* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘aroma.affymetrix’ ...
** package ‘aroma.affymetrix’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘aroma.affymetrix’
finding HTML links ... done
AbstractProbeSequenceNormalization html
AdditiveCovariatesNormalization html
AffineCnPlm html
AffinePlm html
AffineSnpPlm html
AffymetrixCdfFile html
AffymetrixCelFile html
AffymetrixCelSet html
AffymetrixCelSetReporter html
AffymetrixCelSetTuple html
AffymetrixCnChpSet html
AffymetrixFile html
AffymetrixFileSet html
AffymetrixFileSetReporter html
AffymetrixPgfFile html
AffymetrixProbeTabFile html
AlleleSummation html
AllelicCrosstalkCalibration html
AromaChipTypeAnnotationFile html
ArrayExplorer html
AvgCnPlm html
AvgPlm html
AvgSnpPlm html
BackgroundCorrection html
BaseCountNormalization html
BasePositionNormalization html
ChipEffectFile html
ChipEffectGroupMerge html
ChipEffectSet html
ChipEffectTransform html
CnChipEffectFile html
CnChipEffectSet html
CnPlm html
CnProbeAffinityFile html
CnagCfhFile html
CnagCfhSet html
CrlmmParametersFile html
CrlmmParametersSet html
DChipCdfBinFile html
DChipDcpFile html
DChipDcpSet html
DChipGenomeInformation html
DChipQuantileNormalization html
DChipSnpInformation html
ExonChipEffectFile html
ExonChipEffectSet html
ExonProbeAffinityFile html
ExonRmaPlm html
FirmaFile html
FirmaModel html
FirmaSet html
FragmentEquivalentClassNormalization html
FragmentLengthNormalization html
GcContentNormalization html
GcContentNormalization2 html
GcRmaBackgroundCorrection html
GenericReporter html
GenomeInformation html
HetLogAddCnPlm html
HetLogAddPlm html
HetLogAddSnpPlm html
LimmaBackgroundCorrection html
LinearModelProbeSequenceNormalization html
MatNormalization html
MatSmoothing html
MbeiCnPlm html
MbeiPlm html
MbeiSnpPlm html
Model html
MultiArrayUnitModel html
Non-documented_objects html
NormExpBackgroundCorrection html
OpticalBackgroundCorrection html
ParameterCelFile html
ParameterCelSet html
ProbeAffinityFile html
ProbeLevelModel html
ProbeLevelTransform html
ProbeLevelTransform3 html
QualityAssessmentFile html
QualityAssessmentModel html
QualityAssessmentSet html
QuantileNormalization html
ReseqCrosstalkCalibration html
ResidualFile html
ResidualSet html
RmaBackgroundCorrection html
RmaCnPlm html
RmaPlm html
RmaSnpPlm html
ScaleNormalization html
ScaleNormalization3 html
SingleArrayUnitModel html
SmoothMultiarrayModel html
finding level-2 HTML links ... done
SmoothRmaModel html
SnpChipEffectFile html
SnpChipEffectGroupMerge html
SnpChipEffectSet html
SnpInformation html
SnpPlm html
SnpProbeAffinityFile html
SpatialReporter html
TransformReport html
UgpGenomeInformation html
UnitModel html
UnitTypeScaleNormalization html
WeightsFile html
WeightsSet html
allocateFromCdf.AffymetrixCelFile html
allocateFromCdf.AromaUnitTabularBinaryFile
html
aroma.affymetrix-package html
as.AffymetrixCelSet.AffymetrixCelSet html
as.AffymetrixCnChpSet.AffymetrixCnChpSet
html
as.AffymetrixFileSet.AffymetrixFileSet
html
as.CnagCfhSet.CnagCfhSet html
as.DChipDcpSet.DChipDcpSet html
as.character.AffymetrixCelSet html
as.character.AffymetrixCnChpSet html
as.character.CnagCfhSet html
as.character.DChipDcpSet html
averageQuantile.AffymetrixCelSet html
bpmapCluster2Cdf html
byChipType.AromaChipTypeAnnotationFile
html
byChipType.DChipGenomeInformation html
byChipType.DChipSnpInformation html
byChipType.GenomeInformation html
byChipType.SnpInformation html
byChipType.UgpGenomeInformation html
byPath.AffymetrixFileSet html
calculateBaseline.ChipEffectSet html
calculateParametersGsb.AffymetrixCelSet
html
calculateResidualSet.FirmaModel html
clearData.AffymetrixCelFile html
compare.AffymetrixCdfFile html
computeAffinities.AffymetrixCdfFile html
convert.AffymetrixCdfFile html
convertUnits.AffymetrixCdfFile html
createExonByTranscriptCdf.AffymetrixCdfFile
html
createFrom.AffymetrixCelFile html
createMonocellCdf.AffymetrixCdfFile html
createUniqueCdf.AffymetrixCdfFile html
doCRMAv1 html
doCRMAv2 html
doFIRMA html
doGCRMA html
doRMA html
extractAffyBatch.AffymetrixCelSet html
extractDataFrame.ParameterCelSet html
extractExpressionSet.ChipEffectSet html
extractFeatureSet.AffymetrixCelSet html
extractMatrix.AffymetrixCelSet html
extractMatrix.ParameterCelSet html
findByChipType.AffymetrixCdfFile html
findByChipType.AffymetrixPgfFile html
findByChipType.AromaChipTypeAnnotationFile
html
findUnitsTodo.FirmaModel html
findUnitsTodo.ProbeLevelModel html
findUnitsTodo.UnitModel html
fit.FirmaModel html
fit.Model html
fit.ProbeLevelModel html
fit.SingleArrayUnitModel html
fit.SmoothMultiarrayModel html
fitQuantileNormFcn.AffymetrixCelFile html
fromCdf.GenomeInformation html
fromCdf.SnpInformation html
fromDataFile.ChipEffectFile html
fromFile.AffymetrixCdfFile html
fromFile.AffymetrixCelFile html
fromFile.AffymetrixPgfFile html
fromFile.AromaChipTypeAnnotationFile html
fromFile.CnagCfhFile html
getAM.ChipEffectFile html
getAM.ChipEffectSet html
getAlias.GenericReporter html
getAlias.Model html
getAlleleCellPairs.AffymetrixCdfFile html
getAlleleProbePairs.AffymetrixCdfFile html
getAlleleProbePairs3.AffymetrixCdfFile
html
getAverageFile.AffymetrixCelSet html
getAverageFile.CnagCfhSet html
getBaseline.ChipEffectSet html
getCdf.AffymetrixCelFile html
getCdf.AffymetrixCelSet html
getCdf.CnagCfhFile html
getCdf.CnagCfhSet html
getCdf.Model html
getCellIndices.AffymetrixCdfFile html
getCellIndices.ChipEffectFile html
getCellIndices.CnChipEffectFile html
getCellIndices.CnProbeAffinityFile html
getCellIndices.ExonChipEffectFile html
getCellIndices.ExonProbeAffinityFile html
getCellIndices.FirmaFile html
getCellIndices.ProbeAffinityFile html
getCellIndices.ResidualFile html
getCellIndices.SnpChipEffectFile html
getCellIndices.SnpProbeAffinityFile html
getCellIndices.UnitModel html
getCellIndices.WeightsFile html
getChipEffectSet.AlleleSummation html
getChipEffectSet.ProbeLevelModel html
getChipType.AffymetrixCelFile html
getChipType.AffymetrixCelSet html
getChipType.CnagCfhFile html
getChipType.GenomeInformation html
getChipType.SnpInformation html
getCnNames.AffymetrixCdfFile html
getData.GenomeInformation html
getData.SnpInformation html
getDataSet.AffymetrixCelSetReporter html
getDataSet.ArrayExplorer html
getDataSet.Model html
getFirmaSet.FirmaModel html
getFitUnitGroupFunction.AffinePlm html
getFitUnitGroupFunction.AvgPlm html
getFitUnitGroupFunction.ExonRmaPlm html
getFitUnitGroupFunction.FirmaModel html
getFitUnitGroupFunction.HetLogAddPlm html
getFitUnitGroupFunction.MbeiPlm html
getFitUnitGroupFunction.MultiArrayUnitModel
html
getFitUnitGroupFunction.RmaPlm html
getFitUnitGroupFunction.SingleArrayUnitModel
html
getFullName.Model html
getFullName.TransformReport html
getGenomeInformation.AffymetrixCdfFile
html
getHeader.AffymetrixCdfFile html
getHeader.AffymetrixCelFile html
getHeader.AffymetrixPgfFile html
getHeader.AromaChipTypeAnnotationFile html
getHeader.CnagCfhFile html
getImage.AffymetrixCelFile html
getInputDataSet.TransformReport html
getIntensities.AffymetrixCelSet html
getName.GenericReporter html
getName.Model html
getName.TransformReport html
getOutputDataSet.Transform html
getOutputDataSet.TransformReport html
getPath.Model html
getPath.TransformReport html
getPositions.GenomeInformation html
getProbeAffinityFile.ProbeLevelModel html
getResiduals.QualityAssessmentModel html
getRootPath.Model html
getSnpNames.AffymetrixCdfFile html
getTags.GenericReporter html
getTags.Model html
getTags.TransformReport html
getTimestamp.AffymetrixCelFile html
getUnitGroupCellMap.ChipEffectFile html
getUnitIndices.GenomeInformation html
getUnitIntensities.AffymetrixCelSet html
getUnitNames.AffymetrixCdfFile html
getUnitNames.AffymetrixPgfFile html
getUnitTypes.AffymetrixCdfFile html
getWeights.QualityAssessmentModel html
getXAM.ChipEffectFile html
getXAM.ChipEffectSet html
groupUnitsByDimension.AffymetrixCdfFile
html
image270.AffymetrixCelFile html
importFromApt.CnChipEffectSet html
importFromDChip.AffymetrixCelSet html
importFromDChip.CnChipEffectSet html
isDuplicated.AffymetrixCelSet html
isDuplicated.CnagCfhSet html
isPm.AffymetrixCdfFile html
isResequenceChip.AffymetrixCdfFile html
isSnpChip.AffymetrixCdfFile html
justRMA html
nbrOfGroupsPerUnit.AffymetrixCdfFile html
nbrOfSnps.AffymetrixCdfFile html
normalizeQuantile.AffymetrixCelFile html
normalizeQuantile.AffymetrixCelSet html
pdInfo2Cdf html
plotBoxplotStats.list html
plotDensity.AffymetrixCelFile html
plotDensity.AffymetrixCelSet html
plotDensity.GenomeInformation html
plotImage.AffymetrixCelFile html
plotMvsA.AffymetrixCelFile html
plotMvsX.AffymetrixCelFile html
process.AbstractProbeSequenceNormalization
html
process.AdditiveCovariatesNormalization
html
process.AllelicCrosstalkCalibration html
process.ArrayExplorer html
process.BackgroundCorrection html
process.ChipEffectGroupMerge html
process.DChipQuantileNormalization html
process.FragmentEquivalentClassNormalization
html
process.FragmentLengthNormalization html
process.GcContentNormalization html
process.GcRmaBackgroundCorrection html
process.GenericReporter html
process.LimmaBackgroundCorrection html
process.MatNormalization html
process.MatSmoothing html
process.OpticalBackgroundCorrection html
process.QuantileNormalization html
process.ReseqCrosstalkCalibration html
process.RmaBackgroundCorrection html
process.ScaleNormalization html
process.ScaleNormalization3 html
process.SpatialReporter html
process.UnitTypeScaleNormalization html
randomSeed html
readRawData.AffymetrixCelFile html
readUnits.AffymetrixCdfFile html
readUnits.AffymetrixCelFile html
readUnits.CnagCfhFile html
readUnits.MultiArrayUnitModel html
readUnits.SingleArrayUnitModel html
readUnitsByQuartets.AffymetrixCdfFile html
setAlias.GenericReporter html
setAlias.Model html
setArrays.ArrayExplorer html
setCdf.AffymetrixCelFile html
setCdf.AffymetrixCelSet html
setCdf.CnagCfhFile html
setCdf.CnagCfhSet html
setRestructor.AffymetrixCdfFile html
setTags.Model html
setupExampleData.AromaAffymetrix html
smoothScatterMvsA.AffymetrixCelFile html
updateUnits.AffymetrixCelFile html
verify.GenomeInformation html
verify.SnpInformation html
writeCdf.AffyGenePDInfo html
writeImage.AffymetrixCelFile html
** building package indices
** testing if installed package can be loaded from temporary location
Warning in .requireBiocPackage("affxparser", neededBy = getName(pkg)) :
Package 'affxparser' could not be loaded. Without it aroma.affymetrix will not work. Please install it from Bioconductor, cf. https://www.bioconductor.org/
** testing if installed package can be loaded from final location
Warning in .requireBiocPackage("affxparser", neededBy = getName(pkg)) :
Package 'affxparser' could not be loaded. Without it aroma.affymetrix will not work. Please install it from Bioconductor, cf. https://www.bioconductor.org/
** testing if installed package keeps a record of temporary installation path
* DONE (aroma.affymetrix)