Running ‘001.setupExampleData,annotationData.R’ [12s/12s]
  Running ‘002.setupExampleData,rawData.R’ [2s/2s]
  Running ‘AffymetrixCdfFile.R’ [4s/4s]
  Running ‘AffymetrixCelFile.R’ [2s/2s]
  Running ‘AffymetrixCelSet.R’ [2s/3s]
Running the tests in ‘tests/AffymetrixCelSet.R’ failed.
Complete output:
  > library("aroma.affymetrix")
  Loading required package: R.utils
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.21.0 (2016-10-30) successfully loaded. See ?R.oo for help.
  
  Attaching package: 'R.oo'
  
  The following objects are masked from 'package:methods':
  
      getClasses, getMethods
  
  The following objects are masked from 'package:base':
  
      attach, detach, gc, load, save
  
  R.utils v2.6.0 (2017-11-04) successfully loaded. See ?R.utils for help.
  
  Attaching package: 'R.utils'
  
  The following object is masked from 'package:utils':
  
      timestamp
  
  The following objects are masked from 'package:base':
  
      cat, commandArgs, getOption, inherits, isOpen, parse, warnings
  
  Loading required package: aroma.core
  Loading required package: R.filesets
  R.filesets v2.12.0 successfully loaded. See ?R.filesets for help.
  
  Attaching package: 'R.filesets'
  
  The following objects are masked from 'package:R.utils':
  
      extract, validate
  
  The following objects are masked from 'package:base':
  
      append, readLines
  
  Loading required package: R.devices
  R.devices v2.15.1 (2016-11-09) successfully loaded. See ?R.devices for help.
  aroma.core v3.1.1 (2017-09-12) successfully loaded. See ?aroma.core for help.
  
  Attaching package: 'aroma.core'
  
  The following objects are masked from 'package:base':
  
      .Machine, colMeans, colSums, library, require, write
  
  Loading required package: aroma.light
  aroma.light v3.9.1 (2017-12-19) successfully loaded. See ?aroma.light for help.
  
  Attaching package: 'aroma.light'
  
  The following objects are masked from 'package:aroma.affymetrix':
  
      averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
      plotXYCurve
  
  The following objects are masked from 'package:aroma.core':
  
      callNaiveGenotypes, normalizeTumorBoost
  
  Loading required package: affxparser
  
  Attaching package: 'affxparser'
  
  The following object is masked from 'package:aroma.affymetrix':
  
      writeCdf
  
  The following object is masked from 'package:R.utils':
  
      findFiles
  
  The following object is masked _by_ package:aroma.affymetrix:
  
      writeCdf
  
  The following object is masked from package:R.utils:
  
      findFiles
  
  aroma.affymetrix v3.1.0 (2017-03-23) successfully loaded. See ?aroma.affymetrix for help.
  
  Attaching package: 'aroma.affymetrix'
  
  The following objects are masked _by_ 'package:aroma.light':
  
      averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
      plotXYCurve
  
  The following object is masked from 'package:affxparser':
  
      writeCdf
  
  > 
  > ## Empty CEL set
  > ds <- AffymetrixCelSet()
  > print(ds)
  AffymetrixCelSet:
  Name: NA
  Tags: 
  Path: NA
  Platform: Affymetrix
  Chip type: NA
  Number of arrays: 0
  Time period: NA
  Total file size: 0 B
  > 
  > ## Extract non-existing subset on empty set
  > ds <- AffymetrixCelSet()
  > dsT <- extract(ds, "foo", onMissing="NA")
  > print(dsT)
  AffymetrixCelSet:
  Name: NA
  Tags: 
  Path: NA
  Platform: Affymetrix
  Chip type: NA
  Number of arrays: 1
  Names: NA [1]
  Time period: NA -- NA
  Total file size: 0 B
  > 
  > ## CEL set with non-existing CEL file
  > files <- list(AffymetrixCelFile())
  > ds <- AffymetrixCelSet(files)
  > print(ds)
  AffymetrixCelSet:
  Name: NA
  Tags: 
  Path: NA
  Platform: Affymetrix
  Chip type: NA
  Number of arrays: 1
  Names: NA [1]
  Time period: NA -- NA
  Total file size: 0 B
  > 
  > 
  > if (setupExampleData(aroma.affymetrix, mustWork=FALSE)) {
  +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  +   # CDF file
  +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  +   cdf <- AffymetrixCdfFile$byChipType("HG-Focus")
  +   print(cdf)
  + 
  +   # Unit names, types, ...
  +   names <- getUnitNames(cdf)
  +   str(names)
  + 
  +   units <- indexOf(cdf, names=names[42:40])
  +   stopifnot(all.equal(units, 42:40))
  + 
  +   types <- getUnitTypes(cdf)
  +   print(table(types))
  + 
  +   data <- readUnits(cdf, units=1:10)
  +   str(data)
  + 
  +   data <- readDataFrame(cdf, units=1:10)
  +   str(data)
  + 
  +   md5 <- getChecksumFile(cdf)
  +   print(md5)
  + 
  + 
  +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  +   # CEL set / CEL file
  +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  +   cels <- AffymetrixCelSet$byName("FusionSDK_HG-Focus", cdf=cdf)
  +   print(cels)
  + 
  +   # A single file
  +   cel <- cels[[1]]
  +   print(cel)
  + 
  +   # File checksums
  +   md5s <- getChecksumFileSet(cels)
  +   print(md5s)
  + 
  +   # File checksums
  +   md5 <- getChecksumFile(cel)
  +   print(md5)
  + 
  +   # Average CEL file
  +   celR <- getAverageFile(cels)
  +   print(celR)
  + 
  + 
  +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  +   # AromaPlatformInterface
  +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  +   platform <- getAromaPlatform(cdf)
  +   print(platform)
  +   stopifnot(equals(getAromaPlatform(cels), platform))
  +   stopifnot(equals(getAromaPlatform(cel), platform))
  + 
  +   # Unit names file
  +   unf <- getUnitNamesFile(cdf)
  +   print(unf)
  +   stopifnot(equals(getUnitNamesFile(cels), unf))
  +   stopifnot(equals(getUnitNamesFile(cel), unf))
  + } # if (require("AffymetrixDataTestFiles"))
  AffymetrixCdfFile:
  Path: annotationData/chipTypes/HG-Focus
  Filename: HG-Focus.CDF
  File size: 4.06 MiB (4261873 bytes)
  Chip type: HG-Focus
  File format: v4 (binary; XDA)
  Dimension: 448x448
  Number of cells: 200704
  Number of units: 8793
  Cells per unit: 22.83
  Number of QC units: 10
   chr [1:8793] "AFFX-BioB-5_at" "AFFX-BioB-M_at" "AFFX-BioB-3_at" ...
  types
     1 
  8793 
  List of 10
   $ AFFX-BioB-5_at            :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-BioB-5_at:List of 6
    .. .. ..$ x        : int [1:40] 216 216 217 217 218 218 219 219 220 220 ...
    .. .. ..$ y        : int [1:40] 264 265 264 265 264 265 264 265 264 265 ...
    .. .. ..$ pbase    : chr [1:40] "A" "T" "C" "G" ...
    .. .. ..$ tbase    : chr [1:40] "T" "T" "G" "G" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-BioB-M_at            :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-BioB-M_at:List of 6
    .. .. ..$ x        : int [1:40] 218 218 219 219 220 220 221 221 222 222 ...
    .. .. ..$ y        : int [1:40] 266 267 266 267 266 267 266 267 266 267 ...
    .. .. ..$ pbase    : chr [1:40] "C" "G" "T" "A" ...
    .. .. ..$ tbase    : chr [1:40] "G" "G" "A" "A" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-BioB-3_at            :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-BioB-3_at:List of 6
    .. .. ..$ x        : int [1:40] 220 220 221 221 222 222 223 223 224 224 ...
    .. .. ..$ y        : int [1:40] 268 269 268 269 268 269 268 269 268 269 ...
    .. .. ..$ pbase    : chr [1:40] "C" "G" "C" "G" ...
    .. .. ..$ tbase    : chr [1:40] "G" "G" "G" "G" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-BioC-5_at            :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-BioC-5_at:List of 6
    .. .. ..$ x        : int [1:40] 222 222 223 223 224 224 225 225 226 226 ...
    .. .. ..$ y        : int [1:40] 270 271 270 271 270 271 270 271 270 271 ...
    .. .. ..$ pbase    : chr [1:40] "G" "C" "C" "G" ...
    .. .. ..$ tbase    : chr [1:40] "C" "C" "G" "G" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-BioC-3_at            :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-BioC-3_at:List of 6
    .. .. ..$ x        : int [1:40] 224 224 225 225 226 226 227 227 228 228 ...
    .. .. ..$ y        : int [1:40] 272 273 272 273 272 273 272 273 272 273 ...
    .. .. ..$ pbase    : chr [1:40] "A" "T" "T" "A" ...
    .. .. ..$ tbase    : chr [1:40] "T" "T" "A" "A" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-BioDn-5_at           :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-BioDn-5_at:List of 6
    .. .. ..$ x        : int [1:40] 226 226 227 227 228 228 229 229 230 230 ...
    .. .. ..$ y        : int [1:40] 274 275 274 275 274 275 274 275 274 275 ...
    .. .. ..$ pbase    : chr [1:40] "G" "C" "A" "T" ...
    .. .. ..$ tbase    : chr [1:40] "C" "C" "T" "T" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-BioDn-3_at           :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-BioDn-3_at:List of 6
    .. .. ..$ x        : int [1:40] 228 228 229 229 230 230 231 231 232 232 ...
    .. .. ..$ y        : int [1:40] 276 277 276 277 276 277 276 277 276 277 ...
    .. .. ..$ pbase    : chr [1:40] "T" "A" "T" "A" ...
    .. .. ..$ tbase    : chr [1:40] "A" "A" "A" "A" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-CreX-5_at            :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-CreX-5_at:List of 6
    .. .. ..$ x        : int [1:40] 230 230 231 231 232 232 233 233 216 216 ...
    .. .. ..$ y        : int [1:40] 278 279 278 279 278 279 278 279 280 281 ...
    .. .. ..$ pbase    : chr [1:40] "T" "A" "C" "G" ...
    .. .. ..$ tbase    : chr [1:40] "A" "A" "G" "G" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-CreX-3_at            :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-CreX-3_at:List of 6
    .. .. ..$ x        : int [1:40] 232 232 233 233 216 216 217 217 218 218 ...
    .. .. ..$ y        : int [1:40] 280 281 280 281 282 283 282 283 282 283 ...
    .. .. ..$ pbase    : chr [1:40] "C" "G" "A" "T" ...
    .. .. ..$ tbase    : chr [1:40] "G" "G" "T" "T" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ AFFX-HUMISGF3A/M97935_5_at:List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ AFFX-HUMISGF3A/M97935_5_at:List of 6
    .. .. ..$ x        : int [1:40] 443 443 249 249 390 390 266 266 416 416 ...
    .. .. ..$ y        : int [1:40] 331 332 123 124 335 336 285 286 331 332 ...
    .. .. ..$ pbase    : chr [1:40] "C" "G" "G" "C" ...
    .. .. ..$ tbase    : chr [1:40] "G" "G" "C" "C" ...
    .. .. ..$ expos    : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
  'data.frame':	400 obs. of  16 variables:
   $ unit           : int  1 1 1 1 1 1 1 1 1 1 ...
   $ unitName       : chr  "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" ...
   $ unitType       : chr  "expression" "expression" "expression" "expression" ...
   $ unitDirection  : chr  "antisense" "antisense" "antisense" "antisense" ...
   $ unitNbrOfAtoms : int  20 20 20 20 20 20 20 20 20 20 ...
   $ group          : int  1 1 1 1 1 1 1 1 1 1 ...
   $ groupName      : chr  "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" ...
   $ groupDirection : chr  "antisense" "antisense" "antisense" "antisense" ...
   $ groupNbrOfAtoms: int  20 20 20 20 20 20 20 20 20 20 ...
   $ cell           : int  118489 118937 118490 118938 118491 118939 118492 118940 118493 118941 ...
   $ x              : int  216 216 217 217 218 218 219 219 220 220 ...
   $ y              : int  264 265 264 265 264 265 264 265 264 265 ...
   $ pbase          : chr  "A" "T" "C" "G" ...
   $ tbase          : chr  "T" "T" "G" "G" ...
   $ indexPos       : int  0 0 1 1 2 2 3 3 4 4 ...
   $ atom           : int  0 0 1 1 2 2 3 3 4 4 ...
  ChecksumFile:
  Name: HG-Focus.CDF
  Tags: 
  Full name: HG-Focus.CDF
  Pathname: annotationData/chipTypes/HG-Focus/HG-Focus.CDF.md5
  File size: 32 B (32 bytes)
  Checksum on record: 307006493ef52faf137da0bd84c59ca8
  [2018-03-25 18:57:36] Exception: Failed to setup a data set for any of 1 data directories located. The following reasons were reported: (1) Do not know how to unwrap object: SampleAnnotationSet (while trying './rawData/FusionSDK_HG-Focus/HG-Focus').
  
    at #03. byName.AffymetrixCelSet(static, ...)
            - byName.AffymetrixCelSet() is in environment 'aroma.affymetrix'
  
    at #02. byName(static, ...)
            - byName() is in environment 'R.filesets'
  
    at #01. AffymetrixCelSet$byName("FusionSDK_HG-Focus", cdf = cdf)
            - AffymetrixCelSet$byName() is local of the calling function
  
  Error: Failed to setup a data set for any of 1 data directories located. The following reasons were reported: (1) Do not know how to unwrap object: SampleAnnotationSet (while trying './rawData/FusionSDK_HG-Focus/HG-Focus').
  In addition: Warning message:
  In readCdfDataFrame(filename = "annotationData/chipTypes/HG-Focus/HG-Focus.CDF",  :
    Some of the fields were not read: expos
  Execution halted