CRAN Package Check Results for Package aroma.affymetrix

Last updated on 2021-09-24 07:49:10 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.2.0 60.87 312.48 373.35 OK
r-devel-linux-x86_64-debian-gcc 3.2.0 48.42 222.16 270.58 OK
r-devel-linux-x86_64-fedora-clang 3.2.0 447.82 NOTE
r-devel-linux-x86_64-fedora-gcc 3.2.0 438.08 OK
r-devel-windows-x86_64 3.2.0 55.00 242.00 297.00 NOTE
r-devel-windows-x86_64-gcc10-UCRT 3.2.0 ERROR
r-patched-linux-x86_64 3.2.0 67.89 295.47 363.36 OK
r-patched-solaris-x86 3.2.0 493.80 NOTE
r-release-linux-x86_64 3.2.0 48.03 294.31 342.34 OK
r-release-macos-arm64 3.2.0 NOTE
r-release-macos-x86_64 3.2.0 NOTE
r-release-windows-ix86+x86_64 3.2.0 92.00 327.00 419.00 NOTE
r-oldrel-macos-x86_64 3.2.0 NOTE
r-oldrel-windows-ix86+x86_64 3.2.0 73.00 237.00 310.00 NOTE

Check Details

Version: 3.2.0
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-x86_64, r-patched-solaris-x86, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.2.0
Check: tests
Result: ERROR
     Running '001.setupExampleData,annotationData.R'
     Running '002.setupExampleData,rawData.R'
     Running 'AffymetrixCdfFile.R'
     Running 'AffymetrixCelFile.R'
     Running 'AffymetrixCelSet.R'
    Running the tests in 'tests/AffymetrixCelSet.R' failed.
    Complete output:
     > library("aroma.affymetrix")
     Loading required package: R.utils
     Loading required package: R.oo
     Loading required package: R.methodsS3
     R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
     R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.
    
     Attaching package: 'R.oo'
    
     The following object is masked from 'package:R.methodsS3':
    
     throw
    
     The following objects are masked from 'package:methods':
    
     getClasses, getMethods
    
     The following objects are masked from 'package:base':
    
     attach, detach, load, save
    
     R.utils v2.10.1 (2020-08-26 22:50:31 UTC) successfully loaded. See ?R.utils for help.
    
     Attaching package: 'R.utils'
    
     The following object is masked from 'package:utils':
    
     timestamp
    
     The following objects are masked from 'package:base':
    
     cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
     warnings
    
     Loading required package: aroma.core
     Loading required package: R.filesets
     R.filesets v2.14.0 (2020-12-08 07:20:17 UTC) successfully loaded. See ?R.filesets for help.
    
     Attaching package: 'R.filesets'
    
     The following object is masked from 'package:R.utils':
    
     validate
    
     The following objects are masked from 'package:base':
    
     append, readLines
    
     Loading required package: R.devices
     R.devices v2.17.0 (2021-01-19 18:30:06 UTC) successfully loaded. See ?R.devices for help.
     aroma.core v3.2.2 (2021-01-05 05:10:12 UTC) successfully loaded. See ?aroma.core for help.
    
     Attaching package: 'aroma.core'
    
     The following objects are masked from 'package:base':
    
     .Machine, colMeans, colSums, library, require, write
    
     Loading required package: aroma.light
     aroma.light v3.22.0 (2021-05-19) successfully loaded. See ?aroma.light for help.
    
     Attaching package: 'aroma.light'
    
     The following objects are masked from 'package:aroma.affymetrix':
    
     averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
     plotXYCurve
    
     The following objects are masked from 'package:aroma.core':
    
     callNaiveGenotypes, normalizeTumorBoost
    
     Loading required package: affxparser
    
     Attaching package: 'affxparser'
    
     The following object is masked from 'package:aroma.affymetrix':
    
     writeCdf
    
     The following object is masked from 'package:R.utils':
    
     findFiles
    
     The following object is masked _by_ package:aroma.affymetrix:
    
     writeCdf
    
     The following object is masked from package:R.utils:
    
     findFiles
    
     aroma.affymetrix v3.2.0 (2019-06-23 06:00:14 UTC) successfully loaded. See ?aroma.affymetrix for help.
    
     Attaching package: 'aroma.affymetrix'
    
     The following objects are masked _by_ 'package:aroma.light':
    
     averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
     plotXYCurve
    
     The following object is masked from 'package:affxparser':
    
     writeCdf
    
     >
     > ## Empty CEL set
     > ds <- AffymetrixCelSet()
     > print(ds)
     AffymetrixCelSet:
     Name: NA
     Tags:
     Path: NA
     Platform: Affymetrix
     Chip type: NA
     Number of arrays: 0
     Time period: NA
     Total file size: 0 B
     >
     > ## Extract non-existing subset on empty set
     > ds <- AffymetrixCelSet()
     > dsT <- extract(ds, "foo", onMissing="NA")
     > print(dsT)
     AffymetrixCelSet:
     Name: NA
     Tags:
     Path: NA
     Platform: Affymetrix
     Chip type: NA
     Number of arrays: 1
     Names: NA [1]
     Time period: NA -- NA
     Total file size: 0 B
     >
     > ## CEL set with non-existing CEL file
     > files <- list(AffymetrixCelFile())
     > ds <- AffymetrixCelSet(files)
     > print(ds)
     AffymetrixCelSet:
     Name: NA
     Tags:
     Path: NA
     Platform: Affymetrix
     Chip type: NA
     Number of arrays: 1
     Names: NA [1]
     Time period: NA -- NA
     Total file size: 0 B
     >
     >
     > if (setupExampleData(aroma.affymetrix, mustWork=FALSE)) {
     + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     + # CDF file
     + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     + cdf <- AffymetrixCdfFile$byChipType("HG-Focus")
     + print(cdf)
     +
     + # Unit names, types, ...
     + names <- getUnitNames(cdf)
     + str(names)
     +
     + units <- indexOf(cdf, names=names[42:40])
     + stopifnot(all.equal(units, 42:40))
     +
     + types <- getUnitTypes(cdf)
     + print(table(types))
     +
     + data <- readUnits(cdf, units=1:10)
     + str(data)
     +
     + data <- readDataFrame(cdf, units=1:10)
     + str(data)
     +
     + md5 <- getChecksumFile(cdf)
     + print(md5)
     +
     +
     + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     + # CEL set / CEL file
     + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     + cels <- AffymetrixCelSet$byName("FusionSDK_HG-Focus", cdf=cdf)
     + print(cels)
     +
     + # A single file
     + cel <- cels[[1]]
     + print(cel)
     +
     + # File checksums
     + md5s <- getChecksumFileSet(cels)
     + print(md5s)
     +
     + # File checksums
     + md5 <- getChecksumFile(cel)
     + print(md5)
     +
     + # Average CEL file
     + celR <- getAverageFile(cels)
     + print(celR)
     +
     +
     + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     + # AromaPlatformInterface
     + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     + platform <- getAromaPlatform(cdf)
     + print(platform)
     + stopifnot(equals(getAromaPlatform(cels), platform))
     + stopifnot(equals(getAromaPlatform(cel), platform))
     +
     + # Unit names file
     + unf <- getUnitNamesFile(cdf)
     + print(unf)
     + stopifnot(equals(getUnitNamesFile(cels), unf))
     + stopifnot(equals(getUnitNamesFile(cel), unf))
     + } # if (require("AffymetrixDataTestFiles"))
     AffymetrixCdfFile:
     Path: annotationData/chipTypes/HG-Focus
     Filename: HG-Focus.CDF
     File size: 4.06 MiB (4261873 bytes)
     Chip type: HG-Focus
     File format: v4 (binary; XDA)
     Dimension: 448x448
     Number of cells: 200704
     Number of units: 8793
     Cells per unit: 22.83
     Number of QC units: 10
     chr [1:8793] "AFFX-BioB-5_at" "AFFX-BioB-M_at" "AFFX-BioB-3_at" ...
     types
     1
     8793
     List of 10
     $ AFFX-BioB-5_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-BioB-5_at:List of 6
     .. .. ..$ x : int [1:40] 216 216 217 217 218 218 219 219 220 220 ...
     .. .. ..$ y : int [1:40] 264 265 264 265 264 265 264 265 264 265 ...
     .. .. ..$ pbase : chr [1:40] "A" "T" "C" "G" ...
     .. .. ..$ tbase : chr [1:40] "T" "T" "G" "G" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-BioB-M_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-BioB-M_at:List of 6
     .. .. ..$ x : int [1:40] 218 218 219 219 220 220 221 221 222 222 ...
     .. .. ..$ y : int [1:40] 266 267 266 267 266 267 266 267 266 267 ...
     .. .. ..$ pbase : chr [1:40] "C" "G" "T" "A" ...
     .. .. ..$ tbase : chr [1:40] "G" "G" "A" "A" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-BioB-3_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-BioB-3_at:List of 6
     .. .. ..$ x : int [1:40] 220 220 221 221 222 222 223 223 224 224 ...
     .. .. ..$ y : int [1:40] 268 269 268 269 268 269 268 269 268 269 ...
     .. .. ..$ pbase : chr [1:40] "C" "G" "C" "G" ...
     .. .. ..$ tbase : chr [1:40] "G" "G" "G" "G" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-BioC-5_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-BioC-5_at:List of 6
     .. .. ..$ x : int [1:40] 222 222 223 223 224 224 225 225 226 226 ...
     .. .. ..$ y : int [1:40] 270 271 270 271 270 271 270 271 270 271 ...
     .. .. ..$ pbase : chr [1:40] "G" "C" "C" "G" ...
     .. .. ..$ tbase : chr [1:40] "C" "C" "G" "G" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-BioC-3_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-BioC-3_at:List of 6
     .. .. ..$ x : int [1:40] 224 224 225 225 226 226 227 227 228 228 ...
     .. .. ..$ y : int [1:40] 272 273 272 273 272 273 272 273 272 273 ...
     .. .. ..$ pbase : chr [1:40] "A" "T" "T" "A" ...
     .. .. ..$ tbase : chr [1:40] "T" "T" "A" "A" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-BioDn-5_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-BioDn-5_at:List of 6
     .. .. ..$ x : int [1:40] 226 226 227 227 228 228 229 229 230 230 ...
     .. .. ..$ y : int [1:40] 274 275 274 275 274 275 274 275 274 275 ...
     .. .. ..$ pbase : chr [1:40] "G" "C" "A" "T" ...
     .. .. ..$ tbase : chr [1:40] "C" "C" "T" "T" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-BioDn-3_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-BioDn-3_at:List of 6
     .. .. ..$ x : int [1:40] 228 228 229 229 230 230 231 231 232 232 ...
     .. .. ..$ y : int [1:40] 276 277 276 277 276 277 276 277 276 277 ...
     .. .. ..$ pbase : chr [1:40] "T" "A" "T" "A" ...
     .. .. ..$ tbase : chr [1:40] "A" "A" "A" "A" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-CreX-5_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-CreX-5_at:List of 6
     .. .. ..$ x : int [1:40] 230 230 231 231 232 232 233 233 216 216 ...
     .. .. ..$ y : int [1:40] 278 279 278 279 278 279 278 279 280 281 ...
     .. .. ..$ pbase : chr [1:40] "T" "A" "C" "G" ...
     .. .. ..$ tbase : chr [1:40] "A" "A" "G" "G" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-CreX-3_at :List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-CreX-3_at:List of 6
     .. .. ..$ x : int [1:40] 232 232 233 233 216 216 217 217 218 218 ...
     .. .. ..$ y : int [1:40] 280 281 280 281 282 283 282 283 282 283 ...
     .. .. ..$ pbase : chr [1:40] "C" "G" "A" "T" ...
     .. .. ..$ tbase : chr [1:40] "G" "G" "T" "T" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     $ AFFX-HUMISGF3A/M97935_5_at:List of 3
     ..$ type : int 1
     ..$ direction: int 2
     ..$ groups :List of 1
     .. ..$ AFFX-HUMISGF3A/M97935_5_at:List of 6
     .. .. ..$ x : int [1:40] 443 443 249 249 390 390 266 266 416 416 ...
     .. .. ..$ y : int [1:40] 331 332 123 124 335 336 285 286 331 332 ...
     .. .. ..$ pbase : chr [1:40] "C" "G" "G" "C" ...
     .. .. ..$ tbase : chr [1:40] "G" "G" "C" "C" ...
     .. .. ..$ expos : int [1:40] 0 0 1 1 2 2 3 3 4 4 ...
     .. .. ..$ direction: int 2
     'data.frame': 400 obs. of 16 variables:
     $ unit : int 1 1 1 1 1 1 1 1 1 1 ...
     $ unitName : chr "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" ...
     $ unitType : chr "expression" "expression" "expression" "expression" ...
     $ unitDirection : chr "antisense" "antisense" "antisense" "antisense" ...
     $ unitNbrOfAtoms : int 20 20 20 20 20 20 20 20 20 20 ...
     $ group : int 1 1 1 1 1 1 1 1 1 1 ...
     $ groupName : chr "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" ...
     $ groupDirection : chr "antisense" "antisense" "antisense" "antisense" ...
     $ groupNbrOfAtoms: int 20 20 20 20 20 20 20 20 20 20 ...
     $ cell : int 118489 118937 118490 118938 118491 118939 118492 118940 118493 118941 ...
     $ x : int 216 216 217 217 218 218 219 219 220 220 ...
     $ y : int 264 265 264 265 264 265 264 265 264 265 ...
     $ pbase : chr "A" "T" "C" "G" ...
     $ tbase : chr "T" "T" "G" "G" ...
     $ indexPos : int 0 0 1 1 2 2 3 3 4 4 ...
     $ atom : int 0 0 1 1 2 2 3 3 4 4 ...
     ChecksumFile:
     Name: HG-Focus.CDF
     Tags:
     Full name: HG-Focus.CDF
     Pathname: annotationData/chipTypes/HG-Focus/HG-Focus.CDF.md5
     File size: 32 B (32 bytes)
     Checksum on record: 307006493ef52faf137da0bd84c59ca8
     AffymetrixCelSet:
     Name: HG-Focus
     Tags:
     Path: ../../../../lib/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin
     Platform: Affymetrix
     Chip type: HG-Focus
     Number of arrays: 2
     Names: HG-Focus-1-121502, HG-Focus-2-121502 [2]
     Time period: 2002-05-15 10:59:33 -- 2002-05-15 11:07:10
     Total file size: 3.84 MiB
     AffymetrixCelFile:
     Name: HG-Focus-1-121502
     Tags:
     Full name: HG-Focus-1-121502
     Pathname: ../../../../lib/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL
     File size: 1.92 MiB (2012775 bytes)
     File format: v1 (binary; CC)
     Platform: Affymetrix
     Chip type: HG-Focus
     Timestamp: 2002-05-15 11:07:10
     ChecksumFileSet:
     Name: 2.Calvin
     Tags:
     Full name: 2.Calvin
     Number of files: 2
     Names: HG-Focus-1-121502.CEL, HG-Focus-2-121502.CEL [2]
     Path (to the first file): ../../../../lib/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin
     Total file size: 64 B (64 bytes)
     ChecksumFile:
     Name: HG-Focus-1-121502.CEL
     Tags:
     Full name: HG-Focus-1-121502.CEL
     Pathname: ../../../../lib/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL.md5
     File size: 32 B (32 bytes)
     Checksum on record: eb680c1b324e74b649e8b7fc643ee0c5
     Error in file(filename, open = "w+b") : cannot open the connection
     Calls: getAverageFile ... createFrom.AffymetrixCelFile -> .createCel -> <Anonymous> -> file
     In addition: Warning messages:
     1: In readCdfDataFrame(filename = "annotationData/chipTypes/HG-Focus/HG-Focus.CDF", :
     Some of the fields were not read: expos
     2: In file(filename, open = "w+b") :
     cannot open file '../../../../lib/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/.average-intensities-median-mad,b6c18433fdbd8c5edcea9dc2fa49c6aa.CEL.tmp': No such file or directory
     Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 3.2.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'oligo', 'pdInfoBuilder', 'AffymetrixDataTestFiles'
Flavor: r-release-macos-arm64

Version: 3.2.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘oligo’
Flavor: r-release-macos-arm64

Version: 3.2.0
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'pdInfoBuilder', 'AffymetrixDataTestFiles'
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64