Running '001.setupExampleData,annotationData.R' [12s]
  Running '002.setupExampleData,rawData.R' [3s]
  Running 'AffymetrixCdfFile.R' [3s]
  Running 'AffymetrixCelFile.R' [2s]
  Running 'AffymetrixCelSet.R' [3s]
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 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.22.0 (2018-04-21) 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 v2.7.0 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 v2.12.1 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 v2.16.0 (2018-07-21) successfully loaded. See ?R.devices for help.
  aroma.core v3.1.3 (2018-04-29) 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 v3.10.0 (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 v3.1.1 (2018-04-05) 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)
  [2019-01-31 13:49:07] Exception: Failed to create file link: rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL[.lnk] -> D:/temp/Rtmpq2Nol4/RLIBS_29a805453528e/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL
  
    at #04. createLink.default(link = pathnameD, target = pathnameS, skip = TRUE)
            - createLink.default() is in environment 'R.utils'
  
    at #03. createLink(link = pathnameD, target = pathnameS, skip = TRUE)
            - createLink() is in environment 'R.utils'
  
    at #02. setupExampleData.AromaAffymetrix(aroma.affymetrix, dirs = "rawData", 
                mustWork = FALSE)
            - setupExampleData.AromaAffymetrix() is in environment 'aroma.affymetrix'
  
    at #01. setupExampleData(aroma.affymetrix, dirs = "rawData", mustWork = FALSE)
            - setupExampleData() is in environment 'aroma.affymetrix'
  
  Error: Failed to create file link: rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL[.lnk] -> D:/temp/Rtmpq2Nol4/RLIBS_29a805453528e/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL
  In addition: Warning message:
  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:/temp/Rtmpq2Nol4/RLIBS_29a805453528e/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL"' had status 1
  Execution halted
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 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
  R.oo v1.22.0 (2018-04-21) 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 v2.7.0 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 v2.12.1 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 v2.16.0 (2018-07-21) successfully loaded. See ?R.devices for help.
  aroma.core v3.1.3 (2018-04-29) 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 v3.10.0 (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 v3.1.1 (2018-04-05) 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")
  [2019-01-31 13:49:10] Exception: Failed to create file link: annotationData/chipTypes/Test3/Test3.CDF[.lnk] -> D:/temp/Rtmpq2Nol4/RLIBS_29a805453528e/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF
  
    at #04. createLink.default(link = pathnameD, target = pathnameS)
            - createLink.default() is in environment 'R.utils'
  
    at #03. createLink(link = pathnameD, target = pathnameS)
            - createLink() is in environment 'R.utils'
  
    at #02. setupExampleData.AromaAffymetrix(aroma.affymetrix, dataset = "FusionSDK_Test3", 
                dirs = "annotationData", mustWork = FALSE)
            - setupExampleData.AromaAffymetrix() is in environment 'aroma.affymetrix'
  
    at #01. setupExampleData(aroma.affymetrix, dataset = "FusionSDK_Test3", 
                dirs = "annotationData", mustWork = FALSE)
            - setupExampleData() is in environment 'aroma.affymetrix'
  
  Error: Failed to create file link: annotationData/chipTypes/Test3/Test3.CDF[.lnk] -> D:/temp/Rtmpq2Nol4/RLIBS_29a805453528e/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF
  In addition: Warning message:
  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:/temp/Rtmpq2Nol4/RLIBS_29a805453528e/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF"' had status 1
  Execution halted
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 v1.22.0 (2018-04-21) 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 v2.7.0 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 v2.12.1 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 v2.16.0 (2018-07-21) successfully loaded. See ?R.devices for help.
  aroma.core v3.1.3 (2018-04-29) 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 v3.10.0 (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 v3.1.1 (2018-04-05) 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"))
  [2019-01-31 13:49:16] Exception: Pathname not found: rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL (rawData/FusionSDK_HG-Focus/HG-Focus/ exists, but nothing beyond; current directory is 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/tests')
  
    at #07. getReadablePathname.Arguments(static, ...)
            - getReadablePathname.Arguments() is in environment 'R.utils'
  
    at #06. getReadablePathname(static, ...)
            - getReadablePathname() is in environment 'R.utils'
  
    at #05. Arguments$getReadablePathname(link, mustExist = TRUE)
            - Arguments$getReadablePathname() is local of the calling function
  
    at #04. createLink.default(link = pathnameD, target = pathnameS, skip = TRUE)
            - createLink.default() is in environment 'R.utils'
  
    at #03. createLink(link = pathnameD, target = pathnameS, skip = TRUE)
            - createLink() is in environment 'R.utils'
  
    at #02. setupExampleData.AromaAffymetrix(aroma.affymetrix, mustWork = FALSE)
            - setupExampleData.AromaAffymetrix() is in environment 'aroma.affymetrix'
  
    at #01. setupExampleData(aroma.affymetrix, mustWork = FALSE)
            - setupExampleData() is in environment 'aroma.affymetrix'
  
  Error: Pathname not found: rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL (rawData/FusionSDK_HG-Focus/HG-Focus/ exists, but nothing beyond; current directory is 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/tests')
  Execution halted