Running ‘examplewithNAvalues.R’ [23s/29s]
  Running ‘examplewithRNAseq.R’ [23s/31s]
  Running ‘examplewithanchoringdata.R’ [23s/34s]
  Running ‘examplewithinsitudata.R’ [23s/30s]
  Running ‘examplewithmetabolomic.R’ [22s/31s]
  Running ‘examplewithmicroarray.R’ [23s/31s]
  Running ‘examplewithnoreplicate.R’ [22s/28s]
  Running ‘testAIC.R’ [22s/32s]
  Running ‘test_selectgroups.R’ [22s/30s]
  Running ‘testbmdcalc.R’ [23s/31s]
  Running ‘testbmdplotwithgradient.R’ [23s/32s]
  Running ‘testplotfit.R’ [22s/32s]
  Running ‘testresidualtests.R’ [23s/35s]
  Running ‘testscaling.R’ [22s/31s]
  Running ‘testsensitivityplot.R’ [22s/28s]
  Running ‘testthat.R’ [24s/34s]
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
  
  Attaching package: 'BiocGenerics'
  
  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, aperm, 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
  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"))
  converting counts to integer mode
  Error in qr.default(modelMatrix) : object '.F_dqrdc2' not found
  Calls: RNAseqdata ... DESeqDataSetFromMatrix -> DESeqDataSet -> checkFullRank -> qr -> qr.default
  Execution halted
Running the tests in ‘tests/examplewithmetabolomic.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
  
  Attaching package: 'BiocGenerics'
  
  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, aperm, 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
  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 metabolomic data
  > datafilename <- system.file("extdata", "metabolo_sample.txt", package="DRomics")
  > (o <- continuousomicdata(datafilename, check = TRUE))
  Elements of the experimental design in order to check the coding of the data:
  Tested doses and number of replicates for each dose:
  
     0 0.69  1.1 1.79 2.92 4.78 7.76 
    10    6    2    2    2    6    2 
  Number of items: 109 
  Identifiers of the first 20 items:
  
   [1] "P_2"  "P_4"  "P_5"  "P_6"  "P_7"  "P_10" "P_11" "P_12" "P_14" "P_16"
  [11] "P_19" "P_21" "P_22" "P_26" "P_32" "P_34" "P_35" "P_36" "P_37" "P_38"
  Warning message:
  In continuousomicdata(datafilename, check = TRUE) : 
  We recommend you to check that your omic data were correctly pretreated
  before importation. In particular data (e.g. metabolomic signal) should
  have been log-transformed, without replacing 0 values by NA values
  (consider using the half minimum method instead for example).
  > if (visualize)
  + 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))
  Error in qr.default(x) : object '.F_dqrdc2' not found
  Calls: itemselect -> lmFit -> nonEstimable -> qr -> qr.default
  Execution halted
Running the tests in ‘tests/examplewithmicroarray.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
  
  Attaching package: 'BiocGenerics'
  
  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, aperm, 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
  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 data and normalization if needed
  > # options to put in shiny : norm.method (4 methods)
  > ## sample of the transcripto data set
  > datafilename <- system.file("extdata", "transcripto_very_small_sample.txt", package="DRomics")
  > (o <- microarraydata(datafilename, check = TRUE, norm.method = "cyclicloess"))
  Just wait, the normalization using cyclicloess may take a few minutes.
  Elements of the experimental design in order to check the coding of the data:
  Tested doses and number of replicates for each dose:
  
      0  0.69 1.223 2.148 3.774 6.631 
      5     5     5     5     5     5 
  Number of items: 100 
  Identifiers of the first 20 items:
   [1] "1"    "2"    "3"    "4"    "5.1"  "6.1"  "7.1"  "8.1"  "9.1"  "10.1"
  [11] "11.1" "12.1" "13.1" "14.1" "15"   "16.1" "17.1" "18.1" "19.1" "20.1"
  Data were normalized between arrays using the following method: cyclicloess 
  > plot(o)
  > if (visualize) 
  + {
  +   (o.2 <- microarraydata(datafilename, check = TRUE, norm.method = "none"))
  +   (o.3 <- microarraydata(datafilename, check = TRUE, norm.method = "quantile"))
  +   (o.4 <- microarraydata(datafilename, check = TRUE, norm.method = "scale"))
  +   
  +   plot(o.2)
  +   plot(o.3)
  +   plot(o.4)
  + }
  > 
  > 
  > # 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))
  Error in qr.default(x) : object '.F_dqrdc2' not found
  Calls: itemselect -> lmFit -> nonEstimable -> qr -> qr.default
  Execution halted