############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TitanCNA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TitanCNA_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TitanCNA.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TitanCNA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TitanCNA’ version ‘1.30.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘TitanCNA’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’ Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’ Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’ Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’ Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’ Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’ Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’ Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’ Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’ Warning: replacing previous import ‘BiocGenerics::combine’ by ‘dplyr::combine’ when loading ‘TitanCNA’ Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’ Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’ See ‘/Users/biocbuild/bbs-3.13-bioc/meat/TitanCNA.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: data 1.7Mb extdata 4.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE computeSDbwIndex: no visible binding for global variable ‘ClonalCluster’ correctIntegerCN: no visible binding for global variable ‘Median_HaplotypeRatio’ correctIntegerCN: no visible binding for global variable ‘Chromosome’ correctIntegerCN: no visible binding for global variable ‘Copy_Number’ correctIntegerCN: no visible binding for global variable ‘logR_Copy_Number’ correctIntegerCN: no visible binding for global variable ‘Median_logR’ correctIntegerCN: no visible binding for global variable ‘Cellular_Prevalence’ correctIntegerCN: no visible binding for global variable ‘Chr’ correctIntegerCN: no visible binding for global variable ‘LogRatio’ correctIntegerCN: no visible binding for global variable ‘CellularPrevalence’ correctIntegerCN: no visible binding for global variable ‘Corrected_Ratio’ correctIntegerCN: no visible binding for global variable ‘Corrected_Copy_Number’ correctIntegerCN: no visible binding for global variable ‘Corrected_Call’ correctIntegerCN: no visible binding for global variable ‘TITAN_call’ correctIntegerCN: no visible binding for global variable ‘Corrected_MajorCN’ correctIntegerCN: no visible binding for global variable ‘MajorCN’ correctIntegerCN: no visible binding for global variable ‘Corrected_MinorCN’ correctIntegerCN: no visible binding for global variable ‘MinorCN’ correctIntegerCN: no visible binding for global variable ‘CopyNumber’ correctIntegerCN: no visible binding for global variable ‘TITANcall’ correctReadDepth: no visible global function definition for ‘queryHits’ correctReadcount: no visible global function definition for ‘loess’ correctReadcount: no visible global function definition for ‘predict’ correctReadcount: no visible global function definition for ‘approxfun’ correctReadcount: no visible global function definition for ‘lowess’ extendSegments: no visible binding for global variable ‘Start’ extendSegments: no visible binding for global variable ‘End’ extendSegments: no visible binding for global variable ‘Chromosome’ extendSegments: no visible binding for global variable ‘Start.snp’ extendSegments: no visible binding for global variable ‘End.snp’ extendSegments: no visible binding for global variable ‘Start.telo’ extendSegments: no visible binding for global variable ‘seq.info’ extractAlleleReadCounts: no visible global function definition for ‘PileupParam’ extractAlleleReadCounts: no visible global function definition for ‘BcfFile’ extractAlleleReadCounts: no visible global function definition for ‘scanBcf’ extractAlleleReadCounts: no visible global function definition for ‘ScanBamParam’ extractAlleleReadCounts: no visible global function definition for ‘scanBamFlag’ extractAlleleReadCounts: no visible global function definition for ‘BamFile’ extractAlleleReadCounts: no visible global function definition for ‘pileup’ extractAlleleReadCounts: no visible global function definition for ‘write.table’ getHaplotypesFromVCF: no visible global function definition for ‘rowRanges<-’ getHaplotypesFromVCF: no visible global function definition for ‘rowRanges’ getHaplotypesFromVCF: no visible global function definition for ‘na.omit’ getHaplotypesFromVCF: no visible global function definition for ‘unstrsplit’ getHaplotypesFromVCF: no visible global function definition for ‘queryHits’ getHaplotypesFromVCF: no visible global function definition for ‘DataFrame’ getOverlap: no visible global function definition for ‘as’ getOverlap: no visible global function definition for ‘queryHits’ getOverlap: no visible global function definition for ‘subjectHits’ getPositionOverlap: no visible global function definition for ‘as’ getSubcloneProfiles: no visible global function definition for ‘read.delim’ getSubcloneProfiles: no visible binding for global variable ‘CopyNumber’ getSubcloneProfiles: no visible binding for global variable ‘TITANcall’ keepChr: no visible global function definition for ‘as’ loadAlleleCounts: no visible global function definition for ‘read.delim’ loadBXcountsFromBEDDir: no visible binding for global variable ‘BXcounts’ loadBXcountsFromBEDDir: no visible binding for global variable ‘BX’ loadBXcountsFromBEDDir: no visible global function definition for ‘RangedData’ loadHaplotypeAlleleCounts: no visible global function definition for ‘read.delim’ loadHaplotypeAlleleCounts: no visible global function definition for ‘subjectHits’ loadHaplotypeAlleleCounts: no visible global function definition for ‘as’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘phasedAlleleFraction’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘phasedCount’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘depth’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘SNPs’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeFraction’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeDepth.sum’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeBinDepth.sum’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeDepth.mean’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeBinDepth.mean’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘phaseSet’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘haplotypeBin’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeFraction.symmetric’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeDepth.sum.symmetric’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeDepth.mean.symmetric’ loadHaplotypeAlleleCounts: no visible global function definition for ‘.’ loadHaplotypeAlleleCounts: no visible global function definition for ‘na.omit’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘phasedCount.haploSymmetric’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘nonRef’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘phaseSet.aggr’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘HaplotypeRatio’ loadHaplotypeAlleleCounts: no visible binding for global variable ‘tumDepth’ loadReadCountsFromBed: no visible global function definition for ‘excludeCentromere’ loadReadCountsFromBed: no visible global function definition for ‘filterByTargetedSequences’ mergeSegsByCol: no visible binding for global variable ‘Median_Ratio’ mergeSegsByCol: no visible binding for global variable ‘Median_logR’ mergeSegsByCol: no visible binding for global variable ‘End’ mergeSegsByCol: no visible binding for global variable ‘Length.snp.’ outlierObslik: no visible global function definition for ‘dunif’ outputModelParameters: no visible global function definition for ‘write.table’ outputTitanResults: no visible global function definition for ‘write.table’ outputTitanSegments: no visible binding for global variable ‘Sample’ plotAllelicCN: no visible binding for global variable ‘Allele.1’ plotAllelicCN: no visible binding for global variable ‘LogRatio’ plotAllelicCN: no visible binding for global variable ‘Allele.2’ plotAllelicCN: no visible binding for global variable ‘Chr’ plotAllelicCN: no visible binding for global variable ‘TITANcall’ plotAllelicCN: no visible global function definition for ‘par’ plotAllelicCN: no visible binding for global variable ‘CopyNumber’ plotAllelicCN: no visible global function definition for ‘points’ plotAllelicCN: no visible global function definition for ‘lines’ plotAllelicRatio: no visible binding for global variable ‘Chr’ plotAllelicRatio: no visible binding for global variable ‘TITANcall’ plotAllelicRatio: no visible global function definition for ‘par’ plotAllelicRatio: no visible binding for global variable ‘AllelicRatio’ plotAllelicRatio: no visible global function definition for ‘lines’ plotCNlogRByChr: no visible binding for global variable ‘LogRatio’ plotCNlogRByChr: no visible binding for global variable ‘Median_logR’ plotCNlogRByChr: no visible binding for global variable ‘Chr’ plotCNlogRByChr: no visible binding for global variable ‘TITANcall’ plotCNlogRByChr: no visible global function definition for ‘par’ plotCNlogRByChr: no visible global function definition for ‘lines’ plotCNlogRByChr: no visible binding for global variable ‘Chromosome’ plotCNlogRByChr : : no visible global function definition for ‘lines’ plotCNlogRByChr: no visible binding for global variable ‘End_Position.bp.’ plotCNlogRByChr: no visible binding for global variable ‘Start_Position.bp.’ plotChrLines: no visible global function definition for ‘lines’ plotChrLines: no visible global function definition for ‘axis’ plotClonalFrequency: no visible binding for global variable ‘ClonalCluster’ plotClonalFrequency: no visible binding for global variable ‘CellularPrevalence’ plotClonalFrequency: no visible binding for global variable ‘TITANcall’ plotClonalFrequency: no visible binding for global variable ‘Chr’ plotClonalFrequency: no visible global function definition for ‘par’ plotClonalFrequency: no visible global function definition for ‘lines’ plotClonalFrequency: no visible global function definition for ‘mtext’ plotGeneAnnotation: no visible global function definition for ‘abline’ plotGeneAnnotation: no visible global function definition for ‘mtext’ plotHaplotypeFraction: no visible binding for global variable ‘HaplotypeRatio.1’ plotHaplotypeFraction: no visible binding for global variable ‘HaplotypeRatio’ plotHaplotypeFraction: no visible binding for global variable ‘HaplotypeRatio.2’ plotHaplotypeFraction: no visible binding for global variable ‘Chr’ plotHaplotypeFraction: no visible binding for global variable ‘TITANcall’ plotHaplotypeFraction: no visible global function definition for ‘par’ plotHaplotypeFraction: no visible global function definition for ‘points’ plotHaplotypeFraction: no visible binding for global variable ‘AllelicRatio’ plotHaplotypeFraction: no visible global function definition for ‘lines’ plotIdiogram.hg38: no visible global function definition for ‘par’ plotIdiogram.hg38: no visible binding for global variable ‘lsegments’ plotIdiogram.hg38: no visible binding for global variable ‘lpolygon’ plotIdiogram.hg38: no visible global function definition for ‘axis’ plotIdiogram.hg38: no visible global function definition for ‘text’ plotSegmentMedians: no visible binding for global variable ‘Chromosome’ plotSegmentMedians: no visible binding for global variable ‘TITAN_call’ plotSegmentMedians: no visible global function definition for ‘par’ plotSegmentMedians: no visible binding for global variable ‘End_Position.bp.’ plotSegmentMedians: no visible global function definition for ‘.’ plotSegmentMedians: no visible binding for global variable ‘Start_Position.bp.’ plotSegmentMedians: no visible binding for global variable ‘MajorCN’ plotSegmentMedians: no visible binding for global variable ‘MinorCN’ plotSegmentMedians : : no visible global function definition for ‘lines’ plotSegmentMedians: no visible global function definition for ‘lines’ plotSegmentMedians: no visible binding for global variable ‘Copy_Number’ plotSubcloneProfiles: no visible binding for global variable ‘Chr’ plotSubcloneProfiles: no visible global function definition for ‘par’ plotSubcloneProfiles: no visible binding for global variable ‘CopyNumber’ plotSubcloneProfiles: no visible global function definition for ‘axis’ plotSubcloneProfiles: no visible global function definition for ‘points’ plotSubcloneProfiles: no visible global function definition for ‘mtext’ plotSubcloneProfiles: no visible global function definition for ‘lines’ printSDbw: no visible global function definition for ‘write.table’ removeCentromereSegs: no visible binding for global variable ‘Chromosome’ removeCentromereSegs: no visible binding for global variable ‘Start’ removeCentromereSegs: no visible binding for global variable ‘End’ removeEmptyClusters: no visible global function definition for ‘tail’ runEMclonalCN: no visible binding for global variable ‘head’ updateParameters: no visible global function definition for ‘uniroot’ wigToRangedData: no visible global function definition for ‘RangedData’ Undefined global functions or variables: . Allele.1 Allele.2 AllelicRatio BX BXcounts BamFile BcfFile CellularPrevalence Cellular_Prevalence Chr Chromosome ClonalCluster CopyNumber Copy_Number Corrected_Call Corrected_Copy_Number Corrected_MajorCN Corrected_MinorCN Corrected_Ratio DataFrame End End.snp End_Position.bp. HaplotypeBinDepth.mean HaplotypeBinDepth.sum HaplotypeDepth.mean HaplotypeDepth.mean.symmetric HaplotypeDepth.sum HaplotypeDepth.sum.symmetric HaplotypeFraction HaplotypeFraction.symmetric HaplotypeRatio HaplotypeRatio.1 HaplotypeRatio.2 Length.snp. LogRatio MajorCN Median_HaplotypeRatio Median_Ratio Median_logR MinorCN PileupParam RangedData SNPs Sample ScanBamParam Start Start.snp Start.telo Start_Position.bp. TITAN_call TITANcall abline approxfun as axis depth dunif excludeCentromere filterByTargetedSequences haplotypeBin head lines loess logR_Copy_Number lowess lpolygon lsegments mtext na.omit nonRef par phaseSet phaseSet.aggr phasedAlleleFraction phasedCount phasedCount.haploSymmetric pileup points predict queryHits read.delim rowRanges rowRanges<- scanBamFlag scanBcf seq.info subjectHits tail text tumDepth uniroot unstrsplit write.table Consider adding importFrom("graphics", "abline", "axis", "lines", "mtext", "par", "points", "text") importFrom("methods", "as") importFrom("stats", "approxfun", "dunif", "loess", "lowess", "na.omit", "predict", "uniroot") importFrom("utils", "head", "read.delim", "tail", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: correctCN.Rd:51-53: Dropping empty section \details * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘list’ * checking for missing documentation entries ... WARNING Undocumented code objects: ‘plotIdiogram.hg38’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TitanCNA-package 30.798 0.557 31.379 runEMclonalCN 22.695 0.324 23.054 getPositionOverlap 8.975 0.160 9.144 filterData 8.732 0.192 8.931 correctReadDepth 7.288 0.117 7.409 TitanCNA-plotting 6.952 0.205 7.169 computeSDbwIndex 5.234 0.070 5.307 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 6 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/TitanCNA.Rcheck/00check.log’ for details.