* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ICAMS’ ...
** this is package ‘ICAMS’ version ‘3.0.11’
** package ‘ICAMS’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘ICAMS’
finding HTML links ... done
AddAndCheckDBSClassInVCF html
AddAndCheckSBSClassInVCF html
AddDBSClass html
AddRunInformation html
AddSBSClass html
AddSeqContext html
AddTranscript html
AnnotateDBSVCF html
AnnotateIDVCF html
AnnotateSBSVCF html
CalBaseCountsFrom3MerAbundance html
CalculateNumberOfSpace html
Canonicalize1Del html
Canonicalize1ID html
Canonicalize1INS html
CanonicalizeID html
CatalogRowOrder html
CheckAndFixChrNames html
CheckAndFixChrNamesForTransRanges html
CheckAndReorderRownames html
CheckAndReturnDBSCatalogs html
CheckAndReturnDBSMatrix html
CheckAndReturnIDCatalog html
CheckAndReturnIDMatrix html
CheckAndReturnSBSCatalogs html
CheckAndReturnSBSMatrix html
CheckDBSClassInVCF html
CheckSBSClassInVCF html
CheckSeqContextInVCF html
CollapseCatalog html
ConvertCatalogToSigProfilerFormat html
ConvertICAMSCatalogToSigProSBS96 html
CreateDinucAbundance html
CreateExomeStrandedRanges html
CreateOneColDBSMatrix html
CreateOneColIDMatrix html
CreateOneColSBSMatrix html
CreateOnePPMFromSBSVCF html
CreatePPMFromSBSVCFs html
CreatePentanucAbundance html
CreateStrandedDinucAbundance html
CreateStrandedTrinucAbundance html
CreateTetranucAbundance html
CreateTransRanges html
CreateTrinucAbundance html
FindDelMH html
FindMaxRepeatDel html
FindMaxRepeatIns html
GeneExpressionData html
GenerateEmptyKmerCounts html
GenerateKmer html
GeneratePlotPFMmatrix html
GenerateVCFsFromIndelSimpleFile1 html
GenerateVCFsFromIndelSimpleFiles html
Get1BPIndelFlanks html
GetCustomKmerCounts html
GetGenomeKmerCounts html
GetMutationLoadsFromMutectVCFs html
GetMutationLoadsFromStrelkaIDVCFs html
GetMutationLoadsFromStrelkaSBSVCFs html
GetSequenceKmerCounts html
GetStrandedKmerCounts html
GetVAF html
HaplotypePlot html
ICAMS html
InferAbundance html
InferCatalogClassPrefix html
InferCatalogInfo html
InferRefGenomeName html
InferRownames html
IsGRCh37 html
IsGRCh38 html
IsGRCm38 html
IsICAMSCatalog html
IsRefGenomeInstalled html
MakeDataFrameFromVCF html
MakeVCFDBSdf html
MutectVCFFilesToCatalog html
MutectVCFFilesToCatalogAndPlotToPdf html
MutectVCFFilesToZipFile html
NormalizeGenomeArg html
Plot96PartOfCompositeToPDF html
PlotCatalog html
PlotCatalogToPdf html
PlotPFMmatrix html
PlotPPM html
PlotPPMToPdf html
PlotTransBiasGeneExp html
PlotTransBiasGeneExpToPdf html
ReadAndSplitMutectVCFs html
ReadAndSplitStrelkaSBSVCFs html
ReadAndSplitVCFs html
ReadBedRanges html
ReadCatalog html
ReadCatalogErrReturn html
ReadCatalogInternal html
ReadDukeNUSCat192 html
ReadMutectVCF html
ReadMutectVCFs html
ReadStapleGT96SBS html
ReadStrelkaIDVCF html
ReadStrelkaIDVCFs html
ReadStrelkaSBSVCF html
ReadStrelkaSBSVCFs html
ReadTranscriptRanges html
ReadVCF html
ReadVCFs html
RemoveRangesOnBothStrand html
RenameColumnsWithNameEnd html
RenameColumnsWithNameStart html
RenameColumnsWithNameStrand html
RenameColumnsWithNameVAF html
Restaple1536 html
Restaple96 html
RevcDBS144 html
RevcSBS96 html
SelectVariantsByChromName html
SimpleReadVCF html
SplitListOfMutectVCFs html
SplitListOfStrelkaSBSVCFs html
SplitListOfVCFs html
SplitOneMutectVCF html
SplitOneVCF html
SplitSBSVCF html
SplitStrelkaSBSVCF html
StandardChromName html
StandardChromNameNew html
StopIfCatalogTypeIllegal html
StopIfNrowIllegal html
StopIfRegionIllegal html
StopIfTranscribedRegionIllegal html
StrelkaIDVCFFilesToCatalog html
StrelkaIDVCFFilesToCatalogAndPlotToPdf
html
StrelkaIDVCFFilesToZipFile html
StrelkaSBSVCFFilesToCatalog html
StrelkaSBSVCFFilesToCatalogAndPlotToPdf
html
StrelkaSBSVCFFilesToZipFile html
SymmetricalContextsFor1BPIndel html
TCFromCouSigCou html
TCFromDenSigDen html
TestMakeCatalogFromMutectVCFs html
TestMakeCatalogFromStrelkaIDVCFs html
TestMakeCatalogFromStrelkaSBSVCFs html
TestPlotCatCOMPOSITE html
TransRownames.ID.PCAWG.SigPro html
TransRownames.ID.SigPro.PCAWG html
TranscriptRanges html
TransformCatalog html
Unstaple1536 html
Unstaple78 html
Unstaple96 html
VCFsToCatalogs html
VCFsToCatalogsAndPlotToPdf html
VCFsToDBSCatalogs html
VCFsToIDCatalogs html
VCFsToSBSCatalogs html
VCFsToZipFile html
VCFsToZipFileXtra html
WriteCat html
WriteCatalog html
WriteCatalogIndelSigPro html
all.abundance html
as.catalog html
revc html
*** copying figures
** 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 (ICAMS)