Running '001.setupExampleData,annotationData.R' [178s]
  Running '002.setupExampleData,rawData.R' [165s]
  Running 'AffymetrixCdfFile.R' [166s]
  Running 'AffymetrixCelFile.R' [1s]
  Running 'AffymetrixCelSet.R' [160s]
Running the tests in 'tests/001.setupExampleData,annotationData.R' failed.
Complete output:
  > library("aroma.affymetrix")
  Loading required package: R.utils
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help.
  
  Attaching package: 'R.oo'
  
  The following object is masked from 'package:R.methodsS3':
  
      throw
  
  The following objects are masked from 'package:methods':
  
      getClasses, getMethods
  
  The following objects are masked from 'package:base':
  
      attach, detach, load, save
  
  R.utils v2.12.3 (2023-11-18 01:00:02 UTC) 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, isOpen, nullfile, parse, use, warnings
  
  Loading required package: aroma.core
  Loading required package: R.filesets
  R.filesets v2.15.1 (2024-01-24 17:22:49 UTC) successfully loaded. See ?R.filesets for help.
  
  Attaching package: 'R.filesets'
  
  The following object is masked from 'package:R.utils':
  
      validate
  
  The following objects are masked from 'package:base':
  
      append, readLines
  
  Loading required package: R.devices
  R.devices v2.17.2 (2024-01-29 13:30:11 UTC) successfully loaded. See ?R.devices for help.
  aroma.core v3.3.1 (2024-02-19 08:40:02 UTC) 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 v3.32.0 (2023-10-24) 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 v3.2.2 (2024-02-18 20:40:03 UTC) 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
  
  > 
  > setupExampleData(aroma.affymetrix, dirs="annotationData", mustWork=FALSE)
  Reading CDF header...
  Reading CDF header...done
  Reading CDF QC units...
  Reading CDF QC units...done
  Reading CDF units...
  Reading CDF units...done
  Writing CDF structure...
  Timing for writeCdf():
     user  system elapsed 
     6.78    0.08    6.86 
  Writing CDF structure...done
  > 
  > proc.time()
     user  system elapsed 
     9.92    0.42   10.78 
Running the tests in 'tests/002.setupExampleData,rawData.R' failed.
Complete output:
  > library("aroma.affymetrix")
  Loading required package: R.utils
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help.
  
  Attaching package: 'R.oo'
  
  The following object is masked from 'package:R.methodsS3':
  
      throw
  
  The following objects are masked from 'package:methods':
  
      getClasses, getMethods
  
  The following objects are masked from 'package:base':
  
      attach, detach, load, save
  
  R.utils v2.12.3 (2023-11-18 01:00:02 UTC) 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, isOpen, nullfile, parse, use, warnings
  
  Loading required package: aroma.core
  Loading required package: R.filesets
  R.filesets v2.15.1 (2024-01-24 17:22:49 UTC) successfully loaded. See ?R.filesets for help.
  
  Attaching package: 'R.filesets'
  
  The following object is masked from 'package:R.utils':
  
      validate
  
  The following objects are masked from 'package:base':
  
      append, readLines
  
  Loading required package: R.devices
  R.devices v2.17.2 (2024-01-29 13:30:11 UTC) successfully loaded. See ?R.devices for help.
  aroma.core v3.3.1 (2024-02-19 08:40:02 UTC) 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 v3.32.0 (2023-10-24) 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 v3.2.2 (2024-02-18 20:40:03 UTC) 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
  
  > 
  > setupExampleData(aroma.affymetrix, dirs="rawData", mustWork=FALSE)
  Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuführen.
  Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuführen.
  Warning messages:
  1: In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
    running command 'C:\Windows\system32\cmd.exe /c mklink "rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL" "D:/RCompile/CRANpkg/lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL"' had status 1
  2: In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
    running command 'C:\Windows\system32\cmd.exe /c mklink "rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-2-121502.CEL" "D:/RCompile/CRANpkg/lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-2-121502.CEL"' had status 1
  > 
  > proc.time()
     user  system elapsed 
     1.10    0.31    3.03 
Running the tests in 'tests/AffymetrixCdfFile.R' failed.
Complete output:
  > library("aroma.affymetrix")
  Loading required package: R.utils
  Loading required package: R.oo
  Loading required package: R.methodsS3
  R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help.
  
  Attaching package: 'R.oo'
  
  The following object is masked from 'package:R.methodsS3':
  
      throw
  
  The following objects are masked from 'package:methods':
  
      getClasses, getMethods
  
  The following objects are masked from 'package:base':
  
      attach, detach, load, save
  
  R.utils v2.12.3 (2023-11-18 01:00:02 UTC) 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, isOpen, nullfile, parse, use, warnings
  
  Loading required package: aroma.core
  Loading required package: R.filesets
  R.filesets v2.15.1 (2024-01-24 17:22:49 UTC) successfully loaded. See ?R.filesets for help.
  
  Attaching package: 'R.filesets'
  
  The following object is masked from 'package:R.utils':
  
      validate
  
  The following objects are masked from 'package:base':
  
      append, readLines
  
  Loading required package: R.devices
  R.devices v2.17.2 (2024-01-29 13:30:11 UTC) successfully loaded. See ?R.devices for help.
  aroma.core v3.3.1 (2024-02-19 08:40:02 UTC) 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 v3.32.0 (2023-10-24) 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 v3.2.2 (2024-02-18 20:40:03 UTC) 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 CDF
  > cdf <- AffymetrixCdfFile()
  > print(cdf)
  AffymetrixCdfFile:
  Path: NA
  Filename: NA
  File size: NA
  Chip type: NA
  File format: NA
  Dimension: NAxNA
  Number of cells: NA
  > 
  > ## Missing CDF
  > cdf <- AffymetrixCdfFile(NA_character_, mustExist=FALSE)
  > print(cdf)
  AffymetrixCdfFile:
  Path: NA
  Filename: NA
  File size: NA
  Chip type: NA
  File format: NA
  Dimension: NAxNA
  Number of cells: NA
  > 
  > 
  > if (setupExampleData(aroma.affymetrix, dataset="FusionSDK_Test3", dirs="annotationData", mustWork=FALSE)) {
  +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  +   # CDF file
  +   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  +   cdf <- AffymetrixCdfFile$byChipType("Test3")
  +   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)
  + 
  +   ## Get an existing or create a new onocell CDF
  +   cdfM <- getMonocellCdf(cdf, verbose=-10)
  +   print(cdfM)
  +   t0 <- lastModified(getPathname(cdfM))
  +   print(t0)
  + 
  +   ## A monocell CDF can be re-created
  +   cdfM <- getMonocellCdf(cdf, force=TRUE)
  +   print(cdfM)
  +   t1 <- lastModified(getPathname(cdfM))
  +   print(t1)
  +   stopifnot(t1 >= t0)
  + } # if (... "AffymetrixDataTestFiles")
  Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuführen.
  AffymetrixCdfFile:
  Path: ../../../../lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA
  Filename: Test3.CDF
  File size: 243.77 KiB (249624 bytes)
  Chip type: Test3
  File format: v4 (binary; XDA)
  Dimension: 126x126
  Number of cells: 15876
  Number of units: 345
  Cells per unit: 46.02
  Number of QC units: 13
   chr [1:345] "Pae_16SrRNA_s_at" "Pae_23SrRNA_s_at" "PA1178_oprH_at" ...
  types
    1 
  345 
  List of 10
   $ Pae_16SrRNA_s_at:List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ Pae_16SrRNA_s_at:List of 6
    .. .. ..$ x        : int [1:32] 111 111 19 19 95 95 18 18 25 25 ...
    .. .. ..$ y        : int [1:32] 79 80 19 20 39 40 55 56 113 114 ...
    .. .. ..$ pbase    : chr [1:32] "t" "a" "a" "t" ...
    .. .. ..$ tbase    : chr [1:32] "a" "a" "t" "t" ...
    .. .. ..$ expos    : int [1:32] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ Pae_23SrRNA_s_at:List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ Pae_23SrRNA_s_at:List of 6
    .. .. ..$ x        : int [1:32] 124 124 56 56 1 1 85 85 62 62 ...
    .. .. ..$ y        : int [1:32] 95 96 99 100 23 24 41 42 9 10 ...
    .. .. ..$ pbase    : chr [1:32] "a" "t" "t" "a" ...
    .. .. ..$ tbase    : chr [1:32] "t" "t" "a" "a" ...
    .. .. ..$ expos    : int [1:32] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ PA1178_oprH_at  :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ PA1178_oprH_at:List of 6
    .. .. ..$ x        : int [1:24] 41 41 117 117 110 110 60 60 41 41 ...
    .. .. ..$ y        : int [1:24] 49 50 45 46 41 42 75 76 47 48 ...
    .. .. ..$ pbase    : chr [1:24] "a" "t" "g" "c" ...
    .. .. ..$ tbase    : chr [1:24] "t" "t" "c" "c" ...
    .. .. ..$ expos    : int [1:24] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ PA1816_dnaQ_at  :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ PA1816_dnaQ_at:List of 6
    .. .. ..$ x        : int [1:24] 21 21 68 68 119 119 62 62 118 118 ...
    .. .. ..$ y        : int [1:24] 105 106 41 42 49 50 37 38 97 98 ...
    .. .. ..$ pbase    : chr [1:24] "a" "t" "a" "t" ...
    .. .. ..$ tbase    : chr [1:24] "t" "t" "t" "t" ...
    .. .. ..$ expos    : int [1:24] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ PA3183_zwf_at   :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ PA3183_zwf_at:List of 6
    .. .. ..$ x        : int [1:24] 104 104 106 106 79 79 53 53 77 77 ...
    .. .. ..$ y        : int [1:24] 91 92 19 20 27 28 75 76 19 20 ...
    .. .. ..$ pbase    : chr [1:24] "t" "a" "a" "t" ...
    .. .. ..$ tbase    : chr [1:24] "a" "a" "t" "t" ...
    .. .. ..$ expos    : int [1:24] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ PA3640_dnaE_at  :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ PA3640_dnaE_at:List of 6
    .. .. ..$ x        : int [1:24] 113 113 81 81 10 10 110 110 119 119 ...
    .. .. ..$ y        : int [1:24] 41 42 27 28 45 46 103 104 91 92 ...
    .. .. ..$ pbase    : chr [1:24] "a" "t" "a" "t" ...
    .. .. ..$ tbase    : chr [1:24] "t" "t" "t" "t" ...
    .. .. ..$ expos    : int [1:24] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ PA4407_ftsZ_at  :List of 3
    ..$ type     : int 1
    ..$ direction: int 2
    ..$ groups   :List of 1
    .. ..$ PA4407_ftsZ_at:List of 6
    .. .. ..$ x        : int [1:24] 19 19 13 13 100 100 36 36 18 18 ...
    .. .. ..$ y        : int [1:24] 45 46 23 24 115 116 75 76 41 42 ...
    .. .. ..$ pbase    : chr [1:24] "c" "g" "a" "t" ...
    .. .. ..$ tbase    : chr [1:24] "g" "g" "t" "t" ...
    .. .. ..$ expos    : int [1:24] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 2
   $ Pae_16SrRNA_s_st:List of 3
    ..$ type     : int 1
    ..$ direction: int 1
    ..$ groups   :List of 1
    .. ..$ Pae_16SrRNA_s_st:List of 6
    .. .. ..$ x        : int [1:32] 94 94 82 82 79 79 95 95 77 77 ...
    .. .. ..$ y        : int [1:32] 61 62 67 68 21 22 49 50 97 98 ...
    .. .. ..$ pbase    : chr [1:32] "a" "t" "t" "a" ...
    .. .. ..$ tbase    : chr [1:32] "t" "t" "a" "a" ...
    .. .. ..$ expos    : int [1:32] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 1
   $ Pae_23SrRNA_s_st:List of 3
    ..$ type     : int 1
    ..$ direction: int 1
    ..$ groups   :List of 1
    .. ..$ Pae_23SrRNA_s_st:List of 6
    .. .. ..$ x        : int [1:32] 87 87 36 36 32 32 66 66 57 57 ...
    .. .. ..$ y        : int [1:32] 5 6 71 72 17 18 61 62 47 48 ...
    .. .. ..$ pbase    : chr [1:32] "t" "a" "a" "t" ...
    .. .. ..$ tbase    : chr [1:32] "a" "a" "t" "t" ...
    .. .. ..$ expos    : int [1:32] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 1
   $ PA1178_oprH_st  :List of 3
    ..$ type     : int 1
    ..$ direction: int 1
    ..$ groups   :List of 1
    .. ..$ PA1178_oprH_st:List of 6
    .. .. ..$ x        : int [1:24] 37 37 79 79 68 68 51 51 79 79 ...
    .. .. ..$ y        : int [1:24] 33 34 67 68 65 66 111 112 43 44 ...
    .. .. ..$ pbase    : chr [1:24] "t" "a" "c" "g" ...
    .. .. ..$ tbase    : chr [1:24] "a" "a" "g" "g" ...
    .. .. ..$ expos    : int [1:24] 0 0 1 1 2 2 3 3 4 4 ...
    .. .. ..$ direction: int 1
  'data.frame':	272 obs. of  16 variables:
   $ unit           : int  1 1 1 1 1 1 1 1 1 1 ...
   $ unitName       : chr  "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" ...
   $ unitType       : chr  "expression" "expression" "expression" "expression" ...
   $ unitDirection  : chr  "antisense" "antisense" "antisense" "antisense" ...
   $ unitNbrOfAtoms : int  16 16 16 16 16 16 16 16 16 16 ...
   $ group          : int  1 1 1 1 1 1 1 1 1 1 ...
   $ groupName      : chr  "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" ...
   $ groupDirection : chr  "antisense" "antisense" "antisense" "antisense" ...
   $ groupNbrOfAtoms: int  16 16 16 16 16 16 16 16 16 16 ...
   $ cell           : int  10066 10192 2414 2540 5010 5136 6949 7075 14264 14390 ...
   $ x              : int  111 111 19 19 95 95 18 18 25 25 ...
   $ y              : int  79 80 19 20 39 40 55 56 113 114 ...
   $ pbase          : chr  "T" "A" "A" "T" ...
   $ tbase          : chr  "A" "A" "T" "T" ...
   $ 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: Test3.CDF
  Tags: 
  Full name: Test3.CDF
  Pathname: ../../../../lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF.md5
  File size: 32 B (32 bytes)
  Checksum on record: f84c557f0882b82ab1c876f581a133f9
  Retrieving monocell CDF...
   Monocell chip type: Test3,monocell
   Locating monocell CDF...
    Pathname: 
   Locating monocell CDF...done
   Could not locate monocell CDF. Will create one for chip type...
    Creating monocell CDF...
     Chip type: Test3
     Validate (main) CDF...
     Validate (main) CDF...done
     Adding temporary suffix from file...
      Pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF
      Suffix: .tmp
      Rename existing file?: FALSE
      Temporary pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp
     Adding temporary suffix from file...done
     Number of cells per group field: 1
     Reading CDF group names...
     Reading CDF group names...done
               used (Mb) gc trigger (Mb) max used (Mb)
     Ncells  686928 36.7    1199758 64.1  1199758 64.1
     Vcells 1199352  9.2    8388608 64.0  2004062 15.3
               used (Mb) gc trigger (Mb) max used (Mb)
     Ncells  685542 36.7    1199758 64.1  1199758 64.1
     Vcells 1197651  9.2    8388608 64.0  2004062 15.3
     Number of cells per unit:
        Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
           1       1       1       1       1       1 
     Reading CDF QC units...
     Reading CDF QC units...done
     Number of QC cells: 1844 in 13 QC units (59.95 KiB)
     Total number of cells: 2189
     Best array dimension: 47x47 (=2209 cells, i.e. 20 left-over cells)
     Creating CDF header with source CDF as template...
      Setting up header...
       Reading CDF header...
       Reading CDF header...done
       Reading CDF unit names...
       Reading CDF unit names...done
      Setting up header...done
      Writing...
       destHeader:
       List of 12
        $ ncols      : int 47
        $ nrows      : int 47
        $ nunits     : int 345
        $ nqcunits   : int 13
        $ refseq     : chr ""
        $ chiptype   : chr "Test3"
        $ filename   : chr "../../../../lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF"
        $ rows       : int 126
        $ cols       : int 126
        $ probesets  : int 345
        $ qcprobesets: int 13
        $ reference  : chr ""
       unitNames:
        chr [1:345] "Pae_16SrRNA_s_at" "Pae_23SrRNA_s_at" "PA1178_oprH_at" ...
       qcUnitLengths:
        num [1:13] 2106 2106 1434 230 230 ...
       unitLengths:
        num [1:345] 116 116 116 116 116 116 116 116 116 116 ...
                 used (Mb) gc trigger (Mb) max used (Mb)
       Ncells  690025 36.9    1199758 64.1  1199758 64.1
       Vcells 1214354  9.3    8388608 64.0  2004062 15.3
                 used (Mb) gc trigger (Mb) max used (Mb)
       Ncells  691175 37.0    1199758 64.1  1199758 64.1
       Vcells 1216436  9.3    8388608 64.0  2087356 16.0
      Writing...done
     Creating CDF header with source CDF as template...done
     Writing QC units...
      Rearranging QC unit cell indices...
       Units:      
      Rearranging QC unit cell indices...done
                used (Mb) gc trigger (Mb) max used (Mb)
      Ncells  691556 37.0    1199758 64.1  1199758 64.1
      Vcells 1211968  9.3    8388608 64.0  2087356 16.0
     Writing QC units...done
     Number of units: 345
     Argument 'ram': 1.000000
     Average unit length: 116.000000 bytes
     Number of chunks: 1 (34482 units/chunk)
     Reading, extracting, and writing units...
      Chunk #1 of 1 (345 units)
      Reading CDF list structure...
      Reading CDF list structure...done
   => RAM: 1.56 MiB
                used (Mb) gc trigger (Mb) max used (Mb)
      Ncells  692594 37.0    1199758 64.1  1199758 64.1
      Vcells 1214722  9.3    8388608 64.0  2087356 16.0
     Reading, extracting, and writing units...done
     Temporary CDF file created:
     Output pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp
                                                            size isdir mode
     annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp 76542 FALSE  666
                                                                         mtime
     annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp 2024-03-23 11:07:02
                                                                         ctime
     annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp 2024-03-23 11:07:02
                                                                         atime exe
     annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp 2024-03-23 11:07:02  no
               used (Mb) gc trigger (Mb) max used (Mb)
     Ncells  695724 37.2    1199758 64.1  1199758 64.1
     Vcells 1222350  9.4    8388608 64.0  2087356 16.0
     Verifying the written CDF...
      Chunk 1 of 1
     Verifying the written CDF...done
               used (Mb) gc trigger (Mb) max used (Mb)
     Ncells  696860 37.3    1199758 64.1  1199758 64.1
     Vcells 1225281  9.4    8388608 64.0  2087356 16.0
     Dropping temporary suffix from file...
      Temporary pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp
      Suffix: .tmp
      Regular expression for suffix: \.tmp$
      Pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF
      Renaming existing file...
       Result: TRUE
      Renaming existing file...done
     Dropping temporary suffix from file...done
     File pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF
                                                        size isdir mode
     annotationData/chipTypes/Test3/Test3,monocell.CDF 76542 FALSE  666
                                                                     mtime
     annotationData/chipTypes/Test3/Test3,monocell.CDF 2024-03-23 11:07:02
                                                                     ctime
     annotationData/chipTypes/Test3/Test3,monocell.CDF 2024-03-23 11:07:02
                                                                     atime exe
     annotationData/chipTypes/Test3/Test3,monocell.CDF 2024-03-23 11:07:02  no
    Creating monocell CDF...done
   Could not locate monocell CDF. Will create one for chip type...done
   Could not locate monocell CDF. Will create one for chip type...done
  Retrieving monocell CDF...done
  AffymetrixCdfFile:
  Path: annotationData/chipTypes/Test3
  Filename: Test3,monocell.CDF
  File size: 74.75 KiB (76542 bytes)
  Chip type: Test3,monocell
  File format: v4 (binary; XDA)
  Dimension: 47x47
  Number of cells: 2209
  Number of units: 345
  Cells per unit: 6.40
  Number of QC units: 13
  [1] "2024-03-23 11:07:02 CET"
  AffymetrixCdfFile:
  Path: annotationData/chipTypes/Test3
  Filename: Test3,monocell.CDF
  File size: 74.75 KiB (76542 bytes)
  Chip type: Test3,monocell
  File format: v4 (binary; XDA)
  Dimension: 47x47
  Number of cells: 2209
  Number of units: 345
  Cells per unit: 6.40
  Number of QC units: 13
  [1] "2024-03-23 11:07:04 CET"
  Warning messages:
  1: In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
    running command 'C:\Windows\system32\cmd.exe /c mklink "annotationData/chipTypes/Test3/Test3.CDF" "D:/RCompile/CRANpkg/lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF"' had status 1
  2: In readCdfDataFrame(filename = "../../../../lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF",  :
    Some of the fields were not read: expos
  > 
  > proc.time()
     user  system elapsed 
     3.00    0.39    6.57 
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 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help.
  
  Attaching package: 'R.oo'
  
  The following object is masked from 'package:R.methodsS3':
  
      throw
  
  The following objects are masked from 'package:methods':
  
      getClasses, getMethods
  
  The following objects are masked from 'package:base':
  
      attach, detach, load, save
  
  R.utils v2.12.3 (2023-11-18 01:00:02 UTC) 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, isOpen, nullfile, parse, use, warnings
  
  Loading required package: aroma.core
  Loading required package: R.filesets
  R.filesets v2.15.1 (2024-01-24 17:22:49 UTC) successfully loaded. See ?R.filesets for help.
  
  Attaching package: 'R.filesets'
  
  The following object is masked from 'package:R.utils':
  
      validate
  
  The following objects are masked from 'package:base':
  
      append, readLines
  
  Loading required package: R.devices
  R.devices v2.17.2 (2024-01-29 13:30:11 UTC) successfully loaded. See ?R.devices for help.
  aroma.core v3.3.1 (2024-02-19 08:40:02 UTC) 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 v3.32.0 (2023-10-24) 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 v3.2.2 (2024-02-18 20:40:03 UTC) 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
  AffymetrixCelSet:
  Name: HG-Focus
  Tags: 
  Path: ../../../../lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin
  Platform: Affymetrix
  Chip type: HG-Focus
  Number of arrays: 2
  Names: HG-Focus-1-121502, HG-Focus-2-121502 [2]
  Time period: 2002-05-15 10:59:33 -- 2002-05-15 11:07:10
  Total file size: 3.84 MiB
  AffymetrixCelFile:
  Name: HG-Focus-1-121502
  Tags: 
  Full name: HG-Focus-1-121502
  Pathname: ../../../../lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL
  File size: 1.92 MiB (2012775 bytes)
  File format: v1 (binary; CC)
  Platform: Affymetrix
  Chip type: HG-Focus
  Timestamp: 2002-05-15 11:07:10
  ChecksumFileSet:
  Name: 2.Calvin
  Tags: 
  Full name: 2.Calvin
  Number of files: 2
  Names: HG-Focus-1-121502.CEL, HG-Focus-2-121502.CEL [2]
  Path (to the first file): ../../../../lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin
  Total file size: 64 B (64 bytes)
  ChecksumFile:
  Name: HG-Focus-1-121502.CEL
  Tags: 
  Full name: HG-Focus-1-121502.CEL
  Pathname: ../../../../lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL.md5
  File size: 32 B (32 bytes)
  Checksum on record: eb680c1b324e74b649e8b7fc643ee0c5
  AffymetrixCelFile:
  Name: .average-intensities-median-mad
  Tags: b6c18433fdbd8c5edcea9dc2fa49c6aa
  Full name: .average-intensities-median-mad,b6c18433fdbd8c5edcea9dc2fa49c6aa
  Pathname: ../../../../lib/4.4/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/.average-intensities-median-mad,b6c18433fdbd8c5edcea9dc2fa49c6aa.CEL
  File size: 1.91 MiB (2007713 bytes)
  File format: v4 (binary; XDA)
  Platform: Affymetrix
  Chip type: HG-Focus
  Timestamp: 2023-04-08 06:16:18
  AffymetrixPlatform:
  Platform: Affymetrix
  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
  Warning message:
  In readCdfDataFrame(filename = "annotationData/chipTypes/HG-Focus/HG-Focus.CDF",  :
    Some of the fields were not read: expos
  > 
  > proc.time()
     user  system elapsed 
     2.62    0.53    5.21