Mac ARM64 build report for BioC 3.19 - CHECK results for maftools on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4461
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maftools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maftools_2.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/maftools.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maftools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maftools’ version ‘2.20.0’
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maftools’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
Namespace in Imports field not imported from: ‘Rhtslib’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.dnaCopy_plotter: no visible binding for global variable ‘contig’
.dnaCopy_plotter: no visible binding for global variable ‘Chromosome’
.dnaCopy_plotter: no visible global function definition for ‘par’
.dnaCopy_plotter: no visible global function definition for ‘abline’
.dnaCopy_plotter: no visible global function definition for ‘segments’
.dnaCopy_plotter: no visible global function definition for ‘axis’
.getdomains: no visible binding for global variable ‘HGNC’
.getdomains: no visible binding for global variable ‘refseq.ID’
.getdomains: no visible binding for global variable ‘protein.ID’
.getdomains: no visible global function definition for ‘.’
.getdomains: no visible binding for global variable ‘aa.length’
.mafSetKeys: no visible binding for global variable ‘Chromosome’
.mafSetKeys: no visible binding for global variable ‘Start_Position’
.mafSetKeys: no visible binding for global variable ‘End_Position’
add_legend: no visible global function definition for ‘par’
add_legend: no visible global function definition for ‘legend’
add_oncoprint: no visible global function definition for ‘unit’
add_oncoprint: no visible binding for global variable ‘bg’
add_oncoprint2: no visible global function definition for ‘unit’
annovarToMaf: no visible binding for global variable ‘Hugo_Symbol’
annovarToMaf: no visible binding for global variable ‘Gene.refGene’
annovarToMaf: no visible binding for global variable ‘Func.refGene’
annovarToMaf: no visible binding for global variable
  ‘ExonicFunc.refGene’
annovarToMaf: no visible binding for global variable ‘AAChange.refGene’
annovarToMaf: no visible binding for global variable ‘ref_alt_len’
annovarToMaf: no visible binding for global variable ‘Ref’
annovarToMaf: no visible binding for global variable ‘Alt’
annovarToMaf: no visible binding for global variable ‘ref_alt_diff’
annovarToMaf: no visible binding for global variable ‘Variant_Type’
annovarToMaf: no visible binding for global variable ‘ref_alt’
annovarToMaf: no visible binding for global variable ‘ens_id’
annovarToMaf: no visible binding for global variable ‘hgnc_symbol’
annovarToMaf: no visible binding for global variable ‘Entrez_Gene_Id’
annovarToMaf: no visible binding for global variable ‘Entrez’
binconf : bc: no visible global function definition for ‘qf’
binconf : bc: no visible global function definition for ‘qnorm’
bubble_plot: no visible global function definition for ‘layout’
bubble_plot: no visible global function definition for ‘symbols’
bubble_plot: no visible global function definition for ‘axis’
bubble_plot: no visible global function definition for ‘abline’
bubble_plot: no visible global function definition for ‘mtext’
bubble_plot: no visible global function definition for ‘text’
bubble_plot: no visible global function definition for ‘par’
cancerhotspots: no visible global function definition for ‘browseURL’
cancerhotspotsAggr : <anonymous>: no visible global function definition
  for ‘.’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘A’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘G’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘C’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘Ins’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘Del’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘t_depth’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘VAF’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘End_Position’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘Start_Position’
cancerhotspotsAggr: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
clinicalEnrichment : pairwise.fisher.test : compare.levels: no visible
  global function definition for ‘fisher.test’
clinicalEnrichment : pairwise.fisher.test: no visible global function
  definition for ‘pairwise.table’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Gene’
clinicalEnrichment: no visible binding for global variable
  ‘AlteredSamples’
clinicalEnrichment: no visible binding for global variable
  ‘Hugo_Symbol’
clinicalEnrichment: no visible binding for global variable
  ‘MutatedSamples’
clinicalEnrichment : <anonymous> : <anonymous>: no visible global
  function definition for ‘fisher.test’
clinicalEnrichment : <anonymous> : <anonymous>: no visible binding for
  global variable ‘Group’
clinicalEnrichment : <anonymous> : <anonymous>: no visible binding for
  global variable ‘Genotype’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Hugo_Symbol’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Analysis’
clinicalEnrichment : <anonymous>: no visible global function definition
  for ‘.’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Var1’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Var2’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘value’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘fdr’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘cf’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Genotype’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘N’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘n_mutated_Feature’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘N.x’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘N.y’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Feature_1’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Feature_2’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘n_mutated_Feature1’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘n_mutated_Feature2’
clinicalEnrichment: no visible binding for global variable ‘Analysis’
clinicalEnrichment: no visible global function definition for ‘.’
clinicalEnrichment: no visible binding for global variable ‘Feature_1’
clinicalEnrichment: no visible binding for global variable ‘Feature_2’
clinicalEnrichment: no visible binding for global variable
  ‘n_mutated_Feature1’
clinicalEnrichment: no visible binding for global variable
  ‘n_mutated_Feature2’
clinicalEnrichment: no visible binding for global variable ‘fdr’
clinicalEnrichment: no visible binding for global variable ‘Group1’
clinicalEnrichment: no visible binding for global variable ‘Group2’
clinicalEnrichment: no visible binding for global variable
  ‘n_mutated_group1’
clinicalEnrichment: no visible binding for global variable
  ‘n_mutated_group2’
clinicalEnrichment: no visible binding for global variable ‘p_value’
clinicalEnrichment: no visible binding for global variable ‘OR’
clinicalEnrichment: no visible binding for global variable ‘OR_low’
clinicalEnrichment: no visible binding for global variable ‘OR_high’
clinicalEnrichment: no visible global function definition for
  ‘p.adjust’
clinicalEnrichment: no visible binding for global variable ‘cf’
cluster_prot: no visible binding for global variable ‘N’
cluster_prot: no visible binding for global variable ‘distance’
cluster_prot: no visible binding for global variable ‘startDist’
cluster_prot: no visible binding for global variable ‘endDist’
cluster_prot: no visible binding for global variable ‘fraction’
cluster_prot : <anonymous>: no visible binding for global variable
  ‘fraction’
coBarplot: no visible binding for global variable ‘Hugo_Symbol’
coBarplot: no visible binding for global variable ‘ID’
coBarplot: no visible global function definition for ‘.’
coBarplot: no visible binding for global variable ‘AlteredSamples’
coBarplot: no visible global function definition for ‘par’
coBarplot: no visible global function definition for ‘barplot’
coBarplot: no visible global function definition for ‘text’
coBarplot: no visible global function definition for ‘axis’
coBarplot: no visible global function definition for ‘mtext’
coBarplot: no visible global function definition for ‘title’
coBarplot: no visible global function definition for ‘legend’
coGisticChromPlot: no visible binding for global variable ‘Chromosome’
coGisticChromPlot: no visible binding for global variable ‘loc’
coGisticChromPlot: no visible binding for global variable
  ‘Start_Position’
coGisticChromPlot: no visible binding for global variable
  ‘End_Position’
coGisticChromPlot: no visible global function definition for ‘.’
coGisticChromPlot: no visible binding for global variable ‘qvalues’
coGisticChromPlot: no visible binding for global variable ‘Cytoband’
coGisticChromPlot: no visible binding for global variable
  ‘Variant_Classification’
coGisticChromPlot: no visible binding for global variable ‘value’
coGisticChromPlot: no visible global function definition for ‘layout’
coGisticChromPlot: no visible global function definition for ‘par’
coGisticChromPlot: no visible global function definition for ‘text’
coGisticChromPlot: no visible global function definition for ‘segments’
coGisticChromPlot: no visible global function definition for ‘axis’
coGisticChromPlot: no visible global function definition for ‘mtext’
coGisticChromPlot: no visible global function definition for ‘rect’
coGisticChromPlot: no visible global function definition for ‘lines’
coGisticChromPlot: no visible global function definition for ‘head’
coGisticChromPlot: no visible binding for global variable ‘gistic’
coGisticChromPlot: no visible binding for global variable
  ‘Start_Position_updated’
coGisticChromPlot: no visible binding for global variable
  ‘End_Position_updated’
coGisticChromPlot: no visible binding for global variable ‘ystart’
coGisticChromPlot: no visible global function definition for
  ‘complete.cases’
coGisticChromPlot: no visible global function definition for ‘rug’
coGisticChromPlot: no visible binding for global variable ‘Hugo_Symbol’
coGisticChromPlot: no visible binding for global variable ‘VC’
coGisticChromPlot: no visible binding for global variable ‘G_Score’
coGisticChromPlot: no visible binding for global variable
  ‘anno_Position’
coOncoplot: no visible binding for global variable ‘Hugo_Symbol’
coOncoplot: no visible global function definition for ‘.’
coOncoplot: no visible binding for global variable ‘MutatedSamples’
coOncoplot: no visible binding for global variable ‘MutatedSamples_m1’
coOncoplot: no visible binding for global variable ‘MutatedSamples_m2’
coOncoplot: no visible global function definition for ‘plot.new’
coOncoplot: no visible global function definition for ‘par’
coOncoplot: no visible global function definition for ‘image’
coOncoplot: no visible global function definition for ‘text’
coOncoplot: no visible global function definition for ‘legend’
createOncoMatrix: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
createOncoMatrix: no visible binding for global variable ‘Hugo_Symbol’
createOncoMatrix: no visible binding for global variable ‘Variant_Type’
createOncoMatrix: no visible binding for global variable
  ‘Variant_Classification’
createOncoMatrix: no visible binding for global variable
  ‘Variant_Classification_temp’
createOncoMatrix: no visible global function definition for ‘.’
dashboard: no visible binding for global variable ‘statFontSize’
dashboard: no visible binding for global variable ‘fs’
dashboard: no visible binding for global variable ‘pie’
dashboard: no visible global function definition for ‘par’
dashboard: no visible global function definition for ‘barplot’
dashboard: no visible global function definition for ‘abline’
dashboard: no visible global function definition for ‘axis’
dashboard: no visible global function definition for ‘title’
dashboard: no visible binding for global variable ‘value’
dashboard: no visible binding for global variable ‘variable’
dashboard: no visible global function definition for ‘text’
dashboard: no visible global function definition for ‘mtext’
dashboard: no visible binding for global variable ‘ID’
dashboard: no visible binding for global variable ‘Mean’
dashboard: no visible global function definition for ‘lines’
dashboard: no visible binding for global variable ‘Median’
dashboard: no visible binding for global variable ‘N’
dashboard: no visible global function definition for ‘.’
dashboard: no visible binding for global variable
  ‘Variant_Classification’
dashboard: no visible global function definition for ‘boxplot’
dashboard: no visible binding for global variable ‘boxStat’
dashboard: no visible binding for global variable ‘Hugo_Symbol’
dashboard: no visible binding for global variable ‘AlteredSamples’
detect_kataegis: no visible global function definition for
  ‘write.table’
detect_kataegis: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
detect_kataegis_chr: no visible binding for global variable ‘row_idx’
detect_kataegis_chr: no visible binding for global variable
  ‘Start_Position’
detect_kataegis_chr: no visible binding for global variable
  ‘Chromosome’
detect_kataegis_chr: no visible binding for global variable ‘Size’
detect_kataegis_chr: no visible binding for global variable
  ‘End_Position’
detect_kataegis_chr: no visible global function definition for ‘.’
detect_kataegis_chr: no visible binding for global variable ‘con.class’
detect_kataegis_chr: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
dirichletClusters: no visible binding for global variable ‘dp’
drugInteractions: no visible binding for global variable ‘Hugo_Symbol’
drugInteractions: no visible binding for global variable ‘Gene’
drugInteractions: no visible binding for global variable ‘N’
drugInteractions: no visible binding for global variable ‘category’
drugInteractions: no visible global function definition for ‘.’
drugInteractions: no visible binding for global variable ‘V1’
drugInteractions: no visible binding for global variable ‘label’
drugInteractions: no visible global function definition for ‘par’
drugInteractions: no visible global function definition for ‘pie’
drugInteractions: no visible global function definition for
  ‘heat.colors’
drugInteractions: no visible global function definition for ‘barplot’
drugInteractions: no visible global function definition for ‘text’
drugInteractions: no visible global function definition for ‘axis’
drugInteractions: no visible global function definition for ‘mtext’
drugInteractions: no visible global function definition for ‘title’
estimateSignatures: no visible global function definition for ‘png’
filterCopyNumber: no visible global function definition for ‘.’
filterCopyNumber: no visible binding for global variable ‘Hugo_Symbol’
filterCopyNumber: no visible binding for global variable ‘Chromosome’
filterCopyNumber: no visible binding for global variable
  ‘i.Start_Position’
filterCopyNumber: no visible binding for global variable
  ‘i.End_Position’
filterCopyNumber: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
filterCopyNumber: no visible binding for global variable ‘t_vaf’
filterCopyNumber: no visible binding for global variable
  ‘Start_Position’
filterCopyNumber: no visible binding for global variable ‘End_Position’
filterCopyNumber: no visible binding for global variable ‘Segment_Mean’
filterCopyNumber: no visible binding for global variable ‘CN’
filterMaf: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
filterMaf: no visible binding for global variable ‘Hugo_Symbol’
forestPlot: no visible binding for global variable ‘pval’
forestPlot: no visible binding for global variable ‘adjPval’
forestPlot: no visible binding for global variable ‘Cohort’
forestPlot: no visible binding for global variable ‘SampleSize’
forestPlot: no visible binding for global variable ‘pos’
forestPlot: no visible global function definition for ‘par’
forestPlot: no visible global function definition for ‘.’
forestPlot: no visible binding for global variable ‘or’
forestPlot: no visible binding for global variable ‘ci.up’
forestPlot: no visible binding for global variable ‘ci.low’
forestPlot: no visible binding for global variable ‘or_new’
forestPlot: no visible binding for global variable ‘upper’
forestPlot: no visible binding for global variable ‘lower’
forestPlot : <anonymous>: no visible global function definition for
  ‘points’
forestPlot : <anonymous>: no visible global function definition for
  ‘segments’
forestPlot: no visible global function definition for ‘abline’
forestPlot: no visible global function definition for ‘axis’
forestPlot: no visible global function definition for ‘mtext’
forestPlot: no visible global function definition for ‘title’
forestPlot: no visible global function definition for ‘text’
genesToBarcodes: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
genesToBarcodes : <anonymous>: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
genotypeMatrix: no visible binding for global variable ‘id’
genotypeMatrix: no visible binding for global variable ‘Chromosome’
genotypeMatrix: no visible binding for global variable ‘Start_Position’
genotypeMatrix: no visible binding for global variable ‘t_vaf’
get_anno_cols: no visible global function definition for
  ‘colorRampPalette’
get_col_df: no visible binding for global variable ‘Hugo_Symbol’
get_col_df: no visible binding for global variable ‘Var1’
get_col_df: no visible binding for global variable ‘Freq’
get_col_df: no visible global function definition for ‘.’
get_col_df: no visible binding for global variable ‘Gene’
get_lp_data: no visible binding for global variable ‘Hugo_Symbol’
get_lp_data: no visible global function definition for ‘.’
get_lp_data: no visible binding for global variable ‘Variant_Type’
get_lp_data: no visible binding for global variable
  ‘Variant_Classification’
get_lp_data: no visible binding for global variable ‘AAChange’
get_lp_data: no visible binding for global variable ‘HGNC’
get_lp_data: no visible binding for global variable ‘refseq.ID’
get_lp_data: no visible binding for global variable ‘protein.ID’
get_lp_data: no visible binding for global variable ‘aa.length’
get_lp_data: no visible binding for global variable ‘domain_lenght’
get_lp_data: no visible binding for global variable ‘End’
get_lp_data: no visible binding for global variable ‘Start’
get_lp_data: no visible binding for global variable ‘ID’
get_lp_data: no visible binding for global variable ‘MutatedSamples’
get_lp_data: no visible binding for global variable ‘conv’
get_lp_data: no visible binding for global variable ‘count2’
get_lp_data: no visible binding for global variable ‘count’
get_lp_data: no visible binding for global variable ‘posRounded’
get_lp_data: no visible binding for global variable ‘lab’
get_lp_data: no visible binding for global variable ‘Label’
get_pw_summary: no visible binding for global variable ‘Pathway’
get_pw_summary: no visible binding for global variable
  ‘fraction_affected’
get_pw_summary: no visible binding for global variable
  ‘n_affected_genes’
get_pw_summary: no visible binding for global variable ‘N’
get_pw_summary: no visible binding for global variable ‘ID’
get_pw_summary: no visible binding for global variable
  ‘Fraction_mutated_samples’
get_pw_summary: no visible binding for global variable
  ‘Mutated_samples’
get_pw_summary: no visible global function definition for ‘.’
get_threshold : <anonymous>: no visible global function definition for
  ‘dbinom’
gisticBubblePlot: no visible binding for global variable ‘qvalues’
gisticBubblePlot: no visible binding for global variable ‘Chromosome’
gisticBubblePlot: no visible binding for global variable ‘loc’
gisticBubblePlot: no visible binding for global variable
  ‘Start_Position’
gisticBubblePlot: no visible binding for global variable ‘End_Position’
gisticBubblePlot: no visible global function definition for ‘.’
gisticBubblePlot: no visible binding for global variable ‘Cytoband’
gisticBubblePlot: no visible binding for global variable
  ‘Variant_Classification’
gisticBubblePlot: no visible binding for global variable ‘nGenes’
gisticBubblePlot: no visible binding for global variable ‘log_q’
gisticBubblePlot: no visible global function definition for ‘par’
gisticChromPlot: no visible binding for global variable ‘qvalues’
gisticChromPlot: no visible binding for global variable ‘Chromosome’
gisticChromPlot: no visible binding for global variable ‘loc’
gisticChromPlot: no visible binding for global variable
  ‘Start_Position’
gisticChromPlot: no visible binding for global variable ‘End_Position’
gisticChromPlot: no visible global function definition for ‘.’
gisticChromPlot: no visible binding for global variable ‘Cytoband’
gisticChromPlot: no visible binding for global variable
  ‘Variant_Classification’
gisticChromPlot: no visible binding for global variable ‘amp’
gisticChromPlot: no visible global function definition for ‘layout’
gisticChromPlot: no visible global function definition for ‘par’
gisticChromPlot: no visible global function definition for ‘abline’
gisticChromPlot: no visible global function definition for ‘axis’
gisticChromPlot: no visible global function definition for ‘mtext’
gisticChromPlot: no visible global function definition for ‘segments’
gisticChromPlot: no visible global function definition for ‘rect’
gisticChromPlot: no visible global function definition for ‘text’
gisticChromPlot: no visible binding for global variable
  ‘Start_Position_updated’
gisticChromPlot: no visible binding for global variable
  ‘End_Position_updated’
gisticChromPlot: no visible global function definition for
  ‘complete.cases’
gisticChromPlot: no visible binding for global variable ‘Hugo_Symbol’
gisticChromPlot: no visible binding for global variable ‘G_Score’
gisticChromPlot: no visible binding for global variable ‘fdr’
gisticMap: no visible binding for global variable ‘Cytoband’
gisticMap: no visible binding for global variable
  ‘Variant_Classification’
gisticOncoPlot: no visible global function definition for ‘par’
gisticOncoPlot: no visible global function definition for ‘image’
gisticOncoPlot: no visible global function definition for ‘abline’
gisticOncoPlot: no visible global function definition for ‘mtext’
gisticOncoPlot: no visible global function definition for ‘text’
gisticOncoPlot: no visible global function definition for ‘legend’
gtMarkers: no visible global function definition for ‘download.file’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘consequence_type’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘gene_affected’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘assembly_version’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘chromosome’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘chromosome_start’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘chromosome_end’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘Variant_Classification’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘Variant_Type’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘reference_genome_allele’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘mutated_from_allele’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘mutated_to_allele’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘icgc_sample_id’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘verification_status’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘sequencing_strategy’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘verification_platform’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘ens_id’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘Hugo_Symbol’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘hgnc_symbol’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘Entrez_Gene_Id’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘Entrez’
icgcSimpleMutationToMAF: no visible global function definition for
  ‘write.table’
icgcSimpleMutationToMAF: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
inferHeterogeneity: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
inferHeterogeneity: no visible binding for global variable ‘t_vaf’
inferHeterogeneity: no visible binding for global variable
  ‘t_alt_count’
inferHeterogeneity: no visible binding for global variable
  ‘t_ref_count’
inferHeterogeneity: no visible binding for global variable ‘Chromosome’
inferHeterogeneity: no visible binding for global variable
  ‘Start_Position’
inferHeterogeneity: no visible binding for global variable
  ‘End_Position’
inferHeterogeneity: no visible binding for global variable ‘Sample’
inferHeterogeneity: no visible global function definition for ‘.’
inferHeterogeneity: no visible binding for global variable
  ‘Hugo_Symbol’
inferHeterogeneity: no visible global function definition for ‘median’
intersectMAF: no visible binding for global variable ‘Chromosome’
intersectMAF: no visible binding for global variable ‘Start_Position’
intersectMAF: no visible binding for global variable ‘End_Position’
intersectMAF: no visible global function definition for ‘.’
intersectMAF: no visible binding for global variable ‘Reference_Allele’
intersectMAF: no visible binding for global variable
  ‘Tumor_Seq_Allele2’
intersectMAF: no visible binding for global variable ‘variant_ID’
intersectMAF: no visible binding for global variable ‘maf_slot’
label_pos: no visible binding for global variable ‘labThis’
label_pos: no visible binding for global variable ‘pos2’
label_pos: no visible binding for global variable ‘count2’
label_pos: no visible binding for global variable ‘conv’
lollipopPlot: no visible binding for global variable ‘domain_lenght’
lollipopPlot: no visible binding for global variable ‘End’
lollipopPlot: no visible binding for global variable ‘Start’
lollipopPlot: no visible binding for global variable ‘Hugo_Symbol’
lollipopPlot: no visible global function definition for ‘.’
lollipopPlot: no visible binding for global variable ‘Variant_Type’
lollipopPlot: no visible binding for global variable
  ‘Variant_Classification’
lollipopPlot: no visible binding for global variable ‘AAChange_’
lollipopPlot: no visible binding for global variable ‘ID’
lollipopPlot: no visible binding for global variable ‘MutatedSamples’
lollipopPlot: no visible binding for global variable ‘conv’
lollipopPlot: no visible binding for global variable ‘count2’
lollipopPlot: no visible binding for global variable ‘count’
lollipopPlot: no visible binding for global variable ‘posRounded’
lollipopPlot: no visible binding for global variable ‘lab’
lollipopPlot: no visible binding for global variable ‘labThis’
lollipopPlot: no visible binding for global variable ‘pos2’
lollipopPlot: no visible binding for global variable ‘Label’
lollipopPlot: no visible global function definition for ‘par’
lollipopPlot: no visible global function definition for ‘rect’
lollipopPlot: no visible global function definition for ‘axis’
lollipopPlot: no visible global function definition for ‘segments’
lollipopPlot: no visible global function definition for ‘points’
lollipopPlot: no visible binding for global variable ‘domainCol’
lollipopPlot: no visible global function definition for ‘title’
lollipopPlot: no visible binding for global variable ‘refseq.ID’
lollipopPlot: no visible global function definition for ‘text’
lollipopPlot: no visible global function definition for ‘legend’
lollipopPlot2: no visible binding for global variable ‘Label’
lollipopPlot2: no visible binding for global variable
  ‘Variant_Classification’
lollipopPlot2: no visible global function definition for ‘par’
lollipopPlot2: no visible global function definition for ‘rect’
lollipopPlot2: no visible global function definition for ‘axis’
lollipopPlot2: no visible global function definition for ‘segments’
lollipopPlot2: no visible binding for global variable ‘pos2’
lollipopPlot2: no visible binding for global variable ‘count2’
lollipopPlot2: no visible global function definition for ‘points’
lollipopPlot2: no visible binding for global variable ‘domainCol’
lollipopPlot2: no visible binding for global variable ‘Start’
lollipopPlot2: no visible binding for global variable ‘End’
lollipopPlot2: no visible global function definition for ‘.’
lollipopPlot2: no visible global function definition for ‘text’
lollipopPlot2: no visible global function definition for ‘mtext’
lollipopPlot2: no visible binding for global variable ‘refseq.ID’
lollipopPlot2: no visible binding for global variable ‘conv’
lollipopPlot2: no visible global function definition for ‘legend’
mafbarplot: no visible binding for global variable ‘ID’
mafbarplot: no visible global function definition for ‘.’
mafbarplot: no visible binding for global variable ‘Hugo_Symbol’
mafbarplot: no visible binding for global variable ‘AlteredSamples’
mafbarplot: no visible global function definition for ‘par’
mafbarplot: no visible global function definition for ‘barplot’
mafbarplot: no visible global function definition for ‘axis’
mafbarplot: no visible global function definition for ‘text’
mafbarplot: no visible global function definition for ‘abline’
mafbarplot: no visible global function definition for ‘mtext’
mafbarplot: no visible global function definition for ‘legend’
mafCompare: no visible global function definition for ‘.’
mafCompare: no visible binding for global variable ‘Pathway’
mafCompare: no visible binding for global variable ‘Mutated_samples’
mafCompare: no visible binding for global variable ‘AlteredSamples’
mafCompare: no visible binding for global variable ‘Hugo_Symbol’
mafCompare: no visible binding for global variable ‘MutatedSamples’
mafCompare : <anonymous>: no visible global function definition for
  ‘fisher.test’
mafCompare: no visible binding for global variable ‘pval’
mafCompare: no visible binding for global variable ‘adjPval’
mafCompare: no visible global function definition for ‘p.adjust’
mafSurvGroup: no visible binding for global variable ‘Time’
mafSurvGroup: no visible global function definition for ‘.’
mafSurvGroup: no visible global function definition for ‘median’
mafSurvGroup: no visible binding for global variable ‘Group’
mafSurvGroup: no visible global function definition for ‘pchisq’
mafSurvGroup: no visible global function definition for ‘par’
mafSurvGroup: no visible global function definition for ‘abline’
mafSurvGroup: no visible global function definition for ‘points’
mafSurvGroup: no visible binding for global variable ‘survProb’
mafSurvGroup: no visible global function definition for ‘lines’
mafSurvGroup: no visible global function definition for ‘axis’
mafSurvGroup: no visible global function definition for ‘mtext’
mafSurvGroup: no visible global function definition for ‘legend’
mafSurvGroup: no visible global function definition for ‘title’
mafSurvival: no visible binding for global variable ‘Time’
mafSurvival: no visible global function definition for ‘.’
mafSurvival: no visible global function definition for ‘median’
mafSurvival: no visible binding for global variable ‘Group’
mafSurvival: no visible global function definition for ‘pchisq’
mafSurvival: no visible global function definition for ‘par’
mafSurvival: no visible global function definition for ‘abline’
mafSurvival: no visible global function definition for ‘points’
mafSurvival: no visible binding for global variable ‘survProb’
mafSurvival: no visible global function definition for ‘lines’
mafSurvival: no visible global function definition for ‘axis’
mafSurvival: no visible global function definition for ‘mtext’
mafSurvival: no visible global function definition for ‘legend’
mafSurvival: no visible global function definition for ‘title’
mapMutsToSegs: no visible binding for global variable ‘Sample’
mapMutsToSegs: no visible binding for global variable ‘Chromosome’
mapMutsToSegs: no visible binding for global variable ‘Start_Position’
mapMutsToSegs: no visible binding for global variable ‘End_Position’
mapMutsToSegs: no visible binding for global variable ‘Variant_Type’
mapMutsToSegs: no visible global function definition for ‘.’
mapMutsToSegs: no visible binding for global variable ‘Hugo_Symbol’
mapMutsToSegs: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
mapMutsToSegs: no visible binding for global variable
  ‘i.Start_Position’
mapMutsToSegs: no visible binding for global variable ‘i.End_Position’
mapMutsToSegs: no visible binding for global variable ‘Segment_Mean’
mapMutsToSegs: no visible binding for global variable
  ‘Start_Position_updated’
mapMutsToSegs: no visible binding for global variable
  ‘End_Position_updated’
mapMutsToSegs: no visible binding for global variable ‘CN’
math.score: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
math.score: no visible binding for global variable ‘t_ref_count’
math.score: no visible binding for global variable ‘t_alt_count’
math.score: no visible binding for global variable ‘t_vaf’
math.score: no visible global function definition for ‘.’
math.score: no visible binding for global variable ‘Hugo_Symbol’
math.score : <anonymous>: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
math.score : <anonymous>: no visible global function definition for
  ‘median’
mutCountMatrix: no visible binding for global variable
  ‘Variant_Classification’
mutCountMatrix: no visible global function definition for ‘.’
mutCountMatrix: no visible binding for global variable ‘Hugo_Symbol’
mutCountMatrix: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
mutCountMatrix: no visible binding for global variable ‘tot’
oncodrive: no visible global function definition for ‘read.csv’
oncodrive: no visible global function definition for ‘sd’
oncodrive: no visible binding for global variable ‘Hugo_Symbol’
oncodrive: no visible global function definition for ‘pnorm’
oncodrive: no visible global function definition for ‘p.adjust’
oncodrive: no visible binding for global variable
  ‘fract_muts_in_clusters’
oncodrive: no visible binding for global variable ‘muts_in_clusters’
oncodrive: no visible binding for global variable ‘total’
oncodrive: no visible global function definition for ‘glm’
oncodrive: no visible global function definition for ‘poisson’
oncodrive : <anonymous>: no visible global function definition for
  ‘poisson.test’
oncodrive: no visible binding for global variable ‘poissonFdr’
oncodrive: no visible global function definition for ‘.’
oncodrive: no visible binding for global variable ‘tFdr’
oncodrive: no visible binding for global variable ‘fdr’
oncoplot: no visible binding for global variable ‘Gene’
oncoplot: no visible global function definition for ‘.’
oncoplot: no visible binding for global variable ‘Pathway’
oncoplot: no visible binding for global variable ‘AlteredSamples’
oncoplot: no visible binding for global variable ‘Hugo_Symbol’
oncoplot: no visible binding for global variable ‘MutatedSamples’
oncoplot: no visible binding for global variable ‘fractMutated’
oncoplot: no visible binding for global variable ‘mutload’
oncoplot: no visible binding for global variable ‘Tumor_Sample_Barcode’
oncoplot: no visible binding for global variable ‘total’
oncoplot: no visible binding for global variable
  ‘Variant_Classification_temp’
oncoplot: no visible binding for global variable
  ‘Variant_Classification’
oncoplot: no visible binding for global variable ‘value’
oncoplot: no visible binding for global variable ‘CNV_total’
oncoplot: no visible binding for global variable ‘Amp’
oncoplot: no visible binding for global variable ‘Del’
oncoplot: no visible binding for global variable ‘max_alt’
oncoplot: no visible binding for global variable ‘n’
oncoplot : <anonymous>: no visible binding for global variable
  ‘pct_alt’
oncoplot: no visible global function definition for ‘par’
oncoplot: no visible global function definition for ‘axis’
oncoplot: no visible global function definition for ‘rect’
oncoplot: no visible global function definition for ‘mtext’
oncoplot: no visible global function definition for ‘abline’
oncoplot: no visible global function definition for ‘title’
oncoplot: no visible global function definition for ‘image’
oncoplot: no visible global function definition for ‘write.table’
oncoplot: no visible binding for global variable ‘row_id’
oncoplot : <anonymous>: no visible global function definition for
  ‘rect’
oncoplot: no visible binding for global variable ‘temp_af’
oncoplot : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
oncoplot: no visible global function definition for ‘box’
oncoplot: no visible global function definition for ‘text’
oncoplot: no visible global function definition for ‘plot.new’
oncoplot: no visible global function definition for ‘legend’
parse_prot: no visible global function definition for ‘.’
parse_prot: no visible binding for global variable ‘Hugo_Symbol’
parse_prot: no visible binding for global variable
  ‘Variant_Classification’
parse_prot: no visible binding for global variable ‘AAChange’
parse_prot: no visible binding for global variable ‘conv’
parse_prot: no visible binding for global variable ‘aa.length’
parse_prot: no visible binding for global variable ‘total’
parse_prot: no visible global function definition for ‘txtProgressBar’
parse_prot: no visible binding for global variable ‘th’
parse_prot: no visible global function definition for
  ‘setTxtProgressBar’
pathway_load: no visible binding for global variable ‘Gene’
pathway_load: no visible global function definition for ‘.’
pathway_load: no visible binding for global variable ‘Pathway’
pathway_load: no visible binding for global variable
  ‘fraction_affected’
pathway_load: no visible binding for global variable ‘n_affected_genes’
pathway_load: no visible binding for global variable ‘N’
pathway_load: no visible binding for global variable ‘ID’
pathway_load: no visible binding for global variable
  ‘Fraction_mutated_samples’
pathway_load: no visible binding for global variable ‘Mutated_samples’
pathways: no visible binding for global variable ‘n_affected_genes’
pathways: no visible binding for global variable
  ‘Fraction_mutated_samples’
pathways : draw_rect: no visible global function definition for ‘rect’
pathways : draw_text: no visible global function definition for ‘text’
pathways : draw_text_sub: no visible global function definition for
  ‘text’
pathways: no visible binding for global variable ‘ID’
pathways: no visible global function definition for ‘layout’
pathways: no visible global function definition for ‘par’
pathways: no visible global function definition for ‘text’
pathways: no visible global function definition for ‘title’
pathways: no visible global function definition for ‘rect’
pathways: no visible global function definition for ‘axis’
pfamDomains: no visible binding for global variable ‘Variant_Type’
pfamDomains: no visible global function definition for ‘.’
pfamDomains: no visible binding for global variable ‘Hugo_Symbol’
pfamDomains: no visible binding for global variable
  ‘Variant_Classification’
pfamDomains: no visible binding for global variable ‘AAChange’
pfamDomains: no visible binding for global variable ‘conv’
pfamDomains: no visible binding for global variable ‘total’
pfamDomains: no visible binding for global variable ‘N’
pfamDomains: no visible binding for global variable ‘fraction’
pfamDomains: no visible binding for global variable ‘HGNC’
pfamDomains: no visible binding for global variable ‘Start’
pfamDomains: no visible binding for global variable ‘End’
pfamDomains: no visible binding for global variable ‘Label’
pfamDomains: no visible binding for global variable ‘pfam’
pfamDomains: no visible binding for global variable ‘Description’
pfamDomains: no visible binding for global variable ‘idx’
pfamDomains: no visible binding for global variable ‘DomainLabel’
pfamDomains: no visible binding for global variable ‘nMut’
pfamDomains: no visible binding for global variable ‘nGenes’
pfamDomains: no visible global function definition for ‘complete.cases’
pfamDomains: no visible binding for global variable ‘nMuts’
pfamDomains: no visible global function definition for ‘write.table’
pfamDomains: no visible global function definition for ‘par’
pfamDomains: no visible global function definition for ‘mtext’
plotApobecDiff: no visible binding for global variable
  ‘APOBEC_Enriched’
plotApobecDiff: no visible binding for global variable
  ‘fraction_APOBEC_mutations’
plotApobecDiff: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
plotApobecDiff: no visible binding for global variable ‘ID’
plotApobecDiff: no visible global function definition for ‘.’
plotApobecDiff: no visible binding for global variable ‘Mean’
plotApobecDiff: no visible binding for global variable ‘Median’
plotApobecDiff: no visible binding for global variable ‘Cohort’
plotApobecDiff: no visible binding for global variable ‘pval’
plotApobecDiff: no visible binding for global variable ‘Hugo_Symbol’
plotApobecDiff: no visible binding for global variable ‘MutatedSamples’
plotApobecDiff: no visible binding for global variable ‘SampleSize’
plotApobecDiff: no visible binding for global variable ‘nonApobec’
plotApobecDiff: no visible binding for global variable ‘V1’
plotApobecDiff: no visible binding for global variable ‘title’
plotApobecDiff: no visible binding for global variable ‘variable’
plotApobecDiff: no visible binding for global variable ‘value’
plotApobecDiff: no visible global function definition for ‘par’
plotApobecDiff: no visible binding for global variable ‘n_mutations’
plotApobecDiff: no visible global function definition for ‘boxplot’
plotApobecDiff: no visible global function definition for ‘title’
plotApobecDiff: no visible global function definition for ‘axis’
plotApobecDiff: no visible global function definition for ‘na.omit’
plotApobecDiff: no visible binding for global variable ‘N’
plotApobecDiff: no visible global function definition for ‘mtext’
plotApobecDiff: no visible global function definition for ‘wilcox.test’
plotApobecDiff: no visible global function definition for ‘text’
plotApobecDiff: no visible global function definition for ‘segments’
plotApobecDiff: no visible global function definition for ‘pie’
plotApobecDiff: no visible global function definition for ‘symbols’
plotApobecDiff: no visible global function definition for ‘barplot’
plotCBS: no visible binding for global variable ‘Sample’
plotCBS: no visible binding for global variable ‘Chromosome’
plotCBS: no visible binding for global variable ‘Start_Position’
plotCBS: no visible global function definition for ‘par’
plotCBS: no visible global function definition for ‘axis’
plotCBS: no visible global function definition for ‘abline’
plotCBS: no visible global function definition for ‘rect’
plotCBS: no visible global function definition for ‘title’
plotCBS: no visible global function definition for ‘mtext’
plotCBSchr: no visible binding for global variable ‘Sample’
plotCBSchr: no visible binding for global variable ‘Chromosome’
plotCBSsegments: no visible binding for global variable ‘Chromosome’
plotCBSsegments: no visible binding for global variable
  ‘Start_Position’
plotCBSsegments: no visible binding for global variable ‘End_Position’
plotCBSsegments: no visible binding for global variable ‘Sample’
plotCBSsegments: no visible global function definition for
  ‘write.table’
plotCBSsegments: no visible global function definition for ‘.’
plotCBSsegments: no visible binding for global variable ‘Hugo_Symbol’
plotCBSsegments: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
plotCBSsegments: no visible binding for global variable ‘Segment_Start’
plotCBSsegments: no visible binding for global variable ‘Segment_End’
plotCBSsegments: no visible binding for global variable ‘Segment_Mean’
plotCBSsegments: no visible binding for global variable ‘CN’
plotCBSsegments: no visible global function definition for ‘text’
plotCBSsegments: no visible global function definition for ‘segments’
plotClusters: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
plotClusters: no visible global function definition for ‘par’
plotClusters: no visible global function definition for ‘boxplot’
plotClusters: no visible binding for global variable ‘t_vaf’
plotClusters: no visible global function definition for ‘density’
plotClusters: no visible global function definition for ‘lines’
plotClusters: no visible global function definition for ‘abline’
plotClusters: no visible global function definition for ‘axis’
plotClusters: no visible global function definition for ‘points’
plotClusters: no visible global function definition for ‘title’
plotClusters: no visible binding for global variable ‘MATH’
plotClusters: no visible global function definition for ‘segments’
plotClusters: no visible global function definition for ‘text’
plotClusters: no visible binding for global variable ‘Hugo_Symbol’
plotClusters: no visible global function definition for ‘legend’
plotClusters: no visible global function definition for ‘mtext’
plotCophenetic: no visible global function definition for ‘par’
plotCophenetic: no visible global function definition for ‘axis’
plotCophenetic: no visible global function definition for ‘lines’
plotCophenetic: no visible global function definition for ‘points’
plotCophenetic: no visible global function definition for ‘segments’
plotCophenetic: no visible binding for global variable ‘cophenetic’
plotCophenetic: no visible global function definition for ‘title’
plotEnrichmentResults: no visible binding for global variable ‘P_value’
plotEnrichmentResults: no visible binding for global variable ‘OR’
plotEnrichmentResults: no visible binding for global variable ‘Group1’
plotEnrichmentResults : <anonymous>: no visible binding for global
  variable ‘g1_muts’
plotEnrichmentResults : <anonymous>: no visible binding for global
  variable ‘g1_tot’
plotEnrichmentResults : <anonymous>: no visible binding for global
  variable ‘g2_muts’
plotEnrichmentResults : <anonymous>: no visible binding for global
  variable ‘g2_tot’
plotEnrichmentResults: no visible binding for global variable
  ‘g1_title’
plotEnrichmentResults: no visible binding for global variable ‘g1_muts’
plotEnrichmentResults: no visible binding for global variable ‘g1_tot’
plotEnrichmentResults: no visible binding for global variable
  ‘g2_title’
plotEnrichmentResults: no visible binding for global variable ‘g2_muts’
plotEnrichmentResults: no visible binding for global variable ‘g2_tot’
plotEnrichmentResults : add_legend: no visible global function
  definition for ‘par’
plotEnrichmentResults : add_legend: no visible global function
  definition for ‘legend’
plotEnrichmentResults: no visible global function definition for ‘par’
plotEnrichmentResults: no visible global function definition for
  ‘barplot’
plotEnrichmentResults: no visible global function definition for ‘axis’
plotEnrichmentResults: no visible global function definition for
  ‘segments’
plotEnrichmentResults: no visible global function definition for ‘text’
plotEnrichmentResults: no visible global function definition for
  ‘legend’
plotEnrichmentResults: no visible global function definition for
  ‘title’
plotmafSummary: no visible binding for global variable ‘statFontSize’
plotmafSummary: no visible global function definition for ‘par’
plotmafSummary: no visible global function definition for ‘barplot’
plotmafSummary: no visible global function definition for ‘axis’
plotmafSummary: no visible global function definition for ‘title’
plotmafSummary: no visible binding for global variable ‘Mean’
plotmafSummary: no visible binding for global variable ‘Median’
plotmafSummary: no visible global function definition for ‘lines’
plotmafSummary: no visible binding for global variable ‘N’
plotmafSummary: no visible global function definition for ‘.’
plotmafSummary: no visible binding for global variable
  ‘Variant_Classification’
plotmafSummary: no visible global function definition for ‘boxplot’
plotmafSummary: no visible binding for global variable ‘boxStat’
plotmafSummary: no visible global function definition for ‘plot.new’
plotmafSummary: no visible global function definition for ‘legend’
plotMosdepth : <anonymous>: no visible binding for global variable
  ‘chr’
plotMosdepth : <anonymous>: no visible binding for global variable
  ‘Chromosome’
plotMosdepth: no visible binding for global variable ‘Chromosome’
plotMosdepth: no visible binding for global variable ‘Start_Position’
plotMosdepth: no visible binding for global variable ‘End_Position’
plotMosdepth: no visible global function definition for ‘.’
plotMosdepth: no visible binding for global variable ‘logR’
plotMosdepth: no visible binding for global variable ‘doc_t’
plotMosdepth: no visible binding for global variable ‘doc_n’
plotMosdepth: no visible global function definition for ‘par’
plotMosdepth : <anonymous>: no visible global function definition for
  ‘points’
plotMosdepth : <anonymous>: no visible global function definition for
  ‘rect’
plotMosdepth: no visible global function definition for ‘abline’
plotMosdepth: no visible global function definition for ‘axis’
plotMosdepth: no visible global function definition for ‘mtext’
plotMosdepth: no visible global function definition for ‘title’
plotMosdepth_t: no visible binding for global variable ‘chr’
plotMosdepth_t: no visible binding for global variable ‘start’
plotMosdepth_t: no visible global function definition for ‘median’
plotMosdepth_t: no visible binding for global variable ‘doc’
plotMosdepth_t: no visible binding for global variable ‘End_Position’
plotMosdepth_t: no visible global function definition for ‘.’
plotMosdepth_t: no visible binding for global variable ‘Chromosome’
plotMosdepth_t: no visible binding for global variable ‘doc_norm’
plotMosdepth_t: no visible binding for global variable ‘Start_Position’
plotMosdepth_t: no visible global function definition for ‘par’
plotMosdepth_t : <anonymous>: no visible global function definition for
  ‘points’
plotMosdepth_t : <anonymous>: no visible global function definition for
  ‘rect’
plotMosdepth_t : <anonymous>: no visible binding for global variable
  ‘Start_Position_updated’
plotMosdepth_t : <anonymous>: no visible binding for global variable
  ‘End_Position_updated’
plotMosdepth_t: no visible global function definition for ‘abline’
plotMosdepth_t: no visible global function definition for ‘axis’
plotMosdepth_t: no visible global function definition for ‘title’
plotOncodrive: no visible binding for global variable ‘log_fdr’
plotOncodrive: no visible binding for global variable ‘fdr’
plotOncodrive: no visible global function definition for ‘par’
plotOncodrive: no visible binding for global variable ‘significant’
plotOncodrive: no visible global function definition for ‘mtext’
plotPathways: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
plotPathways: no visible global function definition for ‘par’
plotPathways: no visible global function definition for ‘image’
plotPathways: no visible global function definition for ‘abline’
plotPathways: no visible global function definition for ‘mtext’
plotPathways: no visible global function definition for ‘text’
plotProtein: no visible binding for global variable ‘HGNC’
plotProtein: no visible binding for global variable ‘refseq.ID’
plotProtein: no visible binding for global variable ‘protein.ID’
plotProtein: no visible global function definition for ‘.’
plotProtein: no visible binding for global variable ‘aa.length’
plotProtein: no visible binding for global variable ‘domain_lenght’
plotProtein: no visible binding for global variable ‘End’
plotProtein: no visible binding for global variable ‘Start’
plotProtein: no visible binding for global variable ‘Label’
plotProtein: no visible global function definition for ‘par’
plotProtein: no visible global function definition for ‘rect’
plotProtein: no visible binding for global variable ‘domainCol’
plotProtein: no visible global function definition for ‘text’
plotProtein: no visible global function definition for ‘title’
plotProtein: no visible global function definition for ‘legend’
plotSignatures: no visible global function definition for ‘par’
plotSignatures: no visible global function definition for ‘barplot’
plotSignatures: no visible global function definition for ‘axis’
plotSignatures: no visible global function definition for ‘mtext’
plotSignatures: no visible global function definition for ‘plot.new’
plotSignatures: no visible global function definition for ‘legend’
plotSignatures: no visible global function definition for ‘title’
plotSignatures: no visible global function definition for ‘rect’
plotSignatures: no visible global function definition for ‘text’
plotTiTv: no visible binding for global variable ‘value’
plotTiTv: no visible global function definition for ‘.’
plotTiTv: no visible binding for global variable ‘variable’
plotTiTv: no visible binding for global variable ‘V1’
plotTiTv: no visible global function definition for ‘par’
plotTiTv: no visible global function definition for ‘barplot’
plotTiTv: no visible global function definition for ‘axis’
plotTiTv: no visible global function definition for ‘mtext’
plotTiTv: no visible global function definition for ‘boxplot’
plotTiTv: no visible global function definition for ‘abline’
plotVaf: no visible binding for global variable ‘Hugo_Symbol’
plotVaf: no visible binding for global variable ‘t_vaf’
plotVaf: no visible binding for global variable ‘t_alt_count’
plotVaf: no visible binding for global variable ‘t_ref_count’
plotVaf: no visible global function definition for ‘.’
plotVaf: no visible binding for global variable ‘value’
plotVaf: no visible global function definition for ‘median’
plotVaf: no visible binding for global variable ‘V1’
plotVaf: no visible global function definition for ‘par’
plotVaf: no visible global function definition for ‘boxplot’
plotVaf: no visible global function definition for ‘axis’
plotVaf: no visible global function definition for ‘abline’
plotVaf: no visible global function definition for ‘stripchart’
prepareMutSig: no visible binding for global variable
  ‘Variant_Classification’
prepareMutSig: no visible binding for global variable ‘OG_Hugo_Symbol’
prepareMutSig: no visible binding for global variable ‘Hugo_Symbol’
prepareMutSig: no visible global function definition for ‘.’
prepareMutSig: no visible binding for global variable ‘MutSig_Synonym’
prepareMutSig: no visible binding for global variable ‘N’
prepareMutSig: no visible global function definition for ‘write.table’
prepAscat : <anonymous>: no visible binding for global variable ‘loci’
prepAscat : <anonymous>: no visible binding for global variable
  ‘tot_depth’
prepAscat : <anonymous>: no visible global function definition for ‘.’
prepAscat : <anonymous>: no visible binding for global variable ‘A’
prepAscat : <anonymous>: no visible binding for global variable ‘G’
prepAscat : <anonymous>: no visible binding for global variable ‘C’
prepAscat : <anonymous>: no visible binding for global variable ‘baf’
prepAscat : <anonymous>: no visible global function definition for
  ‘runif’
prepAscat_t : <anonymous>: no visible binding for global variable
  ‘loci’
prepAscat_t : <anonymous>: no visible binding for global variable
  ‘tot_depth’
prepAscat_t : <anonymous>: no visible global function definition for
  ‘.’
prepAscat_t : <anonymous>: no visible binding for global variable ‘A’
prepAscat_t : <anonymous>: no visible binding for global variable ‘G’
prepAscat_t : <anonymous>: no visible binding for global variable ‘C’
prepAscat_t : <anonymous>: no visible binding for global variable ‘baf’
prepAscat_t : <anonymous>: no visible global function definition for
  ‘runif’
prepAscat_t: no visible global function definition for ‘median’
print_mat: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
print_mat: no visible global function definition for ‘par’
print_mat: no visible global function definition for ‘image’
print_mat: no visible global function definition for ‘rect’
print_mat : <anonymous>: no visible binding for global variable
  ‘temp_af’
print_mat : <anonymous> : <anonymous> : <anonymous>: no visible global
  function definition for ‘points’
print_mat: no visible global function definition for ‘abline’
print_mat: no visible global function definition for ‘mtext’
rainfallPlot: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
rainfallPlot: no visible global function definition for ‘.’
rainfallPlot: no visible binding for global variable ‘Chromosome’
rainfallPlot: no visible binding for global variable ‘Hugo_Symbol’
rainfallPlot: no visible binding for global variable ‘Start_Position’
rainfallPlot: no visible binding for global variable ‘End_Position’
rainfallPlot: no visible binding for global variable ‘Reference_Allele’
rainfallPlot: no visible binding for global variable
  ‘Tumor_Seq_Allele2’
rainfallPlot: no visible binding for global variable ‘Variant_Type’
rainfallPlot: no visible global function definition for
  ‘complete.cases’
rainfallPlot: no visible global function definition for ‘par’
rainfallPlot: no visible global function definition for ‘segments’
rainfallPlot: no visible global function definition for ‘points’
rainfallPlot: no visible global function definition for ‘axis’
rainfallPlot: no visible global function definition for ‘mtext’
rainfallPlot: no visible global function definition for ‘arrows’
rainfallPlot: no visible global function definition for ‘title’
rainfallPlot: no visible global function definition for ‘legend’
rainfallPlot: no visible global function definition for ‘dev.copy’
read.maf: no visible binding for global variable ‘Mutation_Status’
read.maf: no visible binding for global variable ‘Hugo_Symbol’
read.maf: no visible binding for global variable
  ‘Variant_Classification’
read.maf: no visible global function definition for ‘.’
read.maf: no visible binding for global variable ‘Tumor_Sample_Barcode’
read.maf: no visible binding for global variable ‘Unique_Name’
read.maf: no visible binding for global variable ‘Wide_Peak_Limits’
read.maf: no visible binding for global variable ‘id’
readGistic: no visible binding for global variable ‘Unique_Name’
readGistic: no visible binding for global variable ‘Wide_Peak_Limits’
readGistic: no visible binding for global variable ‘cytoband’
readGistic: no visible binding for global variable ‘value’
readGistic: no visible global function definition for ‘.’
readGistic: no visible binding for global variable ‘variable’
readGistic : <anonymous>: no visible binding for global variable
  ‘variable’
readGistic : <anonymous>: no visible binding for global variable
  ‘cytoband’
readGistic : <anonymous>: no visible binding for global variable
  ‘TumorSampleBarcode’
readGistic: no visible binding for global variable ‘CN’
readGistic: no visible binding for global variable ‘TumorSampleBarcode’
readGistic: no visible binding for global variable ‘Variant_Type’
readGistic: no visible binding for global variable ‘Cytoband’
readGistic: no visible binding for global variable ‘peakID’
readGistic: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
readGistic: no visible binding for global variable ‘qvalues’
readSegs: no visible binding for global variable ‘Chromosome’
readSegs: no visible binding for global variable ‘Start_Position’
readSegs: no visible binding for global variable ‘End_Position’
refineClusters: no visible binding for global variable ‘t_vaf’
repelPoints: no visible binding for global variable ‘pos’
repelPoints: no visible binding for global variable ‘distance’
repelPoints: no visible global function definition for ‘.’
run_surv: no visible binding for global variable ‘Group’
run_surv: no visible global function definition for ‘pchisq’
run_surv: no visible global function definition for ‘par’
run_surv: no visible global function definition for ‘abline’
run_surv: no visible global function definition for ‘points’
run_surv: no visible binding for global variable ‘Time’
run_surv: no visible binding for global variable ‘survProb’
run_surv: no visible global function definition for ‘lines’
run_surv: no visible global function definition for ‘axis’
run_surv: no visible global function definition for ‘mtext’
run_surv: no visible global function definition for ‘legend’
run_surv: no visible global function definition for ‘title’
sampleSwaps: no visible binding for global variable ‘id’
sampleSwaps: no visible binding for global variable ‘chr’
sampleSwaps: no visible binding for global variable ‘start’
sampleSwaps : <anonymous>: no visible global function definition for
  ‘.’
sampleSwaps : <anonymous>: no visible binding for global variable ‘id’
sampleSwaps : <anonymous>: no visible binding for global variable ‘ref’
sampleSwaps : <anonymous>: no visible binding for global variable ‘alt’
sampleSwaps : <anonymous> : <anonymous>: no visible binding for global
  variable ‘vaf’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘loci’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘ref_rc’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘alt_rc’
sampleSwaps : <anonymous>: no visible binding for global variable ‘vaf’
sampleSwaps: no visible binding for global variable ‘vaf’
sampleSwaps: no visible binding for global variable ‘total’
sampleSwaps: no visible binding for global variable ‘ref_rc’
sampleSwaps: no visible binding for global variable ‘alt_rc’
sampleSwaps: no visible global function definition for ‘complete.cases’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘fisher.test’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable ‘ref_rc’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable ‘alt_rc’
sampleSwaps : <anonymous> : <anonymous>: no visible global function
  definition for ‘cor.test’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘XY_possibly_paired’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘fract_concordant_snps’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘cor_coef’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘X_bam’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘Y_bam’
sampleSwaps: no visible binding for global variable
  ‘XY_possibly_paired’
segmentLogR: no visible binding for global variable ‘contig’
segmentLogR: no visible binding for global variable ‘logR’
segmentLogR: no visible binding for global variable ‘pos’
segmentLogR: no visible global function definition for ‘write.table’
segmentLogR: no visible global function definition for ‘png’
setdiffMAF: no visible binding for global variable ‘Chromosome’
setdiffMAF: no visible binding for global variable ‘Start_Position’
setdiffMAF: no visible binding for global variable ‘End_Position’
setdiffMAF: no visible global function definition for ‘.’
setdiffMAF: no visible binding for global variable ‘Reference_Allele’
setdiffMAF: no visible binding for global variable ‘Tumor_Seq_Allele2’
setdiffMAF: no visible binding for global variable ‘variant_ID’
setdiffMAF: no visible binding for global variable ‘maf_slot’
shiftPoints: no visible binding for global variable ‘pos’
signatureEnrichment: no visible global function definition for ‘kmeans’
signatureEnrichment: no visible binding for global variable ‘Cluster’
signatureEnrichment: no visible binding for global variable ‘Signature’
signatureEnrichment : <anonymous>: no visible binding for global
  variable ‘Signature’
signatureEnrichment : <anonymous>: no visible binding for global
  variable ‘Tumor_Sample_Barcode’
signatureEnrichment : <anonymous>: no visible binding for global
  variable ‘sd’
signatureEnrichment : <anonymous>: no visible binding for global
  variable ‘N’
signatureEnrichment : add_legend: no visible global function definition
  for ‘par’
signatureEnrichment : add_legend: no visible global function definition
  for ‘legend’
signatureEnrichment: no visible global function definition for ‘par’
signatureEnrichment: no visible global function definition for
  ‘barplot’
signatureEnrichment: no visible global function definition for
  ‘segments’
signatureEnrichment: no visible global function definition for ‘axis’
signatureEnrichment: no visible global function definition for ‘mtext’
signatureEnrichment: no visible global function definition for ‘title’
signatureEnrichment: no visible global function definition for
  ‘boxplot’
signatureEnrichment: no visible global function definition for ‘.’
signatureEnrichment: no visible global function definition for ‘median’
signatureEnrichment: no visible binding for global variable ‘N’
signatureEnrichment: no visible global function definition for
  ‘write.table’
somaticInteractions: no visible binding for global variable
  ‘Hugo_Symbol’
somaticInteractions: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
somaticInteractions : <anonymous> : <anonymous>: no visible global
  function definition for ‘fisher.test’
somaticInteractions: no visible binding for global variable ‘pAdj’
somaticInteractions: no visible global function definition for
  ‘p.adjust’
somaticInteractions: no visible binding for global variable ‘pValue’
somaticInteractions: no visible global function definition for ‘.’
somaticInteractions: no visible binding for global variable ‘gene1’
somaticInteractions: no visible binding for global variable ‘gene2’
somaticInteractions: no visible binding for global variable
  ‘event_ratio’
somaticInteractions: no visible binding for global variable ‘01’
somaticInteractions: no visible binding for global variable ‘10’
somaticInteractions: no visible binding for global variable ‘11’
somaticInteractions: no visible binding for global variable ‘pair’
somaticInteractions: no visible binding for global variable
  ‘AlteredSamples’
somaticInteractions: no visible global function definition for ‘par’
somaticInteractions: no visible global function definition for ‘image’
somaticInteractions: no visible global function definition for ‘abline’
somaticInteractions: no visible global function definition for ‘mtext’
somaticInteractions: no visible binding for global variable ‘Event’
somaticInteractions: no visible global function definition for ‘text’
somaticInteractions: no visible global function definition for ‘points’
somaticInteractions: no visible global function definition for ‘axis’
sortByMutation: no visible binding for global variable ‘MutatedSamples’
sortByMutation: no visible binding for global variable ‘Hugo_Symbol’
subsetMaf: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
subsetMaf: no visible binding for global variable ‘Variant_Type’
subsetMaf: no visible binding for global variable ‘Hugo_Symbol’
subsetMaf: no visible binding for global variable ‘Chromosome’
subsetMaf: no visible binding for global variable ‘Start_Position’
subsetMaf: no visible binding for global variable ‘End_Position’
summarizeGistic: no visible binding for global variable ‘Hugo_Symbol’
summarizeGistic: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
summarizeGistic: no visible global function definition for ‘.’
summarizeGistic: no visible binding for global variable
  ‘Variant_Classification’
summarizeGistic: no visible binding for global variable ‘total’
summarizeGistic: no visible binding for global variable ‘median’
summarizeGistic: no visible binding for global variable ‘Cytoband’
summarizeMaf: no visible binding for global variable ‘Variant_Type’
summarizeMaf: no visible binding for global variable ‘Hugo_Symbol’
summarizeMaf: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
summarizeMaf: no visible global function definition for ‘.’
summarizeMaf: no visible binding for global variable
  ‘Variant_Classification’
summarizeMaf: no visible binding for global variable ‘total’
summarizeMaf: no visible binding for global variable ‘CNV_total’
summarizeMaf: no visible binding for global variable ‘median’
summarizeMaf: no visible binding for global variable ‘CNV’
summarizeMaf: no visible binding for global variable ‘MutatedSamples’
summarizeMaf: no visible binding for global variable ‘Mean’
summarizeMaf: no visible binding for global variable ‘Median’
survGroup: no visible binding for global variable ‘Hugo_Symbol’
survGroup: no visible global function definition for ‘combn’
survGroup: no visible binding for global variable ‘Time’
survGroup: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
survGroup: no visible binding for global variable ‘P_value’
tcgaCompare: no visible global function definition for ‘.’
tcgaCompare: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
tcgaCompare: no visible binding for global variable ‘total’
tcgaCompare: no visible binding for global variable ‘site’
tcgaCompare: no visible binding for global variable ‘cohort’
tcgaCompare : <anonymous>: no visible global function definition for
  ‘.’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘total’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘cohort’
tcgaCompare: no visible global function definition for
  ‘pairwise.t.test’
tcgaCompare: no visible binding for global variable ‘plot_total’
tcgaCompare: no visible binding for global variable ‘total_perMB’
tcgaCompare: no visible global function definition for ‘median’
tcgaCompare: no visible binding for global variable ‘V2’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘plot_total’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘TCGA’
tcgaCompare: no visible global function definition for ‘rect’
tcgaCompare: no visible global function definition for ‘par’
tcgaCompare: no visible global function definition for ‘abline’
tcgaCompare : <anonymous>: no visible binding for global variable ‘V3’
tcgaCompare : <anonymous>: no visible global function definition for
  ‘points’
tcgaCompare: no visible global function definition for ‘axis’
tcgaCompare: no visible binding for global variable
  ‘Median_Mutations_log10’
tcgaCompare: no visible binding for global variable ‘Median_Mutations’
tcgaCompare: no visible global function definition for ‘mtext’
tcgaCompare : <anonymous>: no visible global function definition for
  ‘segments’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘Median_Mutations_log10’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘Median_Mutations’
tcgaCompare: no visible binding for global variable ‘TCGA’
tcgaCompare: no visible binding for global variable ‘Pval’
tcgaDriverBP: no visible binding for global variable ‘Hugo_Symbol’
tcgaDriverBP: no visible global function definition for ‘.’
tcgaDriverBP: no visible binding for global variable ‘AlteredSamples’
tcgaDriverBP: no visible global function definition for ‘par’
tcgaDriverBP: no visible global function definition for ‘image’
tcgaDriverBP: no visible global function definition for ‘abline’
tcgaDriverBP: no visible global function definition for ‘points’
tcgaDriverBP: no visible global function definition for ‘mtext’
tcgaDriverBP: no visible global function definition for ‘text’
tcgaDriverBP: no visible global function definition for ‘title’
tcgaDriverBP : <anonymous>: no visible binding for global variable
  ‘Gene’
tcgaDriverBP: no visible binding for global variable ‘Cancer_type’
tcgaDriverBP: no visible binding for global variable ‘Pathway’
tcgaDriverBP: no visible binding for global variable ‘ID’
tcgaDriverBP: no visible binding for global variable ‘pctAltered’
tcgaDriverBP: no visible binding for global variable ‘tcga_driver’
titv: no visible binding for global variable ‘Reference_Allele’
titv: no visible binding for global variable ‘Tumor_Seq_Allele2’
titv: no visible binding for global variable ‘con’
titv: no visible global function definition for ‘.’
titv: no visible binding for global variable ‘Tumor_Sample_Barcode’
titv: no visible binding for global variable ‘N’
titv: no visible binding for global variable ‘con.class’
titv: no visible binding for global variable ‘fract’
titv: no visible binding for global variable ‘nVars’
titv: no visible binding for global variable ‘TiTv’
titv: no visible global function definition for ‘write.table’
tmb: no visible global function definition for ‘.’
tmb: no visible binding for global variable ‘Tumor_Sample_Barcode’
tmb: no visible binding for global variable ‘total’
tmb: no visible binding for global variable ‘total_perMB’
tmb: no visible binding for global variable ‘total_perMB_log’
tmb: no visible global function definition for ‘median’
tmb: no visible global function definition for ‘par’
tmb: no visible global function definition for ‘abline’
tmb: no visible global function definition for ‘points’
tmb: no visible global function definition for ‘title’
tmb: no visible global function definition for ‘axis’
tmb: no visible global function definition for ‘mtext’
transformSegments: no visible binding for global variable
  ‘Start_Position’
transformSegments: no visible binding for global variable
  ‘End_Position’
transformSegments: no visible binding for global variable ‘Chromosome’
trinucleotideMatrix: no visible binding for global variable ‘pkgname’
trinucleotideMatrix: no visible binding for global variable
  ‘Chromosome’
trinucleotideMatrix: no visible binding for global variable
  ‘Start_Position’
trinucleotideMatrix: no visible binding for global variable
  ‘End_Position’
trinucleotideMatrix: no visible binding for global variable ‘N’
trinucleotideMatrix: no visible binding for global variable ‘Start’
trinucleotideMatrix: no visible binding for global variable ‘End’
trinucleotideMatrix: no visible binding for global variable ‘upstream’
trinucleotideMatrix: no visible binding for global variable
  ‘downstream’
trinucleotideMatrix: no visible global function definition for ‘.’
trinucleotideMatrix: no visible binding for global variable ‘A’
trinucleotideMatrix: no visible binding for global variable ‘C’
trinucleotideMatrix: no visible binding for global variable ‘G’
trinucleotideMatrix: no visible binding for global variable
  ‘trinucleotide’
trinucleotideMatrix: no visible binding for global variable ‘updown’
trinucleotideMatrix: no visible binding for global variable ‘TCA’
trinucleotideMatrix: no visible binding for global variable ‘TCT’
trinucleotideMatrix: no visible binding for global variable ‘AGA’
trinucleotideMatrix: no visible binding for global variable ‘TGA’
trinucleotideMatrix: no visible binding for global variable ‘tcw’
trinucleotideMatrix: no visible binding for global variable ‘wga’
trinucleotideMatrix: no visible binding for global variable
  ‘Substitution’
trinucleotideMatrix: no visible binding for global variable
  ‘SubstitutionType’
trinucleotideMatrix: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
trinucleotideMatrix: no visible binding for global variable ‘n_A’
trinucleotideMatrix: no visible binding for global variable ‘A>C’
trinucleotideMatrix: no visible binding for global variable ‘A>G’
trinucleotideMatrix: no visible binding for global variable ‘A>T’
trinucleotideMatrix: no visible binding for global variable ‘n_T’
trinucleotideMatrix: no visible binding for global variable ‘T>A’
trinucleotideMatrix: no visible binding for global variable ‘T>C’
trinucleotideMatrix: no visible binding for global variable ‘T>G’
trinucleotideMatrix: no visible binding for global variable ‘n_G’
trinucleotideMatrix: no visible binding for global variable ‘G>A’
trinucleotideMatrix: no visible binding for global variable ‘G>C’
trinucleotideMatrix: no visible binding for global variable ‘G>T’
trinucleotideMatrix: no visible binding for global variable ‘n_C’
trinucleotideMatrix: no visible binding for global variable ‘C>A’
trinucleotideMatrix: no visible binding for global variable ‘C>G’
trinucleotideMatrix: no visible binding for global variable ‘C>T’
trinucleotideMatrix: no visible binding for global variable
  ‘n_mutations’
trinucleotideMatrix: no visible binding for global variable
  ‘SubstitutionMotif’
trinucleotideMatrix: no visible binding for global variable ‘tCw_to_A’
trinucleotideMatrix: no visible binding for global variable ‘T[C>A]A’
trinucleotideMatrix: no visible binding for global variable ‘T[C>A]T’
trinucleotideMatrix: no visible binding for global variable ‘tCw_to_G’
trinucleotideMatrix: no visible binding for global variable ‘T[C>G]A’
trinucleotideMatrix: no visible binding for global variable ‘T[C>G]T’
trinucleotideMatrix: no visible binding for global variable ‘tCw_to_T’
trinucleotideMatrix: no visible binding for global variable ‘T[C>T]A’
trinucleotideMatrix: no visible binding for global variable ‘T[C>T]T’
trinucleotideMatrix: no visible binding for global variable ‘tCw’
trinucleotideMatrix: no visible binding for global variable ‘wGa_to_C’
trinucleotideMatrix: no visible binding for global variable ‘A[G>C]A’
trinucleotideMatrix: no visible binding for global variable ‘T[G>C]A’
trinucleotideMatrix: no visible binding for global variable ‘wGa_to_T’
trinucleotideMatrix: no visible binding for global variable ‘A[G>T]A’
trinucleotideMatrix: no visible binding for global variable ‘T[G>T]A’
trinucleotideMatrix: no visible binding for global variable ‘wGa_to_A’
trinucleotideMatrix: no visible binding for global variable ‘A[G>A]A’
trinucleotideMatrix: no visible binding for global variable ‘T[G>A]A’
trinucleotideMatrix: no visible binding for global variable ‘wGa’
trinucleotideMatrix: no visible binding for global variable
  ‘tCw_to_G+tCw_to_T’
trinucleotideMatrix: no visible binding for global variable
  ‘APOBEC_Enrichment’
trinucleotideMatrix: no visible binding for global variable
  ‘n_C>G_and_C>T’
trinucleotideMatrix: no visible binding for global variable
  ‘non_APOBEC_mutations’
trinucleotideMatrix: no visible binding for global variable
  ‘fraction_APOBEC_mutations’
trinucleotideMatrix : <anonymous>: no visible global function
  definition for ‘fisher.test’
trinucleotideMatrix: no visible binding for global variable
  ‘fisher_pvalue’
trinucleotideMatrix: no visible binding for global variable ‘fdr’
trinucleotideMatrix: no visible global function definition for
  ‘p.adjust’
trinucleotideMatrix: no visible binding for global variable
  ‘APOBEC_Enriched’
trinucleotideMatrix: no visible binding for global variable
  ‘SubstitutionTypeMotif’
trinucleotideMatrix: no visible global function definition for
  ‘write.table’
vafCompare: no visible binding for global variable ‘Hugo_Symbol’
vafCompare: no visible binding for global variable ‘t_vaf’
vafCompare: no visible binding for global variable ‘t_alt_count’
vafCompare: no visible binding for global variable ‘t_ref_count’
vafCompare: no visible global function definition for ‘.’
vafCompare: no visible binding for global variable ‘Cohort’
vafCompare: no visible global function definition for ‘layout’
vafCompare: no visible global function definition for ‘par’
vafCompare: no visible global function definition for ‘boxplot’
vafCompare: no visible global function definition for ‘stripchart’
vafCompare: no visible global function definition for ‘axis’
vafCompare: no visible global function definition for ‘title’
vafCompare: no visible global function definition for ‘abline’
vafCompare: no visible global function definition for ‘t.test’
vafCompare: no visible global function definition for ‘text’
validateMaf: no visible binding for global variable ‘variantId’
validateMaf: no visible binding for global variable ‘Chromosome’
validateMaf: no visible binding for global variable ‘Start_Position’
validateMaf: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
validateMaf: no visible binding for global variable ‘Reference_Allele’
validateMaf: no visible binding for global variable ‘Tumor_Seq_Allele2’
validateMaf: no visible binding for global variable ‘Hugo_Symbol’
validateMaf: no visible binding for global variable
  ‘Variant_Classification’
validateMaf: no visible binding for global variable ‘Variant_Type’
validateMaf: no visible binding for global variable ‘End_Position’
write.GisticSummary: no visible global function definition for
  ‘write.table’
write.mafSummary: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  . 01 10 11 A A[G>A]A A[G>C]A A[G>T]A A>C A>G A>T aa.length AAChange
  AAChange_ AAChange.refGene abline adjPval AGA alt Alt alt_rc
  AlteredSamples amp Amp Analysis anno_Position APOBEC_Enriched
  APOBEC_Enrichment arrows assembly_version axis baf barplot bg box
  boxplot boxStat browseURL C C>A C>G C>T Cancer_type category cf chr
  chromosome Chromosome chromosome_end chromosome_start ci.low ci.up
  Cluster CN CNV CNV_total cohort Cohort colorRampPalette combn
  complete.cases con con.class consequence_type contig conv cophenetic
  cor_coef cor.test count count2 cytoband Cytoband dbinom Del density
  Description dev.copy distance doc doc_n doc_norm doc_t domain_lenght
  domainCol DomainLabel download.file downstream dp End End_Position
  End_Position_updated endDist ens_id Entrez Entrez_Gene_Id Event
  event_ratio ExonicFunc.refGene fdr Feature_1 Feature_2 fisher_pvalue
  fisher.test fract fract_concordant_snps fract_muts_in_clusters
  fraction fraction_affected fraction_APOBEC_mutations
  Fraction_mutated_samples fractMutated Freq fs Func.refGene G G_Score
  G>A G>C G>T g1_muts g1_title g1_tot g2_muts g2_title g2_tot Gene
  gene_affected Gene.refGene gene1 gene2 Genotype gistic glm Group
  Group1 Group2 head heat.colors HGNC hgnc_symbol Hugo_Symbol
  i.End_Position i.Start_Position icgc_sample_id id ID idx image Ins
  kmeans lab label Label labThis layout legend lines loc loci log_fdr
  log_q logR lower maf_slot MATH max_alt Mean median Median
  Median_Mutations Median_Mutations_log10 mtext mutated_from_allele
  Mutated_samples mutated_to_allele MutatedSamples MutatedSamples_m1
  MutatedSamples_m2 Mutation_Status mutload muts_in_clusters
  MutSig_Synonym n N n_A n_affected_genes n_C n_C>G_and_C>T n_G
  n_mutated_Feature n_mutated_Feature1 n_mutated_Feature2
  n_mutated_group1 n_mutated_group2 n_mutations n_T N.x N.y na.omit
  nGenes nMut nMuts non_APOBEC_mutations nonApobec nVars OG_Hugo_Symbol
  or OR OR_high OR_low or_new p_value P_value p.adjust pAdj pair
  pairwise.t.test pairwise.table par Pathway pchisq pct_alt pctAltered
  peakID pfam pie pkgname plot_total plot.new png pnorm points poisson
  poisson.test poissonFdr pos pos2 posRounded protein.ID pval Pval
  pValue qf qnorm qvalues read.csv rect ref Ref ref_alt ref_alt_diff
  ref_alt_len ref_rc Reference_Allele reference_genome_allele refseq.ID
  row_id row_idx rug runif Sample SampleSize sd Segment_End
  Segment_Mean Segment_Start segments sequencing_strategy
  setTxtProgressBar Signature significant site Size start Start
  Start_Position Start_Position_updated startDist statFontSize
  stripchart Substitution SubstitutionMotif SubstitutionType
  SubstitutionTypeMotif survProb symbols t_alt_count t_depth
  t_ref_count t_vaf t.test T[C>A]A T[C>A]T T[C>G]A T[C>G]T T[C>T]A
  T[C>T]T T[G>A]A T[G>C]A T[G>T]A T>A T>C T>G TCA TCGA tcga_driver TCT
  tcw tCw tCw_to_A tCw_to_G tCw_to_G+tCw_to_T tCw_to_T temp_af text
  tFdr TGA th Time title TiTv tot tot_depth total total_perMB
  total_perMB_log trinucleotide Tumor_Sample_Barcode Tumor_Seq_Allele2
  TumorSampleBarcode txtProgressBar Unique_Name unit updown upper
  upstream V1 V2 V3 vaf VAF value Var1 Var2 variable
  Variant_Classification Variant_Classification_temp variant_ID
  Variant_Type variantId VC verification_platform verification_status
  wga wGa wGa_to_A wGa_to_C wGa_to_T Wide_Peak_Limits wilcox.test
  write.table X_bam XY_possibly_paired Y_bam ystart
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
             "boxplot", "image", "layout", "legend", "lines", "mtext",
             "par", "pie", "plot.new", "points", "rect", "rug",
             "segments", "stripchart", "symbols", "text", "title")
  importFrom("grDevices", "colorRampPalette", "dev.copy", "heat.colors",
             "png")
  importFrom("stats", "C", "complete.cases", "cophenetic", "cor.test",
             "dbinom", "density", "fisher.test", "glm", "kmeans",
             "median", "na.omit", "p.adjust", "pairwise.t.test",
             "pairwise.table", "pchisq", "pnorm", "poisson",
             "poisson.test", "qf", "qnorm", "runif", "sd", "start",
             "t.test", "wilcox.test")
  importFrom("utils", "browseURL", "combn", "download.file", "head",
             "read.csv", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/maftools/libs/maftools.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/maftools.Rcheck/00check.log’
for details.
name	user	system	elapsed
MAF	0.070	0.010	0.081
annovarToMaf	0.051	0.004	0.055
clinicalEnrichment	0	0	0
coBarplot	0.097	0.007	0.104
coGisticChromPlot	0	0	0
coOncoplot	0.093	0.006	0.099
drugInteractions	0.136	0.015	0.152
estimateSignatures	0	0	0
extractSignatures	0	0	0
filterMaf	0.262	0.017	0.279
forestPlot	0.067	0.004	0.071
genesToBarcodes	0.104	0.008	0.113
genotypeMatrix	0.097	0.009	0.106
getClinicalData	0.093	0.006	0.100
getCytobandSummary	0.161	0.010	0.173
getFields	0.106	0.009	0.115
getGeneSummary	0.099	0.006	0.106
getSampleSummary	0.100	0.007	0.106
gisticBubblePlot	0.248	0.007	0.256
gisticChromPlot	0.184	0.009	0.193
gisticOncoPlot	0.164	0.009	0.174
icgcSimpleMutationToMAF	0.022	0.002	0.025
inferHeterogeneity	0	0	0
lollipopPlot	0.296	0.011	0.308
lollipopPlot2	0.454	0.010	0.464
maf2mae	4.342	0.098	4.441
mafCompare	0.060	0.005	0.065
mafSummary	0.171	0.011	0.182
mafSurvGroup	0.124	0.013	0.136
mafSurvival	0.101	0.006	0.107
mafbarplot	0.085	0.004	0.089
math.score	0.091	0.004	0.095
mutCountMatrix	0.162	0.182	0.354
oncodrive	0.642	0.021	0.665
oncoplot	0.154	0.006	0.161
oncostrip	0.108	0.009	0.117
pathways	0.161	0.007	0.167
pfamDomains	0.335	0.012	0.347
plotApobecDiff	0	0	0
plotCBSsegments	0.010	0.001	0.011
plotClusters	0	0	0
plotOncodrive	0.321	0.021	0.343
plotPathways	0.413	0.012	0.424
plotProtein	0.336	0.006	0.342
plotTiTv	0.120	0.007	0.127
plotVaf	0.107	0.009	0.117
plotmafSummary	0.113	0.006	0.120
prepareMutSig	0.125	0.010	0.135
read.maf	0.093	0.005	0.098
readGistic	0.166	0.008	0.172
setMaf	0.127	0.006	0.133
somaticInteractions	0.137	0.006	0.143
subsetMaf	0.178	0.010	0.188
survGroup	0.181	0.009	0.190
tcgaAvailable	0.008	0.003	0.245
tcgaCompare	0.191	0.014	0.206
tcgaLoad	0.067	0.008	0.851
titv	0.180	0.009	0.189
tmb	0.119	0.014	0.134
trinucleotideMatrix	0.000	0.000	0.001
write.GisticSummary	0.172	0.015	0.188
write.mafSummary	0.112	0.009	0.126
CHECK results for maftools on kjohnson3

Summary

Command output

Installation output

Tests output

Example timings
