ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame]

[HenrikBengtsson]

$ for pkg in $pkgs; do echo "$pkg:"; (cd "$pkg"; grep -E "^[ \t]*[^#].*data[.]frame" -- */*.R | grep -vF stringsAsFactors;); echo; read -r -p "Press ENTER to continue ..."; done
aroma.affymetrix:
R/AffymetrixCdfFile.getUnitGroupCellMap.R:    map <- data.frame(unit=units, group=groups, cell=cells)
R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R:  res <- data.frame(
R/AffymetrixCdfFile.groupUnitsByDimension.R:  dims <- as.data.frame(dims)
R/AffymetrixCelFile.R:    class(cel) <- "data.frame"
R/AffymetrixNetAffxCsvFile.R:  data <- data.frame(unitName=data[[1]], fln)
R/AlleleSummation.R:        data <- as.data.frame(data[c("intensities", "stdvs", "pixels")])
R/AromaUfcFile.R:  ## 'data.frame':   1879547 obs. of  3 variables:
R/ChipEffectFile.R:    map <- data.frame(unit=integer(0), group=integer(0), cell=integer(0))
R/ChipEffectFile.R:  map <- data.frame(unit=units2, group=groups, cell=cells)
R/ChipEffectFile.R:  data <- as.data.frame(data)
R/ChromosomalModel.getPositionChipTypeUnit.R:  pcu <- data.frame(position=pos, chipType=chipType, unit=units)
R/CrlmmModel.R:  data <- data.frame(gender=rep("female", times=nbrOfArrays))
R/FirmaFile.R:    map <- data.frame(unit=integer(0), group=integer(0), cell=integer(0))
R/FirmaFile.R:  map <- data.frame(unit=units, group=groups, cell=cells)
R/FirmaFile.R:  data <- as.data.frame(data)
R/isUnitGroupCellMap.R:setMethodS3("isUnitGroupCellMap", "data.frame", function(this, ...) {
R/justRMA.R:  data <- data.frame(ScanDate=getTimestamps(csR))
R/MatNormalization.R:  #ss<-split(data.frame(resid),cuts)
R/ParameterCelFile.extractNnn.R:    ugcMap <- as.data.frame(ugcMap)
R/ParameterCelFile.extractNnn.R:    ugNames <- as.data.frame(ugNames)
R/ParameterCelSet.R:    ugcMap <- as.data.frame(ugcMap)
R/ParameterCelSet.R:    ugNames <- as.data.frame(ugNames)
R/readCfhHeader.R:  references <- data.frame(sd=as.double(references[,1]), sample=I(references[,2]))
R/ResidualFile.R:    map <- data.frame(unit=integer(0), group=integer(0), cell=integer(0))
R/ResidualFile.R:  map <- data.frame(unit=units, group=groups, cell=cells)
R/ResidualFile.R:  data <- as.data.frame(data)
R/SmoothMultiarrayModel.fit.R:  pcu <- data.frame(position=pos, chipType=chipType, unit=units)
R/SmoothMultiarrayModel.fit.R:        outData <- data.frame(cell=map[,"cell"], theta=rep(0, nrow(map)))
R/SnpChipEffectNnn.extractCNT.R:  dataHead <- data.frame(
R/UnitModel.fitCnProbes.R:      data <- data.frame(cell=cellsM, theta=y, sdTheta=sdTheta, outliers=FALSE)
R/UnitTypeScaleNormalization.R:  data <- data.frame(cell=NULL, y=NULL)
R/UnitTypeScaleNormalization.R:    dataKK <- data.frame(cell=cells, y=y)
R/WeightsFile.R:    map <- data.frame(unit=integer(0), group=integer(0), cell=integer(0))
R/WeightsFile.R:  map <- data.frame(unit=units, group=groups, cell=cells)
R/WeightsFile.R:  data <- as.data.frame(data)