Last updated on 2019-06-18 22:49:59 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.1.1 | 53.20 | 244.69 | 297.89 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.1.1 | 43.54 | 192.69 | 236.23 | OK | |
| r-devel-linux-x86_64-fedora-clang | 3.1.1 | 354.63 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 3.1.1 | 346.02 | OK | |||
| r-devel-windows-ix86+x86_64 | 3.1.1 | 108.00 | 351.00 | 459.00 | ERROR | |
| r-patched-linux-x86_64 | 3.1.1 | 50.08 | 244.71 | 294.79 | OK | |
| r-patched-solaris-x86 | 3.1.1 | 446.50 | NOTE | |||
| r-release-linux-x86_64 | 3.1.1 | 51.02 | 244.81 | 295.83 | OK | |
| r-release-windows-ix86+x86_64 | 3.1.1 | 114.00 | 328.00 | 442.00 | ERROR | |
| r-release-osx-x86_64 | 3.1.1 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 3.1.1 | 63.00 | 320.00 | 383.00 | ERROR | |
| r-oldrel-osx-x86_64 | 3.1.1 | NOTE |
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' [3s]
Running 'AffymetrixCelSet.R' [6s]
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 v2.9.0 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$byChipType("Test3")
+ print(cdf)
+
+ # Unit names, types, ...
+ names <- getUnitNames(cdf)
+ str(names)
+
+ units <- indexOf(cdf, names=names[42:40])
+ stopifnot(all.equal(units, 42:40))
+
+ types <- getUnitTypes(cdf)
+ print(table(types))
+
+ data <- readUnits(cdf, units=1:10)
+ str(data)
+
+ data <- readDataFrame(cdf, units=1:10)
+ str(data)
+
+ md5 <- getChecksumFile(cdf)
+ print(md5)
+
+ ## Get an existing or create a new onocell CDF
+ cdfM <- getMonocellCdf(cdf, verbose=-10)
+ print(cdfM)
+ t0 <- lastModified(getPathname(cdfM))
+ print(t0)
+
+ ## A monocell CDF can be re-created
+ cdfM <- getMonocellCdf(cdf, force=TRUE)
+ print(cdfM)
+ t1 <- lastModified(getPathname(cdfM))
+ print(t1)
+ stopifnot(t1 >= t0)
+ } # if (... "AffymetrixDataTestFiles")
Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuf<c2><81>hren.[2019-06-17 15:01:24] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension 'cdf'.
at #03. byChipType.UnitAnnotationDataFile(static, ...)
- byChipType.UnitAnnotationDataFile() is in environment 'aroma.core'
at #02. byChipType(static, ...)
- byChipType() is in environment 'aroma.core'
at #01. AffymetrixCdfFile$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/RtmpoLxHmx/RLIBS_5b84061727e/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 v2.9.0 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
[2019-06-17 15:01:33] 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 message:
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' [19s]
Running '002.setupExampleData,rawData.R' [5s]
Running 'AffymetrixCdfFile.R' [5s]
Running 'AffymetrixCelFile.R' [3s]
Running 'AffymetrixCelSet.R' [6s]
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 v2.9.0 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$byChipType("Test3")
+ print(cdf)
+
+ # Unit names, types, ...
+ names <- getUnitNames(cdf)
+ str(names)
+
+ units <- indexOf(cdf, names=names[42:40])
+ stopifnot(all.equal(units, 42:40))
+
+ types <- getUnitTypes(cdf)
+ print(table(types))
+
+ data <- readUnits(cdf, units=1:10)
+ str(data)
+
+ data <- readDataFrame(cdf, units=1:10)
+ str(data)
+
+ md5 <- getChecksumFile(cdf)
+ print(md5)
+
+ ## Get an existing or create a new onocell CDF
+ cdfM <- getMonocellCdf(cdf, verbose=-10)
+ print(cdfM)
+ t0 <- lastModified(getPathname(cdfM))
+ print(t0)
+
+ ## A monocell CDF can be re-created
+ cdfM <- getMonocellCdf(cdf, force=TRUE)
+ print(cdfM)
+ t1 <- lastModified(getPathname(cdfM))
+ print(t1)
+ stopifnot(t1 >= t0)
+ } # if (... "AffymetrixDataTestFiles")
Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuf<c2><81>hren.[2019-06-17 14:16:26] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension 'cdf'.
at #03. byChipType.UnitAnnotationDataFile(static, ...)
- byChipType.UnitAnnotationDataFile() is in environment 'aroma.core'
at #02. byChipType(static, ...)
- byChipType() is in environment 'aroma.core'
at #01. AffymetrixCdfFile$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/Rtmpi8TeGl/RLIBS_f8471b92192/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 v2.9.0 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
[2019-06-17 14:16:35] 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 message:
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' [17s]
Running '002.setupExampleData,rawData.R' [5s]
Running 'AffymetrixCdfFile.R' [4s]
Running 'AffymetrixCelFile.R' [3s]
Running 'AffymetrixCelSet.R' [6s]
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$byChipType("Test3")
+ print(cdf)
+
+ # Unit names, types, ...
+ names <- getUnitNames(cdf)
+ str(names)
+
+ units <- indexOf(cdf, names=names[42:40])
+ stopifnot(all.equal(units, 42:40))
+
+ types <- getUnitTypes(cdf)
+ print(table(types))
+
+ data <- readUnits(cdf, units=1:10)
+ str(data)
+
+ data <- readDataFrame(cdf, units=1:10)
+ str(data)
+
+ md5 <- getChecksumFile(cdf)
+ print(md5)
+
+ ## Get an existing or create a new onocell CDF
+ cdfM <- getMonocellCdf(cdf, verbose=-10)
+ print(cdfM)
+ t0 <- lastModified(getPathname(cdfM))
+ print(t0)
+
+ ## A monocell CDF can be re-created
+ cdfM <- getMonocellCdf(cdf, force=TRUE)
+ print(cdfM)
+ t1 <- lastModified(getPathname(cdfM))
+ print(t1)
+ stopifnot(t1 >= t0)
+ } # if (... "AffymetrixDataTestFiles")
Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuf<c2><81>hren.[2019-06-10 10:49:18] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'Test3' (without requiring any tags) and with filename extension 'cdf'.
at #03. byChipType.UnitAnnotationDataFile(static, ...)
- byChipType.UnitAnnotationDataFile() is in environment 'aroma.core'
at #02. byChipType(static, ...)
- byChipType() is in environment 'aroma.core'
at #01. AffymetrixCdfFile$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/RtmpCYhb0x/RLIBS_5a2c75b32b22/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
[2019-06-10 10:49:27] 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/RtmpCYhb0x/RLIBS_5a2c75b32b22/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/RtmpCYhb0x/RLIBS_5a2c75b32b22/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