* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ICAMS’ ...
** 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  
    finding level-2 HTML links ... done

    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  
    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  
    GetConsensusVAF                         html  
    GetCustomKmerCounts                     html  
    GetGenomeKmerCounts                     html  
    GetMutationLoadsFromMutectVCFs          html  
    GetMutationLoadsFromStrelkaIDVCFs       html  
    GetMutationLoadsFromStrelkaSBSVCFs      html  
    GetSequenceKmerCounts                   html  
    GetStrandedKmerCounts                   html  
    GetVAF                                  html  
    ICAMS                                   html  
    InferAbundance                          html  
    InferCatalogClassPrefix                 html  
    InferCatalogInfo                        html  
    InferRownames                           html  
    IsGRCh37                                html  
    IsGRCh38                                html  
    IsGRCm38                                html  
    MakeDataFrameFromVCF                    html  
    MakeVCFDBSdf                            html  
    MutectVCFFilesToCatalog                 html  
    MutectVCFFilesToCatalogAndPlotToPdf     html  
    MutectVCFFilesToZipFile                 html  
    NormalizeGenomeArg                      html  
    Plot96PartOfCompositeToPDF              html  
    PlotCatalog                             html  
    PlotCatalogToPdf                        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  
    RenameColumnsWithNameStrand             html  
    RenameColumnsWithNameVAF                html  
    Restaple1536                            html  
    Restaple96                              html  
    RevcDBS144                              html  
    RevcSBS96                               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  
    StrelkaIDVCFFilesToZipFile              html  
    StrelkaSBSVCFFilesToCatalog             html  
    StrelkaSBSVCFFilesToZipFile             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