* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘PSCBS’ ... ** package ‘PSCBS’ 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 ‘PSCBS’ finding HTML links ... done AbstractCBS html CBS html Non-documented_objects html NonPairedPSCBS html PSCBS-package html PSCBS html PairedPSCBS html Restructuring_AbstractCBS_objects html as.CBS.DNAcopy html finding level-2 HTML links ... done as.DNAcopy.CBS html as.data.frame.AbstractCBS html as.data.frame.CBS html bootstrapTCNandDHByRegion.PairedPSCBS html c.CBS html callAB.PairedPSCBS html callAllelicBalanceByDH.PairedPSCBS html callAmplifications.CBS html callCopyNeutral.PairedPSCBS html callCopyNeutralByTCNofAB.PairedPSCBS html callGNL.PairedPSCBS html callGainsAndLosses.CBS html callLOH.PairedPSCBS html callOutliers.CBS html callROH.PairedPSCBS html callSegmentationOutliers html dropChangePoints.AbstractCBS html dropRegions.AbstractCBS html estimateDeltaAB.PairedPSCBS html estimateDeltaABBySmallDH.PairedPSCBS html estimateDeltaCN.PairedPSCBS html estimateDeltaLOH.PairedPSCBS html estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS html estimateKappa.PairedPSCBS html estimateKappaByC1Density.PairedPSCBS html estimateStandardDeviation.CBS html exampleData html extractMinorMajorCNs.PairedPSCBS html extractSegmentMeansByLocus.CBS html extractTCNAndDHs.PairedPSCBS html findLargeGaps html findNeutralCopyNumberState html gapsToSegments.data.frame html getBootstrapLocusSets.PairedPSCBS html getCallStatistics.CBS html getChromosomes.AbstractCBS html getFractionOfGenomeLost.CBS html getLocusData.AbstractCBS html getSampleName.AbstractCBS html getSegments.AbstractCBS html getSegments.PSCBS html getSmoothLocusData.CBS html hclustCNs.AbstractCBS html installDNAcopy html joinSegments.CBS html mergeNonCalledSegments.CBS html mergeThreeSegments.AbstractCBS html mergeTwoSegments.AbstractCBS html mergeTwoSegments.PairedPSCBS html nbrOfChangePoints.AbstractCBS html nbrOfChromosomes.AbstractCBS html nbrOfLoci.AbstractCBS html nbrOfSegments.AbstractCBS html normalizeTotalCNs.AbstractCBS html ploidy.AbstractCBS html plotTracks.AbstractCBS html plotTracks.CBS html plotTracks1.PairedPSCBS html pruneByDP.AbstractCBS html pruneByHClust.AbstractCBS html pruneBySdUndo.CBS html randomSeed html report.AbstractCBS html resetSegments.AbstractCBS html segmentByCBS html segmentByNonPairedPSCBS html segmentByPairedPSCBS html setSampleName.AbstractCBS html testROH.numeric html updateMeans.AbstractCBS html updateMeansTogether.AbstractCBS html weightedQuantile html writeSegments.CBS html writeSegments.PSCBS html *** copying figures ** building package indices ** installing vignettes ** 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 (PSCBS)