Found the following significant warnings:
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/AbstractProbeSequenceNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/AbstractProbeSequenceNormalization.Rd:90: file link ‘AromaCellSequenceFile’ in package ‘aroma.core’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/AdditiveCovariatesNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/AffymetrixCelSetTuple.Rd:31: file link ‘ChipEffectSetTuple’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/AffymetrixCelSetTuple.Rd:31: file link ‘CnChipEffectSetTuple’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/AffymetrixFile.Rd:37: file link ‘AffymetrixCnChpFile’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/AffymetrixFile.Rd:37: file link ‘AffymetrixTsvFile’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/AllelicCrosstalkCalibration.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/BackgroundCorrection.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/BaseCountNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/BasePositionNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ChipEffectGroupMerge.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ChipEffectTransform.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ChipEffectTransform.Rd:34: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/CnChipEffectFile.Rd:46: file link ‘CopyNumberDataFile’ in package ‘aroma.core’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/CnChipEffectFile.Rd:54: file link ‘CopyNumberDataFile’ in package ‘aroma.core’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/CnChipEffectSet.Rd:42: file link ‘CopyNumberDataSet’ in package ‘aroma.core’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/CnChipEffectSet.Rd:50: file link ‘CopyNumberDataSet’ in package ‘aroma.core’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/DChipQuantileNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/FragmentEquivalentClassNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/FragmentLengthNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/GcContentNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/GcContentNormalization2.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/GcRmaBackgroundCorrection.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/GenomeInformation.Rd:33: file link ‘AffymetrixCsvGenomeInformation’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/LimmaBackgroundCorrection.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/LimmaBackgroundCorrection.Rd:109: file link ‘backgroundCorrect’ in package ‘limma’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/LinearModelProbeSequenceNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/MatNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/MatSmoothing.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/Model.Rd:27: file link ‘CrlmmModel’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/NormExpBackgroundCorrection.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/NormExpBackgroundCorrection.Rd:56: file link ‘backgroundCorrect’ in package ‘limma’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/NormExpBackgroundCorrection.Rd:91: file link ‘backgroundCorrect’ in package ‘limma’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/OpticalBackgroundCorrection.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ProbeLevelTransform.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ProbeLevelTransform.Rd:31: file link ‘SpatialRowColumnNormalization’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ProbeLevelTransform.Rd:34: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ProbeLevelTransform3.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/QuantileNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ReseqCrosstalkCalibration.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/RmaBackgroundCorrection.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ScaleNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/ScaleNormalization3.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/SmoothMultiarrayModel.Rd:27: file link ‘SmoothSaModel’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/SnpChipEffectGroupMerge.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/SnpInformation.Rd:33: file link ‘UflSnpInformation’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/UnitTypeScaleNormalization.Rd:26: file link ‘Transform’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/averageQuantile.AffymetrixCelSet.Rd:39: file link ‘approx’ in package ‘stats’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/averageQuantile.AffymetrixCelSet.Rd:58: file link ‘averageQuantile.list’ in package ‘aroma.light’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/createExonByTranscriptCdf.AffymetrixCdfFile.Rd:32: file link ‘AffymetrixNetAffxCsvFile’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/createExonByTranscriptCdf.AffymetrixCdfFile.Rd:44: file link ‘AffymetrixNetAffxCsvFile’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/extractExpressionSet.ChipEffectSet.Rd:30: file link ‘extractMatrix.ChipEffectSet’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/extractExpressionSet.ChipEffectSet.Rd:44: file link ‘ExpressionSet-class’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/extractFeatureSet.AffymetrixCelSet.Rd:39: file link ‘FeatureSet-class’ in package ‘oligoClasses’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/extractFeatureSet.AffymetrixCelSet.Rd:46: file link ‘ExpressionSet-class’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/getImage.AffymetrixCelFile.Rd:40: file link ‘readRawDataRectangle.AffymetrixCelFile’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/getIntensities.AffymetrixCelSet.Rd:25: file link ‘getData.AffymetrixCelSet’ in package ‘aroma.affymetrix’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/justRMA.Rd:23: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/justRMA.Rd:40: file link ‘ExpressionSet’ in package ‘Biobase’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/justRMA.Rd:44: file link ‘justRMA’ in package ‘affy’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/normalizeQuantile.AffymetrixCelFile.Rd:50: file link ‘normalizeQuantile’ in package ‘aroma.light’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/normalizeQuantile.AffymetrixCelSet.Rd:57: file link ‘normalizeQuantileRank.numeric’ in package ‘aroma.light’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/plotDensity.AffymetrixCelFile.Rd:38: file link ‘plotDensity.numeric’ in package ‘aroma.light’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/plotMvsA.AffymetrixCelFile.Rd:33: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/plotMvsX.AffymetrixCelFile.Rd:33: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/process.DChipQuantileNormalization.Rd:26: file link ‘normalizeQuantileSpline.numeric’ in package ‘aroma.light’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/randomSeed.Rd:29: file link ‘RNGkind’ in package ‘base’ does not exist and so has been treated as a topic
  Rd warning: /home/hornik/tmp/scratch/RtmpEWwwSm/R.INSTALL70e22ea80bf5/aroma.affymetrix/man/smoothScatterMvsA.AffymetrixCelFile.Rd:33: file link ‘plot’ in package ‘graphics’ does not exist and so has been treated as a topic
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/aroma.affymetrix.Rcheck/00install.out’ for details.