R Under development (unstable) (2024-02-17 r85935 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.affymetrix") Loading required package: R.utils Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help. Attaching package: 'R.oo' The following object is masked from 'package:R.methodsS3': throw The following objects are masked from 'package:methods': getClasses, getMethods The following objects are masked from 'package:base': attach, detach, load, save R.utils v2.12.3 (2023-11-18 01:00:02 UTC) successfully loaded. See ?R.utils for help. Attaching package: 'R.utils' The following object is masked from 'package:utils': timestamp The following objects are masked from 'package:base': cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings Loading required package: aroma.core Loading required package: R.filesets R.filesets v2.15.1 (2024-01-24 17:22:49 UTC) successfully loaded. See ?R.filesets for help. Attaching package: 'R.filesets' The following object is masked from 'package:R.utils': validate The following objects are masked from 'package:base': append, readLines Loading required package: R.devices R.devices v2.17.2 (2024-01-29 13:30:11 UTC) successfully loaded. See ?R.devices for help. aroma.core v3.3.0 (2022-11-15 18:30:13 UTC) successfully loaded. See ?aroma.core for help. Attaching package: 'aroma.core' The following objects are masked from 'package:base': .Machine, colMeans, colSums, library, require, write Loading required package: aroma.light aroma.light v3.32.0 (2023-10-24) successfully loaded. See ?aroma.light for help. Attaching package: 'aroma.light' The following objects are masked from 'package:aroma.affymetrix': averageQuantile, normalizeQuantile, plotDensity, plotMvsA, plotXYCurve The following objects are masked from 'package:aroma.core': callNaiveGenotypes, normalizeTumorBoost Loading required package: affxparser Attaching package: 'affxparser' The following object is masked from 'package:aroma.affymetrix': writeCdf The following object is masked from 'package:R.utils': findFiles The following object is masked _by_ package:aroma.affymetrix: writeCdf The following object is masked from package:R.utils: findFiles aroma.affymetrix v3.2.2 successfully loaded. See ?aroma.affymetrix for help. Attaching package: 'aroma.affymetrix' The following objects are masked _by_ 'package:aroma.light': averageQuantile, normalizeQuantile, plotDensity, plotMvsA, plotXYCurve The following object is masked from 'package:affxparser': writeCdf > > ## Empty CDF > cdf <- AffymetrixCdfFile() > print(cdf) AffymetrixCdfFile: Path: NA Filename: NA File size: NA Chip type: NA File format: NA Dimension: NAxNA Number of cells: NA > > ## Missing CDF > cdf <- AffymetrixCdfFile(NA_character_, mustExist=FALSE) > print(cdf) AffymetrixCdfFile: Path: NA Filename: NA File size: NA Chip type: NA File format: NA Dimension: NAxNA Number of cells: NA > > > if (setupExampleData(aroma.affymetrix, dataset="FusionSDK_Test3", dirs="annotationData", mustWork=FALSE)) { + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # CDF file + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + cdf <- AffymetrixCdfFile$byChipType("Test3") + print(cdf) + + # Unit names, types, ... + names <- getUnitNames(cdf) + str(names) + + units <- indexOf(cdf, names=names[42:40]) + stopifnot(all.equal(units, 42:40)) + + types <- getUnitTypes(cdf) + print(table(types)) + + data <- readUnits(cdf, units=1:10) + str(data) + + data <- readDataFrame(cdf, units=1:10) + str(data) + + md5 <- getChecksumFile(cdf) + print(md5) + + ## Get an existing or create a new onocell CDF + cdfM <- getMonocellCdf(cdf, verbose=-10) + print(cdfM) + t0 <- lastModified(getPathname(cdfM)) + print(t0) + + ## A monocell CDF can be re-created + cdfM <- getMonocellCdf(cdf, force=TRUE) + print(cdfM) + t1 <- lastModified(getPathname(cdfM)) + print(t1) + stopifnot(t1 >= t0) + } # if (... "AffymetrixDataTestFiles") Ihre Berechtigungen reichen nicht aus, um diesen Vorgang auszuführen. AffymetrixCdfFile: Path: ../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA Filename: Test3.CDF File size: 243.77 KiB (249624 bytes) Chip type: Test3 File format: v4 (binary; XDA) Dimension: 126x126 Number of cells: 15876 Number of units: 345 Cells per unit: 46.02 Number of QC units: 13 chr [1:345] "Pae_16SrRNA_s_at" "Pae_23SrRNA_s_at" "PA1178_oprH_at" ... types 1 345 List of 10 $ Pae_16SrRNA_s_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ Pae_16SrRNA_s_at:List of 6 .. .. ..$ x : int [1:32] 111 111 19 19 95 95 18 18 25 25 ... .. .. ..$ y : int [1:32] 79 80 19 20 39 40 55 56 113 114 ... .. .. ..$ pbase : chr [1:32] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:32] "a" "a" "t" "t" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ Pae_23SrRNA_s_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ Pae_23SrRNA_s_at:List of 6 .. .. ..$ x : int [1:32] 124 124 56 56 1 1 85 85 62 62 ... .. .. ..$ y : int [1:32] 95 96 99 100 23 24 41 42 9 10 ... .. .. ..$ pbase : chr [1:32] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:32] "t" "t" "a" "a" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA1178_oprH_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA1178_oprH_at:List of 6 .. .. ..$ x : int [1:24] 41 41 117 117 110 110 60 60 41 41 ... .. .. ..$ y : int [1:24] 49 50 45 46 41 42 75 76 47 48 ... .. .. ..$ pbase : chr [1:24] "a" "t" "g" "c" ... .. .. ..$ tbase : chr [1:24] "t" "t" "c" "c" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA1816_dnaQ_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_at:List of 6 .. .. ..$ x : int [1:24] 21 21 68 68 119 119 62 62 118 118 ... .. .. ..$ y : int [1:24] 105 106 41 42 49 50 37 38 97 98 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA3183_zwf_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA3183_zwf_at:List of 6 .. .. ..$ x : int [1:24] 104 104 106 106 79 79 53 53 77 77 ... .. .. ..$ y : int [1:24] 91 92 19 20 27 28 75 76 19 20 ... .. .. ..$ pbase : chr [1:24] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:24] "a" "a" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA3640_dnaE_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA3640_dnaE_at:List of 6 .. .. ..$ x : int [1:24] 113 113 81 81 10 10 110 110 119 119 ... .. .. ..$ y : int [1:24] 41 42 27 28 45 46 103 104 91 92 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA4407_ftsZ_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA4407_ftsZ_at:List of 6 .. .. ..$ x : int [1:24] 19 19 13 13 100 100 36 36 18 18 ... .. .. ..$ y : int [1:24] 45 46 23 24 115 116 75 76 41 42 ... .. .. ..$ pbase : chr [1:24] "c" "g" "a" "t" ... .. .. ..$ tbase : chr [1:24] "g" "g" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ Pae_16SrRNA_s_st:List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ Pae_16SrRNA_s_st:List of 6 .. .. ..$ x : int [1:32] 94 94 82 82 79 79 95 95 77 77 ... .. .. ..$ y : int [1:32] 61 62 67 68 21 22 49 50 97 98 ... .. .. ..$ pbase : chr [1:32] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:32] "t" "t" "a" "a" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ Pae_23SrRNA_s_st:List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ Pae_23SrRNA_s_st:List of 6 .. .. ..$ x : int [1:32] 87 87 36 36 32 32 66 66 57 57 ... .. .. ..$ y : int [1:32] 5 6 71 72 17 18 61 62 47 48 ... .. .. ..$ pbase : chr [1:32] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:32] "a" "a" "t" "t" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ PA1178_oprH_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA1178_oprH_st:List of 6 .. .. ..$ x : int [1:24] 37 37 79 79 68 68 51 51 79 79 ... .. .. ..$ y : int [1:24] 33 34 67 68 65 66 111 112 43 44 ... .. .. ..$ pbase : chr [1:24] "t" "a" "c" "g" ... .. .. ..$ tbase : chr [1:24] "a" "a" "g" "g" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 'data.frame': 272 obs. of 16 variables: $ unit : int 1 1 1 1 1 1 1 1 1 1 ... $ unitName : chr "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" ... $ unitType : chr "expression" "expression" "expression" "expression" ... $ unitDirection : chr "antisense" "antisense" "antisense" "antisense" ... $ unitNbrOfAtoms : int 16 16 16 16 16 16 16 16 16 16 ... $ group : int 1 1 1 1 1 1 1 1 1 1 ... $ groupName : chr "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" ... $ groupDirection : chr "antisense" "antisense" "antisense" "antisense" ... $ groupNbrOfAtoms: int 16 16 16 16 16 16 16 16 16 16 ... $ cell : int 10066 10192 2414 2540 5010 5136 6949 7075 14264 14390 ... $ x : int 111 111 19 19 95 95 18 18 25 25 ... $ y : int 79 80 19 20 39 40 55 56 113 114 ... $ pbase : chr "T" "A" "A" "T" ... $ tbase : chr "A" "A" "T" "T" ... $ indexPos : int 0 0 1 1 2 2 3 3 4 4 ... $ atom : int 0 0 1 1 2 2 3 3 4 4 ... ChecksumFile: Name: Test3.CDF Tags: Full name: Test3.CDF Pathname: ../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF.md5 File size: 32 B (32 bytes) Checksum on record: f84c557f0882b82ab1c876f581a133f9 Retrieving monocell CDF... Monocell chip type: Test3,monocell Locating monocell CDF... Pathname: Locating monocell CDF...done Could not locate monocell CDF. Will create one for chip type... Creating monocell CDF... Chip type: Test3 Validate (main) CDF... Validate (main) CDF...done Adding temporary suffix from file... Pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF Suffix: .tmp Rename existing file?: FALSE Temporary pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp Adding temporary suffix from file...done Number of cells per group field: 1 Reading CDF group names... Reading CDF group names...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 686558 36.7 1198944 64.1 1198944 64.1 Vcells 1198851 9.2 8388608 64.0 2003062 15.3 used (Mb) gc trigger (Mb) max used (Mb) Ncells 685175 36.6 1198944 64.1 1198944 64.1 Vcells 1197155 9.2 8388608 64.0 2003062 15.3 Number of cells per unit: Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 Reading CDF QC units... Reading CDF QC units...done Number of QC cells: 1844 in 13 QC units (59.95 KiB) Total number of cells: 2189 Best array dimension: 47x47 (=2209 cells, i.e. 20 left-over cells) Creating CDF header with source CDF as template... Setting up header... Reading CDF header... Reading CDF header...done Reading CDF unit names... Reading CDF unit names...done Setting up header...done Writing... destHeader: List of 12 $ ncols : int 47 $ nrows : int 47 $ nunits : int 345 $ nqcunits : int 13 $ refseq : chr "" $ chiptype : chr "Test3" $ filename : chr "../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF" $ rows : int 126 $ cols : int 126 $ probesets : int 345 $ qcprobesets: int 13 $ reference : chr "" unitNames: chr [1:345] "Pae_16SrRNA_s_at" "Pae_23SrRNA_s_at" "PA1178_oprH_at" ... qcUnitLengths: num [1:13] 2106 2106 1434 230 230 ... unitLengths: num [1:345] 116 116 116 116 116 116 116 116 116 116 ... used (Mb) gc trigger (Mb) max used (Mb) Ncells 689658 36.9 1198944 64.1 1198944 64.1 Vcells 1213858 9.3 8388608 64.0 2003062 15.3 used (Mb) gc trigger (Mb) max used (Mb) Ncells 690808 36.9 1198944 64.1 1198944 64.1 Vcells 1215940 9.3 8388608 64.0 2086862 16.0 Writing...done Creating CDF header with source CDF as template...done Writing QC units... Rearranging QC unit cell indices... Units: Rearranging QC unit cell indices...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 691189 37.0 1198944 64.1 1198944 64.1 Vcells 1211472 9.3 8388608 64.0 2086862 16.0 Writing QC units...done Number of units: 345 Argument 'ram': 1.000000 Average unit length: 116.000000 bytes Number of chunks: 1 (34482 units/chunk) Reading, extracting, and writing units... Chunk #1 of 1 (345 units) Reading CDF list structure... Reading CDF list structure...done => RAM: 1.56 MiB used (Mb) gc trigger (Mb) max used (Mb) Ncells 692227 37.0 1198944 64.1 1198944 64.1 Vcells 1214226 9.3 8388608 64.0 2086862 16.0 Reading, extracting, and writing units...done Temporary CDF file created: Output pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp size isdir mode annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp 76542 FALSE 666 mtime annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp 2024-02-18 21:22:56 ctime annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp 2024-02-18 21:22:56 atime exe annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp 2024-02-18 21:22:56 no used (Mb) gc trigger (Mb) max used (Mb) Ncells 695357 37.2 1198944 64.1 1198944 64.1 Vcells 1221854 9.4 8388608 64.0 2086862 16.0 Verifying the written CDF... Chunk 1 of 1 Verifying the written CDF...done used (Mb) gc trigger (Mb) max used (Mb) Ncells 696493 37.2 1198944 64.1 1198944 64.1 Vcells 1224785 9.4 8388608 64.0 2086862 16.0 Dropping temporary suffix from file... Temporary pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF.tmp Suffix: .tmp Regular expression for suffix: \.tmp$ Pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF Renaming existing file... Result: TRUE Renaming existing file...done Dropping temporary suffix from file...done File pathname: annotationData/chipTypes/Test3/Test3,monocell.CDF size isdir mode annotationData/chipTypes/Test3/Test3,monocell.CDF 76542 FALSE 666 mtime annotationData/chipTypes/Test3/Test3,monocell.CDF 2024-02-18 21:22:56 ctime annotationData/chipTypes/Test3/Test3,monocell.CDF 2024-02-18 21:22:56 atime exe annotationData/chipTypes/Test3/Test3,monocell.CDF 2024-02-18 21:22:56 no Creating monocell CDF...done Could not locate monocell CDF. Will create one for chip type...done Could not locate monocell CDF. Will create one for chip type...done Retrieving monocell CDF...done AffymetrixCdfFile: Path: annotationData/chipTypes/Test3 Filename: Test3,monocell.CDF File size: 74.75 KiB (76542 bytes) Chip type: Test3,monocell File format: v4 (binary; XDA) Dimension: 47x47 Number of cells: 2209 Number of units: 345 Cells per unit: 6.40 Number of QC units: 13 [1] "2024-02-18 21:22:56 CET" AffymetrixCdfFile: Path: annotationData/chipTypes/Test3 Filename: Test3,monocell.CDF File size: 74.75 KiB (76542 bytes) Chip type: Test3,monocell File format: v4 (binary; XDA) Dimension: 47x47 Number of cells: 2209 Number of units: 345 Cells per unit: 6.40 Number of QC units: 13 [1] "2024-02-18 21:22:58 CET" Warning messages: 1: In system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait, : running command 'C:\Windows\system32\cmd.exe /c mklink "annotationData/chipTypes/Test3/Test3.CDF" "D:/RCompile/CRANpkg/lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF"' had status 1 2: In readCdfDataFrame(filename = "../../../../CRANpkg/lib/4.4/AffymetrixDataTestFiles/annotationData/chipTypes/Test3/1.XDA/Test3.CDF", : Some of the fields were not read: expos > > proc.time() user system elapsed 2.23 0.20 5.71