• using R Under development (unstable) (2023-10-01 r85245)
• using platform: x86_64-pc-linux-gnu
• R was compiled by
      gcc-13 (Debian 13.2.0-4) 13.2.0
      GNU Fortran (Debian 13.2.0-4) 13.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘aroma.affymetrix/DESCRIPTION’ ... OK
• this is package ‘aroma.affymetrix’ version ‘3.2.1’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘aroma.affymetrix’ can be installed ... OK
  See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/2s] OK
• checking whether startup messages can be suppressed ... [1s/2s] 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 ... [122s/189s] OK
• checking Rd files ... [4s/6s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... NOTE
  Documented arguments not in \usage in documentation object 'AromaUnitTabularBinaryFile$allocateFromCdf':
    ‘path’ ‘tags’ ‘footer’
  
  Documented arguments not in \usage in documentation object 'byChipType.DChipSnpInformation':
    ‘rootPath’ ‘pattern’ ‘verbose’
  
  Documented arguments not in \usage in documentation object 'UgpGenomeInformation$byChipType':
    ‘version’
  
  Documented arguments not in \usage in documentation object 'calculateResidualSet.FirmaModel':
    ‘verbose’
  
  Documented arguments not in \usage in documentation object 'findByChipType.AromaChipTypeAnnotationFile':
    ‘chipType’ ‘tags’
  
  Documented arguments not in \usage in documentation object 'fit.SmoothMultiarrayModel':
    ‘data’
  
  Documented arguments not in \usage in documentation object 'getCellIndices.ExonChipEffectFile':
    ‘units’
  
  Documented arguments not in \usage in documentation object 'getImage.AffymetrixCelFile':
    ‘palette’
  
  Documented arguments not in \usage in documentation object 'getOutputDataSet.Transform':
    ‘force’
  
  Documented arguments not in \usage in documentation object 'getUnitTypes.AffymetrixCdfFile':
    ‘map’
  
  Documented arguments not in \usage in documentation object 'plotMvsX.AffymetrixCelFile':
    ‘xlim’ ‘xlab’
  
  Documented arguments not in \usage in documentation object 'process.BackgroundCorrection':
    ‘force’ ‘verbose’
  
  Documented arguments not in \usage in documentation object 'readUnits.CnagCfhFile':
    ‘cdf’
  
  Documented arguments not in \usage in documentation object 'setArrays.ArrayExplorer':
    ‘arrays’
  
  Documented arguments not in \usage in documentation object 'setRestructor.AffymetrixCdfFile':
    ‘units’
  
  Documented arguments not in \usage in documentation object 'setupExampleData':
    ‘dirs’
  
  Functions with \usage entries need to have the appropriate \alias
  entries, and all their arguments documented.
  The \usage entries must correspond to syntactically valid R code.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking examples ... [2s/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [25s/41s] OK
    Running ‘001.setupExampleData,annotationData.R’ [12s/19s]
    Running ‘002.setupExampleData,rawData.R’ [1s/3s]
    Running ‘AffymetrixCdfFile.R’ [5s/8s]
    Running ‘AffymetrixCelFile.R’ [2s/3s]
    Running ‘AffymetrixCelSet.R’ [5s/9s]
• checking PDF version of manual ... [29s/52s] OK
• checking HTML version of manual ... [17s/39s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE