• using R Under development (unstable) (2013-04-22 r62639)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘aroma.affymetrix/DESCRIPTION’ ... OK
• this is package ‘aroma.affymetrix’ version ‘2.8.0’
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Packages suggested but not available for checking:
  ‘affyPLM’ ‘dChipIO’ ‘oligo’ ‘pdInfoBuilder’ ‘AffymetrixDataTestFiles’
• 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 whether package ‘aroma.affymetrix’ can be installed ... [16s/17s] 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 R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking for unstated 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 ... NOTE
  extractSnpFeatureSet.AffymetrixCelSet: no visible global function
  definition for ‘read.celfiles’
  pdInfo2Cdf: no visible global function definition for ‘read.celfiles’
  pdInfo2Cdf: no visible global function definition for
  ‘getPlatformDesign’
  writeCdf.AffyGenePDInfo: no visible global function definition for
  ‘cleanPlatformName’
• checking Rd files ... WARNING
  checkRd: (3) allocateFromCdf.AffymetrixCelFile.Rd:23: \synopsis will be removed in R 3.1.0
  checkRd: (3) allocateFromCdf.AromaUnitTabularBinaryFile.Rd:23: \synopsis will be removed in R 3.1.0
  checkRd: (3) byChipType.AromaChipTypeAnnotationFile.Rd:26: \synopsis will be removed in R 3.1.0
  checkRd: (3) byChipType.GenomeInformation.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) byChipType.UgpGenomeInformation.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) byPath.AffymetrixFileSet.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) clearData.AffymetrixCelFile.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) findByChipType.AffymetrixCdfFile.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) findByChipType.AffymetrixPgfFile.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) fromCdf.GenomeInformation.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) fromCdf.SnpInformation.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) fromDataFile.ChipEffectFile.Rd:23: \synopsis will be removed in R 3.1.0
  checkRd: (3) fromFile.AffymetrixCdfFile.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) fromFile.AffymetrixCelFile.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) fromFile.AffymetrixPgfFile.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) fromFile.AromaChipTypeAnnotationFile.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) fromFile.CnagCfhFile.Rd:22: \synopsis will be removed in R 3.1.0
  checkRd: (3) getFitUnitGroupFunction.MultiArrayUnitModel.Rd:24: \synopsis will be removed in R 3.1.0
  checkRd: (3) getFitUnitGroupFunction.SingleArrayUnitModel.Rd:25: \synopsis will be removed in R 3.1.0
  checkRd: (3) importFromApt.CnChipEffectSet.Rd:24: \synopsis will be removed in R 3.1.0
  checkRd: (3) importFromDChip.AffymetrixCelSet.Rd:29: \synopsis will be removed in R 3.1.0
  checkRd: (3) importFromDChip.CnChipEffectSet.Rd:25: \synopsis will be removed in R 3.1.0
• 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 ... OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 2 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/aroma.affymetrix.Rcheck/00check.log’
  for details.