* using log directory 'd:/Rcompile/CRANpkg/local/4.4/dChipIO.Rcheck' * using R Under development (unstable) (2024-03-22 r86169 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'dChipIO/DESCRIPTION' ... OK * this is package 'dChipIO' version '0.1.5' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'dChipIO' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s] OK * checking whether the package can be loaded with stated dependencies ... [0s] OK * checking whether the package can be unloaded cleanly ... [0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s] OK * checking whether the namespace can be unloaded cleanly ... [0s] OK * checking loading without being on the library search path ... [0s] OK * checking whether startup messages can be suppressed ... [0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [2s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... [1s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [173s] ERROR Running 'readCdfBin.R' [172s] Running 'readDcp.R' [0s] Running 'readDcpRectangle.R' [1s] Running the tests in 'tests/readCdfBin.R' failed. Complete output: > library("dChipIO") dChipIO v0.1.5 (2016-01-12) successfully loaded. See ?dChipIO for help. > > path <- system.file("exData", package="dChipIO") > chipType <- "Test3" > filename <- sprintf("%s.CDF.bin", chipType) > pathname <- file.path(path, filename) > > hdr <- readCdfBinHeader(pathname) > print(hdr) $FileName [1] "C:\\Documents and Settings\\hb\\braju.com.R\\aroma.affymetrix\\reengineeringdChip\\annotationData\\Test3.CDF.bin" $Format [1] 4 $ChipType [1] "Test3" $CellDim [1] 126 $NumUnit [1] 345 > > data <- readCdfBin(pathname) > str(data) List of 4 $ header :List of 5 ..$ FileName: chr "C:\\Documents and Settings\\hb\\braju.com.R\\aroma.affymetrix\\reengineeringdChip\\annotationData\\Test3.CDF.bin" ..$ Format : int 4 ..$ ChipType: chr "Test3" ..$ CellDim : int 126 ..$ NumUnit : int 345 $ unitNames: chr [1:345] "Pae_16SrRNA_s_at" "Pae_23SrRNA_s_at" "PA1178_oprH_at" "PA1816_dnaQ_at" ... $ numProbes: int [1:345] 32 32 24 24 24 24 24 32 32 24 ... $ CellPos : int [1:345] 0 0 0 0 0 0 0 0 0 0 ... > > # Read a subset of the units > units <- c(10:11, 15:20, 150:105, 2,2,2) > dataT <- readCdfBin(pathname, units=units) > str(dataT) List of 4 $ header :List of 5 ..$ FileName: chr "C:\\Documents and Settings\\hb\\braju.com.R\\aroma.affymetrix\\reengineeringdChip\\annotationData\\Test3.CDF.bin" ..$ Format : int 4 ..$ ChipType: chr "Test3" ..$ CellDim : int 126 ..$ NumUnit : int 345 $ unitNames: chr [1:57] "PA1178_oprH_st" "PA1816_dnaQ_st" "AFFX-Athal-Actin_5_r_at" "AFFX-Athal-Actin_M_at" ... $ numProbes: int [1:57] 24 24 32 32 32 32 32 32 32 32 ... $ CellPos : int [1:57] 0 0 0 0 0 0 0 0 0 0 ... > > # Assert correctness > for (ff in c("unitNames", "numProbes", "CellPos")) { + stopifnot(length(dataT[[ff]]) == length(units)) + stopifnot(identical(dataT[[ff]], data[[ff]][units])) + } > > proc.time() user system elapsed 0.26 0.06 0.31 * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... [1s] OK * DONE Status: 1 ERROR