CRAN Package Check Results for Maintainer ‘Henrik Bengtsson <henrikb at braju.com>’

Last updated on 2019-05-26 00:47:42 CEST.

Package FAIL ERROR NOTE OK
ACNE 1 11
aroma.affymetrix 4 3 5
aroma.apd 1 11
aroma.cn 1 1 10
aroma.core 1 11
calmate 1 11
dChipIO 12
doFuture 12
future 12
future.apply 12
future.BatchJobs 12
future.batchtools 12
future.callr 12
globals 12
listenv 12
matrixStats 7 5
profmem 12
PSCBS 1 11
R.cache 12
R.devices 1 1 10
R.filesets 12
R.huge 12
R.matlab 12
R.methodsS3 12
R.oo 12
R.rsp 1 11
R.utils 12
startup 12

Package ACNE

Current CRAN status: ERROR: 1, OK: 11

Version: 0.8.1
Check: package dependencies
Result: ERROR
    Packages required but not available: 'aroma.affymetrix', 'aroma.core'
    
    Package suggested but not available for checking: ‘DNAcopy’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Package aroma.affymetrix

Current CRAN status: ERROR: 4, NOTE: 3, OK: 5

Version: 3.1.1
Check: installed package size
Result: NOTE
     installed size is 5.8Mb
     sub-directories of 1Mb or more:
     R 2.3Mb
     help 1.1Mb
     testScripts 1.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 3.1.1
Check: tests
Result: ERROR
     Running '001.setupExampleData,annotationData.R' [20s]
     Running '002.setupExampleData,rawData.R' [6s]
     Running 'AffymetrixCdfFile.R' [5s]
     Running 'AffymetrixCelFile.R' [4s]
     Running 'AffymetrixCelSet.R' [8s]
    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 v2.8.0 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, nullfile, parse,
     warnings
    
     Loading required package: aroma.core
     Loading required package: R.filesets
     R.filesets v2.13.0 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 v2.16.0 (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 v3.14.0 (2018-09-04) 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")
     Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuführen.[2019-05-24 21:02:31] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension 'cdf'.
    
     at #03. byChipType.UnitAnnotationDataFile(static, ...)
     - byChipType.UnitAnnotationDataFile() is in environment 'aroma.core'
    
     at #02. byChipType(static, ...)
     - byChipType() is in environment 'aroma.core'
    
     at #01. AffymetrixCdfFile$byChipType("Test3")
     - AffymetrixCdfFile$byChipType() is local of the calling function
    
     Error: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension '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/Rtmpq0BqBL/RLIBS_2142448bf4874/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 v2.8.0 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, nullfile, parse,
     warnings
    
     Loading required package: aroma.core
     Loading required package: R.filesets
     R.filesets v2.13.0 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 v2.16.0 (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 v3.14.0 (2018-09-04) 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"))
     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: NA
     Tags:
     Path: NA
     Platform: Affymetrix
     Chip type: NA
     Number of arrays: 0
     Time period: NA
     Total file size: 0 B
     [2019-05-24 21:02:42] Exception: Argument 'idx' is out of range [0,0]: 1
    
     at #13. getNumerics.Arguments(static, ..., asMode = "integer", disallow = disallow)
     - getNumerics.Arguments() is in environment 'R.utils'
    
     at #12. getNumerics(static, ..., asMode = "integer", disallow = disallow)
     - getNumerics() is in environment 'R.utils'
    
     at #11. getIntegers.Arguments(static, x, ..., range = range, .name = .name)
     - getIntegers.Arguments() is in environment 'R.utils'
    
     at #10. getIntegers(static, x, ..., range = range, .name = .name)
     - getIntegers() is in environment 'R.utils'
    
     at #09. getIndices.Arguments(static, ..., length = length)
     - getIndices.Arguments() is in environment 'R.utils'
    
     at #08. getIndices(static, ..., length = length)
     - getIndices() is in environment 'R.utils'
    
     at #07. getIndex.Arguments(static, ...)
     - getIndex.Arguments() is in environment 'R.utils'
    
     at #06. getIndex(static, ...)
     - getIndex() is in environment 'R.utils'
    
     at #05. Arguments$getIndex(idx, max = n)
     - Arguments$getIndex() is local of the calling function
    
     at #04. getFile.GenericDataFileSet(x, i, ...)
     - getFile.GenericDataFileSet() is in environment 'R.filesets'
    
     at #03. getFile(x, i, ...)
     - getFile() is in environment 'R.filesets'
    
     at #02. `[[.GenericDataFileSet`(cels, 1)
     - `[[.GenericDataFileSet`() is in environment 'R.filesets'
    
     at #01. cels[[1]]
     - NULL[[]]() is local of the calling function
    
     Error: Argument 'idx' is out of range [0,0]: 1
     In addition: Warning messages:
     1: In createLink.default(link = pathnameD, target = pathnameS, skip = TRUE) :
     Existing link ('rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL'; current working directory: 'd:/Rcompile/CRANpkg/local/3.7/aroma.affymetrix.Rcheck/tests') was skipped, but it links to different target file than requested: 'd:/Rcompile/CRANpkg/local/3.7/aroma.affymetrix.Rcheck/tests' != 'D:/temp/Rtmpq0BqBL/RLIBS_2142448bf4874/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL'
     2: In createLink.default(link = pathnameD, target = pathnameS, skip = TRUE) :
     Existing link ('rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-2-121502.CEL'; current working directory: 'd:/Rcompile/CRANpkg/local/3.7/aroma.affymetrix.Rcheck/tests') was skipped, but it links to different target file than requested: 'd:/Rcompile/CRANpkg/local/3.7/aroma.affymetrix.Rcheck/tests' != 'D:/temp/Rtmpq0BqBL/RLIBS_2142448bf4874/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-2-121502.CEL'
     3: In readCdfDataFrame(filename = "annotationData/chipTypes/HG-Focus/HG-Focus.CDF", :
     Some of the fields were not read: expos
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 3.1.1
Check: tests
Result: ERROR
     Running '001.setupExampleData,annotationData.R' [15s]
     Running '002.setupExampleData,rawData.R' [5s]
     Running 'AffymetrixCdfFile.R' [3s]
     Running 'AffymetrixCelFile.R' [3s]
     Running 'AffymetrixCelSet.R' [5s]
    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 v2.8.0 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, nullfile, parse,
     warnings
    
     Loading required package: aroma.core
     Loading required package: R.filesets
     R.filesets v2.13.0 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 v2.16.0 (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 v3.14.0 (2018-09-04) 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")
     Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuführen.[2019-05-25 10:32:21] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension 'cdf'.
    
     at #03. byChipType.UnitAnnotationDataFile(static, ...)
     - byChipType.UnitAnnotationDataFile() is in environment 'aroma.core'
    
     at #02. byChipType(static, ...)
     - byChipType() is in environment 'aroma.core'
    
     at #01. AffymetrixCdfFile$byChipType("Test3")
     - AffymetrixCdfFile$byChipType() is local of the calling function
    
     Error: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension '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/RtmpKAMNnv/RLIBS_d2407e452a67/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 v2.8.0 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, nullfile, parse,
     warnings
    
     Loading required package: aroma.core
     Loading required package: R.filesets
     R.filesets v2.13.0 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 v2.16.0 (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 v3.14.0 (2018-09-04) 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"))
     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: NA
     Tags:
     Path: NA
     Platform: Affymetrix
     Chip type: NA
     Number of arrays: 0
     Time period: NA
     Total file size: 0 B
     [2019-05-25 10:32:28] Exception: Argument 'idx' is out of range [0,0]: 1
    
     at #13. getNumerics.Arguments(static, ..., asMode = "integer", disallow = disallow)
     - getNumerics.Arguments() is in environment 'R.utils'
    
     at #12. getNumerics(static, ..., asMode = "integer", disallow = disallow)
     - getNumerics() is in environment 'R.utils'
    
     at #11. getIntegers.Arguments(static, x, ..., range = range, .name = .name)
     - getIntegers.Arguments() is in environment 'R.utils'
    
     at #10. getIntegers(static, x, ..., range = range, .name = .name)
     - getIntegers() is in environment 'R.utils'
    
     at #09. getIndices.Arguments(static, ..., length = length)
     - getIndices.Arguments() is in environment 'R.utils'
    
     at #08. getIndices(static, ..., length = length)
     - getIndices() is in environment 'R.utils'
    
     at #07. getIndex.Arguments(static, ...)
     - getIndex.Arguments() is in environment 'R.utils'
    
     at #06. getIndex(static, ...)
     - getIndex() is in environment 'R.utils'
    
     at #05. Arguments$getIndex(idx, max = n)
     - Arguments$getIndex() is local of the calling function
    
     at #04. getFile.GenericDataFileSet(x, i, ...)
     - getFile.GenericDataFileSet() is in environment 'R.filesets'
    
     at #03. getFile(x, i, ...)
     - getFile() is in environment 'R.filesets'
    
     at #02. `[[.GenericDataFileSet`(cels, 1)
     - `[[.GenericDataFileSet`() is in environment 'R.filesets'
    
     at #01. cels[[1]]
     - NULL[[]]() is local of the calling function
    
     Error: Argument 'idx' is out of range [0,0]: 1
     In addition: Warning messages:
     1: In createLink.default(link = pathnameD, target = pathnameS, skip = TRUE) :
     Existing link ('rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL'; current working directory: 'd:/Rcompile/CRANpkg/local/3.6/aroma.affymetrix.Rcheck/tests') was skipped, but it links to different target file than requested: 'd:/Rcompile/CRANpkg/local/3.6/aroma.affymetrix.Rcheck/tests' != 'D:/temp/RtmpKAMNnv/RLIBS_d2407e452a67/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL'
     2: In createLink.default(link = pathnameD, target = pathnameS, skip = TRUE) :
     Existing link ('rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-2-121502.CEL'; current working directory: 'd:/Rcompile/CRANpkg/local/3.6/aroma.affymetrix.Rcheck/tests') was skipped, but it links to different target file than requested: 'd:/Rcompile/CRANpkg/local/3.6/aroma.affymetrix.Rcheck/tests' != 'D:/temp/RtmpKAMNnv/RLIBS_d2407e452a67/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-2-121502.CEL'
     3: In readCdfDataFrame(filename = "annotationData/chipTypes/HG-Focus/HG-Focus.CDF", :
     Some of the fields were not read: expos
     Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 3.1.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘aroma.core’
    
    Packages suggested but not available for checking:
     'Biobase', 'BiocGenerics', 'affxparser', 'affy', 'affyPLM',
     'aroma.light', 'gcrma', 'limma', 'oligo', 'oligoClasses',
     'pdInfoBuilder', 'preprocessCore', 'AffymetrixDataTestFiles'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Version: 3.1.1
Check: tests
Result: ERROR
     Running '001.setupExampleData,annotationData.R' [13s]
     Running '002.setupExampleData,rawData.R' [4s]
     Running 'AffymetrixCdfFile.R' [3s]
     Running 'AffymetrixCelFile.R' [2s]
     Running 'AffymetrixCelSet.R' [5s]
    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 v2.8.0 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 v2.13.0 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 v2.16.0 (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 v3.12.0 (2018-09-04) 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")
     Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuf<c2><81>hren.[2019-05-23 10:26:28] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension 'cdf'.
    
     at #03. byChipType.UnitAnnotationDataFile(static, ...)
     - byChipType.UnitAnnotationDataFile() is in environment 'aroma.core'
    
     at #02. byChipType(static, ...)
     - byChipType() is in environment 'aroma.core'
    
     at #01. AffymetrixCdfFile$byChipType("Test3")
     - AffymetrixCdfFile$byChipType() is local of the calling function
    
     Error: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension '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/Rtmp69bnRk/RLIBS_fd0ca372b5a/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 v2.8.0 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 v2.13.0 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 v2.16.0 (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 v3.12.0 (2018-09-04) 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"))
     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: NA
     Tags:
     Path: NA
     Platform: Affymetrix
     Chip type: NA
     Number of arrays: 0
     Time period: NA
     Total file size: 0 B
     [2019-05-23 10:26:35] Exception: Argument 'idx' is out of range [0,0]: 1
    
     at #13. getNumerics.Arguments(static, ..., asMode = "integer", disallow = disallow)
     - getNumerics.Arguments() is in environment 'R.utils'
    
     at #12. getNumerics(static, ..., asMode = "integer", disallow = disallow)
     - getNumerics() is in environment 'R.utils'
    
     at #11. getIntegers.Arguments(static, x, ..., range = range, .name = .name)
     - getIntegers.Arguments() is in environment 'R.utils'
    
     at #10. getIntegers(static, x, ..., range = range, .name = .name)
     - getIntegers() is in environment 'R.utils'
    
     at #09. getIndices.Arguments(static, ..., length = length)
     - getIndices.Arguments() is in environment 'R.utils'
    
     at #08. getIndices(static, ..., length = length)
     - getIndices() is in environment 'R.utils'
    
     at #07. getIndex.Arguments(static, ...)
     - getIndex.Arguments() is in environment 'R.utils'
    
     at #06. getIndex(static, ...)
     - getIndex() is in environment 'R.utils'
    
     at #05. Arguments$getIndex(idx, max = n)
     - Arguments$getIndex() is local of the calling function
    
     at #04. getFile.GenericDataFileSet(x, i, ...)
     - getFile.GenericDataFileSet() is in environment 'R.filesets'
    
     at #03. getFile(x, i, ...)
     - getFile() is in environment 'R.filesets'
    
     at #02. `[[.GenericDataFileSet`(cels, 1)
     - `[[.GenericDataFileSet`() is in environment 'R.filesets'
    
     at #01. cels[[1]]
     - NULL[[]]() is local of the calling function
    
     Error: Argument 'idx' is out of range [0,0]: 1
     In addition: Warning messages:
     1: In createLink.default(link = pathnameD, target = pathnameS, skip = TRUE) :
     Existing link ('rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-1-121502.CEL'; current working directory: 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/tests') was skipped, but it links to different target file than requested: 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/tests' != 'D:/temp/Rtmp69bnRk/RLIBS_fd0ca372b5a/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL'
     2: In createLink.default(link = pathnameD, target = pathnameS, skip = TRUE) :
     Existing link ('rawData/FusionSDK_HG-Focus/HG-Focus/HG-Focus-2-121502.CEL'; current working directory: 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/tests') was skipped, but it links to different target file than requested: 'd:/Rcompile/CRANpkg/local/3.5/aroma.affymetrix.Rcheck/tests' != 'D:/temp/Rtmp69bnRk/RLIBS_fd0ca372b5a/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-2-121502.CEL'
     3: In readCdfDataFrame(filename = "annotationData/chipTypes/HG-Focus/HG-Focus.CDF", :
     Some of the fields were not read: expos
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 3.1.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
Flavor: r-oldrel-osx-x86_64

Package aroma.apd

Current CRAN status: NOTE: 1, OK: 11

Version: 0.6.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘affxparser’
Flavor: r-release-osx-x86_64

Version: 0.6.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘affxparser’
Flavor: r-release-osx-x86_64

Package aroma.cn

Current CRAN status: ERROR: 1, NOTE: 1, OK: 10

Version: 1.6.1
Check: package dependencies
Result: ERROR
    Packages required but not available: 'aroma.core', 'PSCBS'
    
    Packages suggested but not available for checking:
     'aroma.light', 'DNAcopy', 'GLAD'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Version: 1.6.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘GLAD’
Flavor: r-oldrel-osx-x86_64

Package aroma.core

Current CRAN status: ERROR: 1, NOTE: 11

Version: 3.1.3
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 3.1.3
Check: package dependencies
Result: ERROR
    Package required but not available: ‘PSCBS’
    
    Packages suggested but not available for checking:
     'EBImage', 'preprocessCore', 'aroma.light', 'DNAcopy', 'GLAD',
     'sfit', 'expectile', 'HaarSeg', 'mpcbs'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Version: 3.1.3
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'sfit' 'expectile' 'HaarSeg' 'mpcbs'
Flavor: r-oldrel-windows-ix86+x86_64

Version: 3.1.3
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Flavor: r-oldrel-osx-x86_64

Version: 3.1.3
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘GLAD’
Flavor: r-oldrel-osx-x86_64

Package calmate

Current CRAN status: ERROR: 1, OK: 11

Version: 0.12.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘aroma.core’
    
    Package suggested but not available for checking: ‘DNAcopy’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Package dChipIO

Current CRAN status: OK: 12

Package doFuture

Current CRAN status: OK: 12

Package future

Current CRAN status: OK: 12

Package future.apply

Current CRAN status: OK: 12

Package future.BatchJobs

Current CRAN status: OK: 12

Version: 0.16.1
Check: tests
Result: FAIL
    
Flavor: r-release-osx-x86_64

Package future.batchtools

Current CRAN status: OK: 12

Package future.callr

Current CRAN status: OK: 12

Package globals

Current CRAN status: OK: 12

Package listenv

Current CRAN status: OK: 12

Package matrixStats

Current CRAN status: NOTE: 7, OK: 5

Version: 0.54.0
Check: installed package size
Result: NOTE
     installed size is 9.7Mb
     sub-directories of 1Mb or more:
     libs 9.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Package profmem

Current CRAN status: OK: 12

Package PSCBS

Current CRAN status: ERROR: 1, OK: 11

Version: 0.65.0
Check: package dependencies
Result: ERROR
    Packages required but not available: 'aroma.light', 'DNAcopy'
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64

Package R.cache

Current CRAN status: OK: 12

Package R.devices

Current CRAN status: FAIL: 1, ERROR: 1, OK: 10

Version: 2.16.0
Check: tests
Result: ERROR
     Running ‘DevEvalFileProduct.R’
     Running ‘DevEvalProduct.R’
     Running ‘capabilitiesX11.R’
     Running ‘capturePlot.R’
     Running ‘dataURI.R’
     Running ‘devAll.R’
     Running ‘devDump.R’
     Running ‘devEqualTypes.R’
     Running ‘devEval,error.R’
     Running ‘devEval.R’ [6s/21s]
     Running ‘devIsInteractive.R’
     Running ‘devIsOpen.R’
     Running ‘devList.R’
     Running ‘devListIndexOf.R’
     Running ‘devNew.R’
     Running ‘devOptions.R’
     Running ‘devSet.R’
     Running ‘devTypeName.R’
     Running ‘favicon.R’
     Running ‘toNNN.R’
     Running ‘withPar.R’
    Running the tests in ‘tests/devEval.R’ failed.
    Complete output:
     > message("*** devEval() ...")
     *** devEval() ...
     >
     > library("R.devices")
     R.devices v2.16.0 (2018-07-21) successfully loaded. See ?R.devices for help.
     > library("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 v2.8.0 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, nullfile, parse,
     warnings
    
     > graphics.off()
     >
     > png <- grDevices::png
     > jpeg <- grDevices::jpeg
     > tiff <- grDevices::tiff
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > # Various types of single and multiple device outputs
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > message("*** devEval() - single and multiple device outputs ...")
     *** devEval() - single and multiple device outputs ...
     >
     > types <- list(
     + character(0L),
     + "png",
     + "jpg",
     + "nulldev",
     + c("png", "png", "jpeg"),
     + "png,nulldev,pdf"
     + )
     >
     > for (type in types) {
     + cat("Device types: ", paste(sQuote(type), collapse=", "), "\n", sep="")
     + devList0 <- devList()
     + res <- devEval(type, name="multi", aspectRatio=2/3, {
     + plot(1:10)
     + })
     + print(res)
     + stopifnot(length(res) == length(unlist(strsplit(type, split=","))))
     + stopifnot(all.equal(devList(), devList0))
     + }
     Device types:
     character(0)
     Device types: 'png'
     [1] "figures/multi.png"
     Device types: 'jpg'
     [1] "figures/multi.jpg"
     Device types: 'nulldev'
     [1] "/dev/null"
     Device types: 'png', 'png', 'jpeg'
     $png
     [1] "figures/multi.png"
    
     $png
     [1] "figures/multi.png"
    
     $jpeg
     [1] "figures/multi.jpg"
    
     Device types: 'png,nulldev,pdf'
     $png
     [1] "figures/multi.png"
    
     $nulldev
     [1] "/dev/null"
    
     $pdf
     [1] "figures/multi.pdf"
    
     >
     > # Sanity checks
     > print(devList())
     named integer(0)
     > stopifnot(length(devList()) == 0L)
     >
     > message("*** devEval() - single and multiple device outputs ... DONE")
     *** devEval() - single and multiple device outputs ... DONE
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > # With 'initially' and 'finally' expression
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > message("*** devEval() - initially and finally ...")
     *** devEval() - initially and finally ...
     >
     > devList0 <- devList()
     > devEval(c("png", "jpg"), name="count", {
     + plot(1:10)
     + count <- count + 1L
     + }, initially = {
     + # Emulate an overhead
     + cat("Initiate...")
     + count <- 0L
     + Sys.sleep(1)
     + cat("done\n")
     + }, finally = {
     + cat("Number of image files created: ", count, "\n", sep="")
     + })
     Initiate...done
     Number of image files created: 2
     $png
     [1] "figures/count.png"
    
     $jpeg
     [1] "figures/count.jpg"
    
     > stopifnot(all.equal(devList(), devList0))
     >
     > # Sanity checks
     > print(devList())
     named integer(0)
     > stopifnot(length(devList()) == 0L)
     >
     > message("*** devEval() - initially and finally ... DONE")
     *** devEval() - initially and finally ... DONE
     >
     >
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > # Try several devices until first successful device is found
     > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     > message("*** devEval() - first successful device ...")
     *** devEval() - first successful device ...
     >
     > types <- list(
     + "png|jpg|pdf", # PNG, JPG and then PDF
     + "dummy|png|jpg|pdf", # "Non-existing", PNG, JPG and then PDF
     + "quartz|x11|windows", # Any interactive device (depending on OS)
     + c("png|jpg", "x11|windows"), # PNG or JPG and then x11 or windows
     + "eps|postscript|pdf", # EPS, Postscript or PDF
     + "jpeg2|jpeg", # JPEG via bitmap() or via jpeg()
     + "png,jpg|x11|windows", # == c("png", "jpg|x11|windows")
     + "nulldev|jpeg" # NULL devices, otherwise jpeg
     + )
     >
     > if (!capabilitiesX11()) {
     + message("Skipping test for X11")
     + types <- lapply(types, FUN=function(x) gsub("x11|", "", x, fixed=TRUE))
     + }
     >
     > devList0 <- devList()
     >
     > for (type in types) {
     + printf("Any of %s\n", paste(sQuote(type), collapse=" + "))
     +
     + # Use try-catch in case not supported on some test systems
     + tryCatch({
     + res <- devEval(type, name="any", aspectRatio=2/3, scale=1.2, {
     + plot(100:1)
     + })
     + printf("Result: %s (%s)\n\n", sQuote(res), attr(res, "type"))
     +
     + if (length(devList()) > 0) devOff()
     + }, error = function(ex) {
     + printf("Failed: %s\n\n", sQuote(ex$message))
     + })
     + } # for (type ...)
     Any of 'png|jpg|pdf'
     Any of 'dummy|png|jpg|pdf'
     Any of 'quartz|x11|windows'
     Failed: 'Failed to open graphics device: quartz'
    
     Any of 'png|jpg' + 'x11|windows'
     Any of 'eps|postscript|pdf'
     Any of 'jpeg2|jpeg'
     Any of 'png,jpg|x11|windows'
    
     *** caught segfault ***
     address f8066018, cause 'memory not mapped'
    
     Traceback:
     1: .External2(C_X11, d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, d$maxcubesize, d$bg, d$canvas, d$fonts, NA_integer_, d$xpos, d$ypos, d$title, type, antialias, d$family)
     2: (function (display = "", width, height, pointsize, gamma, bg, canvas, fonts, family, xpos, ypos, title, type, antialias, ...) { if (display != "XImage") { check <- Sys.getenv("_R_CHECK_SCREEN_DEVICE_", "") msg <- "screen devices should not be used in examples etc" if (identical(check, "stop")) stop(msg, domain = NA) else if (identical(check, "warn")) warning(msg, immediate. = TRUE, noBreaks. = TRUE, domain = NA) } if (display == "" && .Platform$GUI == "AQUA" && is.na(Sys.getenv("DISPLAY", NA))) Sys.setenv(DISPLAY = ":0") new <- list() if (!missing(display)) new$display <- display if (!missing(width)) new$width <- width if (!missing(height)) new$height <- height if (!missing(gamma)) new$gamma <- gamma if (!missing(pointsize)) new$pointsize <- pointsize if (!missing(bg)) new$bg <- bg if (!missing(canvas)) new$canvas <- canvas if (!missing(xpos)) new$xpos <- xpos if (!missing(ypos)) new$ypos <- ypos if (!missing(title)) new$title <- title if (!checkIntFormat(new$title)) stop("invalid 'title'") if (!missing(type)) { new$type <- match.arg(type, c("Xlib", "cairo", "nbcairo", "dbcairo")) if (!capabilities("cairo") && type != "Xlib") warning("cairo-based types are not supported on this build - using \"Xlib\"") } if (!missing(family)) new$family <- family if (!missing(fonts)) new$fonts <- fonts if (!missing(antialias) && type != "Xlib") new$antialias <- match.arg(antialias, aa.cairo) d <- check.options(new, name.opt = ".X11.Options", envir = .X11env) if (d$type == "Xlib" && !missing(family)) { fns <- X11Fonts() if (!family %in% names(fns)) stop("unknown family for X11(type = \"XLib\")") d$fonts[1] <- fns[[family]] } type <- if (capabilities("cairo")) switch(d$type, cairo = 1L, nbcairo = 2L, dbcairo = 3L, 0L) else 0L if (display == "XImage") type <- 0L antialias <- match(d$antialias, aa.cairo) if (grepl("darwin", R.version$os)) check_for_XQuartz() .External2(C_X11, d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, d$maxcubesize, d$bg, d$canvas, d$fonts, NA_integer_, d$xpos, d$ypos, d$title, type, antialias, d$family) invisible()})()
     3: do.call(typeT, args = args)
     4: devNew(type, which = fullname, ..., .allowUnknownArgs = .allowUnknownArgs)
     5: devEval(type = type, expr = expr, initially = NULL, finally = NULL, envir = envir, name = nameOrg, tags = tags, sep = sep, ..., ext = ext, filename = filename, path = path, field = field, onIncomplete = onIncomplete, force = force, .exprAsIs = TRUE, .allowUnknownArgs = TRUE)
     6: FUN(X[[i]], ...)
     7: lapply(types, FUN = function(type) { devEval(type = type, expr = expr, initially = NULL, finally = NULL, envir = envir, name = nameOrg, tags = tags, sep = sep, ..., ext = ext, filename = filename, path = path, field = field, onIncomplete = onIncomplete, force = force, .exprAsIs = TRUE, .allowUnknownArgs = TRUE)})
     8: devEval(type, name = "any", aspectRatio = 2/3, scale = 1.2, { plot(100:1)})
     9: doTryCatch(return(expr), name, parentenv, handler)
     10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11: tryCatchList(expr, classes, parentenv, handlers)
     12: tryCatch({ res <- devEval(type, name = "any", aspectRatio = 2/3, scale = 1.2, { plot(100:1) }) printf("Result: %s (%s)\n\n", sQuote(res), attr(res, "type")) if (length(devList()) > 0) devOff()}, error = function(ex) { printf("Failed: %s\n\n", sQuote(ex$message))})
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.16.0
Check: whether package can be installed
Result: FAIL
    
Flavor: r-release-osx-x86_64

Package R.filesets

Current CRAN status: OK: 12

Package R.huge

Current CRAN status: OK: 12

Package R.matlab

Current CRAN status: OK: 12

Package R.methodsS3

Current CRAN status: OK: 12

Package R.oo

Current CRAN status: OK: 12

Package R.rsp

Current CRAN status: FAIL: 1, OK: 11

Version: 0.43.1
Check: dependencies in R code
Result: FAIL
    
Flavor: r-release-osx-x86_64

Package R.utils

Current CRAN status: OK: 12

Package startup

Current CRAN status: NOTE: 12

Version: 0.11.0
Check: for hidden files and directories
Result: NOTE
    Found the following hidden files and directories:
     inst/.Renviron.d
     inst/.Rprofile.d
    These were most likely included in error. See section 'Package
    structure' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64