* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘aroma.core’ ...
** this is package ‘aroma.core’ version ‘3.3.2’
** package ‘aroma.core’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function write to write.default, which was defined in environment aroma.core.
** help
*** installing help indices
  converting help for package ‘aroma.core’
    finding HTML links ... done
    AbstractCNData                          html  
    AbstractPSCNData                        html  
    AromaCellCpgFile                        html  
    AromaCellPositionFile                   html  
    AromaCellTabularBinaryFile              html  
    AromaGenomeTextFile                     html  
    AromaMicroarrayDataFile                 html  
    AromaMicroarrayDataSet                  html  
    AromaMicroarrayDataSetTuple             html  
    AromaMicroarrayTabularBinaryFile        html  
    AromaPlatform                           html  
    AromaPlatformInterface                  html  
    AromaRepository                         html  
    AromaTabularBinaryFile                  html  
    AromaTabularBinarySet                   html  
    AromaTransform                          html  
    AromaUnitCallFile                       html  
    AromaUnitCallSet                        html  
    AromaUnitFracBCnBinaryFile              html  
    AromaUnitFracBCnBinarySet               html  
    AromaUnitGenotypeCallFile               html  
    AromaUnitGenotypeCallSet                html  
    AromaUnitPscnBinaryFile                 html  
    AromaUnitPscnBinarySet                  html  
    AromaUnitSignalBinaryFile               html  
    AromaUnitSignalBinarySet                html  
    AromaUnitTabularBinaryFile              html  
    AromaUnitTotalCnBinaryFile              html  
    AromaUnitTotalCnBinarySet               html  
    AromaUnitTypesFile                      html  
    BinnedScatter                           html  
    CacheKeyInterface                       html  
    CbsModel                                html  
    ChromosomalModel                        html  
    ChromosomeExplorer                      html  
    CopyNumberChromosomalModel              html  
    CopyNumberSegmentationModel             html  
    Explorer                                html  
    FileCacheKeyInterface                   html  
    GladModel                               html  
    HaarSegModel                            html  
    Non-documented_objects                  html  
    NonPairedPSCNData                       html  
    PairedPSCNData                          html  
    ParametersInterface                     html  
    RawAlleleBFractions                     html  
    RawCopyNumberModel                      html  
    RawCopyNumbers                          html  
    RawGenomicSignals                       html  
    RawMirroredAlleleBFractions             html  
    RawSequenceReads                        html  
    SegmentedAlleleBFractions               html  
    SegmentedCopyNumbers                    html  
    SegmentedGenomicSignalsInterface        html  
    UnitAnnotationDataFile                  html  
    UnitNamesFile                           html  
    UnitTypesFile                           html  
    allocate.AromaTabularBinaryFile         html  
    aroma.core-package                      html  
    as.GrayscaleImage.matrix                html  
    colBinnedSmoothing.matrix               html  
    colKernelSmoothing.matrix               html  
    display.Explorer                        html  
    doCBS                                   html  
    downloadChipTypeFile.AromaRepository    html  
    downloadFile.AromaRepository            html  
    estimateSds.CopyNumberChromosomalModel
                                            html  
    estimateStandardDeviation.RawGenomicSignals
                                            html  
    exportAromaUnitPscnBinarySet            html  
    extractRawCopyNumbers.CopyNumberChromosomalModel
                                            html  
    findAnnotationData                      html  
    findAnnotationDataByChipType            html  
    findFilesTodo.AromaTransform            html  
    fit.CopyNumberChromosomalModel          html  
    fit.CopyNumberSegmentationModel         html  
    fitGenotypeCone.matrix                  html  
    fitGenotypeConeBySfit.matrix            html  
    fitMultiDimensionalCone.matrix          html  
    getAlias.Explorer                       html  
    getAromaPlatform.AromaPlatformInterface
                                            html  
    getCacheKey.CacheKeyInterface           html  
    getCacheKey.FileCacheKeyInterface       html  
    getChipType.AromaPlatformInterface      html  
    getChipType.ChromosomalModel            html  
    getChromosomes.ChromosomalModel         html  
    getChromosomes.ChromosomeExplorer       html  
    getFullName.AromaTransform              html  
    getInputDataSet.AromaTransform          html  
    getModel.ChromosomeExplorer             html  
    getName.AromaTransform                  html  
    getName.Explorer                        html  
    getNames.ChromosomalModel               html  
    getNames.Explorer                       html  
    getOutputDataSet.AromaTransform         html  
    getParameters.ParametersInterface       html  
    getParametersAsString.ParametersInterface
                                            html  
    getPath.AromaTransform                  html  
    getPath.Explorer                        html  
    getPlatform.AromaPlatformInterface      html  
    getRootPath.AromaTransform              html  
    getRootPath.Explorer                    html  
    getTags.AromaTransform                  html  
    getTags.Explorer                        html  
    getUnitAnnotationDataFile.AromaPlatformInterface
                                            html  
    indexOf.UnitNamesFile                   html  
    isCompatibleWith.AromaPlatformInterface
                                            html  
    isDone.AromaTransform                   html  
    listFiles.AromaRepository               html  
    matrixBlockPolish.matrix                html  
    mergeBoxplotStats.list                  html  
    nbrOfArrays.ChromosomalModel            html  
    nbrOfArrays.Explorer                    html  
    nbrOfChipTypes.AromaMicroarrayDataSetTuple
                                            html  
    nbrOfChipTypes.ChromosomalModel         html  
    plotTracks.PairedPSCNData               html  
    process.AromaTransform                  html  
    process.ChromosomeExplorer              html  
    process.Explorer                        html  
    processTime                             html  
    readFooter.AromaTabularBinaryFile       html  
    segmentByCBS.RawGenomicSignals          html  
    segmentByGLAD.RawGenomicSignals         html  
    segmentByHaarSeg.RawGenomicSignals      html  
    segmentByMPCBS.RawGenomicSignals        html  
    setAlias.Explorer                       html  
    setArrays.ChromosomeExplorer            html  
    setArrays.Explorer                      html  
    updateSetupExplorerFile.ChromosomeExplorer
                                            html  
    writeDataFrame.AromaUnitSignalBinaryFile
                                            html  
    writeDataFrame.AromaUnitSignalBinarySet
                                            html  
    writeDataFrame.AromaUnitTabularBinaryFile
                                            html  
    writeFooter.AromaTabularBinaryFile      html  
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (aroma.core)