BiocParallel
  
  Attaching package: 'DelayedArray'
  
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      colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
  
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      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
  Elements of the experimental design in order to check the coding of the data :
  Tested doses and number of replicates for each dose:
  
     0 0.22 0.67    2    6 
     2    3    3    3    3 
  Number of items:  999 
  Identifiers of the first 20 items:
   [1] "NM_144958"    "NR_102758"    "NM_172405"    "NM_029777"    "NM_001130188"
   [6] "NM_207141"    "NM_001162368" "NM_008117"    "NM_001168290" "NM_010910"   
  [11] "NM_001004147" "NM_001146318" "NM_145597"    "NM_001161797" "NM_021483"   
  [16] "NR_002862"    "NR_033520"    "NM_134027"    "NM_010381"    "NM_019388"   
  Data were normalized with respect to library size
          and  tranformed using the following method:  rlog  
  > plot(o)
  > 
  > # item selection using the quadratic method
  > # options to put in shiny : select.method (3 methods), FDR (numerical positive value < 1)
  > (s_quad <- itemselect(o, select.method = "quadratic", FDR = 0.001))
  converting counts to integer mode
    the design formula contains a numeric variable with integer values,
    specifying a model with increasing fold change for higher values.
    did you mean for this to be a factor? if so, first convert
    this variable to a factor using the factor() function
  estimating size factors
  estimating dispersions
  gene-wise dispersion estimates
  mean-dispersion relationship
  final dispersion estimates
  fitting model and testing
  Error in .wrap_in_length_one_list_like_object(value, name, x) : 
    failed to coerce 'list(value)' to a DESeqResults object of length 1
  Calls: itemselect ... .append_list_element -> .wrap_in_length_one_list_like_object
  Execution halted