Package: maftools

Version: 1.4.28

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings maftools_1.4.28.tar.gz

StartedAt: 2018-04-12 00:44:18 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:48:37 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 259.5 seconds

RetCode: 0

Status:  OK

CheckDir: maftools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings maftools_1.4.28.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/maftools.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maftools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maftools’ version ‘1.4.28’
* 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
* checking installed package size ... NOTE
  installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       5.5Mb
    extdata   4.5Mb
* 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
add_oncoprint: no visible binding for global variable ‘bg’
annovarToMaf: no visible binding for global variable
  ‘ExonicFunc.refGene’
annovarToMaf: no visible binding for global variable ‘uid’
annovarToMaf: no visible binding for global variable ‘ens_id’
annovarToMaf: no visible binding for global variable ‘Hugo_Symbol’
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’
annovarToMaf: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
annovarToMaf: no visible binding for global variable
  ‘Variant_Classification’
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’
coOncoplot: no visible global function definition for ‘.’
coOncoplot: no visible binding for global variable ‘Hugo_Symbol’
coOncoplot: no visible binding for global variable ‘MutatedSamples’
coOncoplot: no visible binding for global variable ‘MutatedSamples.x’
coOncoplot: no visible binding for global variable ‘MutatedSamples.y’
createOncoMatrix: no visible global function definition for ‘.’
createOncoMatrix: no visible binding for global variable ‘Hugo_Symbol’
createOncoMatrix: no visible binding for global variable
  ‘Variant_Classification’
createOncoMatrix: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
createOncoMatrix: no visible binding for global variable ‘sampleId’
dashboard: no visible binding for global variable ‘statFontSize’
dashboard: no visible binding for global variable ‘fs’
dashboard: no visible binding for global variable ‘Mean’
dashboard: no visible binding for global variable ‘Median’
dashboard: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
dashboard: no visible binding for global variable ‘N’
dashboard: no visible binding for global variable
  ‘Variant_Classification’
dashboard: no visible binding for global variable ‘x’
dashboard: no visible binding for global variable ‘y’
dashboard: no visible binding for global variable ‘label’
dashboard: no visible global function definition for ‘.’
dashboard: no visible binding for global variable ‘value’
dashboard: no visible binding for global variable ‘variable’
dashboard: no visible binding for global variable ‘Hugo_Symbol’
detectCP : <anonymous>: no visible binding for global variable
  ‘Start_Position’
detectCP : <anonymous>: no visible binding for global variable
  ‘Chromosome’
detectCP : <anonymous>: no visible binding for global variable
  ‘End_Position’
detectCP : <anonymous>: no visible binding for global variable ‘nMuts’
detectCP : <anonymous>: no visible binding for global variable
  ‘Avg_intermutation_dist’
detectCP : <anonymous>: no visible binding for global variable
  ‘i.Start_Position’
detectCP : <anonymous>: no visible binding for global variable ‘Size’
detectCP : <anonymous>: no visible global function definition for ‘.’
detectCP : <anonymous>: no visible binding for global variable
  ‘con.class’
detectCP : <anonymous>: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
detectCP: no visible binding for global variable ‘Tumor_Sample_Barcode’
dirichletClusters: no visible binding for global variable ‘dp’
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’
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 ‘log10OR’
forestPlot: no visible binding for global variable ‘or’
forestPlot: no visible global function definition for ‘.’
forestPlot: no visible binding for global variable ‘statLeft’
forestPlot: no visible binding for global variable ‘statRight’
forestPlot: no visible binding for global variable ‘Hugo_Symbol’
forestPlot: no visible binding for global variable ‘label’
forestPlot: no visible binding for global variable ‘flow’
forestPlot: no visible binding for global variable ‘ci.low’
forestPlot: no visible binding for global variable ‘ci.up’
geneCloud: no visible binding for global variable ‘Cytoband’
geneCloud: no visible binding for global variable ‘qvalues’
geneCloud: no visible binding for global variable ‘MutatedSamples’
geneCloud: no visible binding for global variable ‘Hugo_Symbol’
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’
getOncoPlot: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
getOncoPlot: no visible binding for global variable ‘ID’
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 ‘nSamples’
gisticBubblePlot: no visible binding for global variable ‘pos’
gisticBubblePlot: no visible binding for global variable ‘lab’
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
  ‘Start_Position_updated’
gisticChromPlot: no visible binding for global variable
  ‘End_Position_updated’
gisticChromPlot: no visible binding for global variable ‘ystart’
gisticChromPlot: no visible binding for global variable ‘amp’
gisticChromPlot: no visible binding for global variable ‘ysmall’
gisticChromPlot: no visible binding for global variable ‘ybig’
gisticChromPlot: no visible binding for global variable ‘labPos’
gisticMap: no visible binding for global variable ‘Cytoband’
gisticMap: no visible binding for global variable
  ‘Variant_Classification’
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 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’
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 ‘HGNC’
lollipopPlot: no visible binding for global variable ‘refseq.ID’
lollipopPlot: no visible binding for global variable ‘protein.ID’
lollipopPlot: no visible binding for global variable ‘aa.length’
lollipopPlot: no visible binding for global variable ‘Label’
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 ‘pos2’
lollipopPlot: no visible binding for global variable ‘Start’
lollipopPlot: no visible binding for global variable ‘End’
lollipopPlot: no visible binding for global variable ‘labThis’
lollipopPlot: no visible binding for global variable ‘mutations’
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: no visible global function definition for ‘.’
mafCompare: no visible binding for global variable ‘adjPval’
mafSurvival: no visible global function definition for ‘.’
mafSurvival: no visible binding for global variable ‘Time’
mafSurvival: no visible binding for global variable ‘Group’
mafSurvival: no visible binding for global variable ‘survProb’
mafSurvival: no visible binding for global variable ‘survLower’
mafSurvival: no visible binding for global variable ‘survUp’
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_vaf’
math.score: no visible binding for global variable ‘t_alt_count’
math.score: no visible binding for global variable ‘t_ref_count’
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’
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 binding for global variable ‘Hugo_Symbol’
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 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 ‘FDR’
oncoplot: no visible binding for global variable ‘gene’
oncoplot: no visible global function definition for ‘.’
oncoplot: no visible binding for global variable ‘Hugo_Symbol’
oncoplot: no visible binding for global variable ‘Tumor_Sample_Barcode’
oncoplot : anno_column_bar: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
oncostrip: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
oncostrip: no visible binding for global variable ‘Hugo_Symbol’
oncostrip : anno_pct: no visible binding for global variable ‘numMat’
oncotate: no visible binding for global variable ‘anno.df’
pancanComparison: no visible binding for global variable ‘gene’
pancanComparison: no visible global function definition for ‘.’
pancanComparison: no visible binding for global variable ‘nMut’
pancanComparison: no visible binding for global variable
  ‘SampleFraction’
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 binding for global variable ‘th’
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 binding for global variable ‘nMuts’
plotApobecDiff: no visible binding for global variable ‘n_mutations’
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 ‘variable’
plotApobecDiff: no visible binding for global variable ‘value’
plotApobecDiff: no visible binding for global variable ‘N’
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 binding for global variable
  ‘Start_Position_updated’
plotCBS: no visible binding for global variable ‘End_Position_updated’
plotCBS: no visible binding for global variable ‘Segment_Mean’
plotCBSchr: no visible binding for global variable ‘Sample’
plotCBSchr: no visible binding for global variable ‘Chromosome’
plotCBSchr: no visible binding for global variable ‘Start_Position’
plotCBSchr: no visible binding for global variable ‘End_Position’
plotCBSchr: no visible binding for global variable ‘Segment_Mean’
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 binding for global variable ‘Hugo_Symbol’
plotCBSsegments: no visible binding for global variable ‘CN’
plotCBSsegments: no visible binding for global variable ‘Segment_Mean’
plotCBSsegments: no visible binding for global variable
  ‘Start_Position_updated’
plotCBSsegments: no visible global function definition for ‘.’
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’
plotClusters: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
plotClusters: no visible binding for global variable ‘t_vaf’
plotClusters: no visible binding for global variable ‘MATH’
plotClusters: no visible binding for global variable ‘Hugo_Symbol’
plotOncodrive: no visible binding for global variable
  ‘fract_muts_in_clusters’
plotOncodrive: no visible binding for global variable ‘fdr’
plotOncodrive: no visible binding for global variable ‘clusters’
plotOncodrive: no visible binding for global variable ‘significant’
plotOncodrive: no visible binding for global variable ‘label’
plotOncodrive: no visible binding for global variable
  ‘muts_in_clusters’
plotSignatures: no visible binding for global variable ‘Var2’
plotSignatures: no visible binding for global variable ‘value’
plotSignatures: no visible binding for global variable ‘Var1’
plotTiTv: no visible binding for global variable ‘variable’
plotTiTv: no visible binding for global variable ‘value’
plotTiTv: no visible global function definition for ‘.’
plotTiTv: no visible binding for global variable ‘V1’
plotTiTv: no visible binding for global variable ‘Tumor_Sample_Barcode’
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 binding for global variable ‘V1’
plotmafSummary: no visible binding for global variable ‘Mean’
plotmafSummary: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
plotmafSummary: no visible binding for global variable ‘N’
plotmafSummary: no visible binding for global variable
  ‘Variant_Classification’
plotmafSummary: no visible binding for global variable ‘x’
plotmafSummary: no visible binding for global variable ‘y’
plotmafSummary: no visible binding for global variable ‘label’
plotmafSummary: no visible binding for global variable ‘Median’
plotmafSummary: no visible global function definition for ‘.’
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’
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 binding for global variable
  ‘Start_Position_updated’
rainfallPlot: no visible binding for global variable ‘con.class’
rainfallPlot: no visible binding for global variable ‘id’
rainfallPlot: no visible binding for global variable ‘minDiff’
rainfallPlot: no visible binding for global variable
  ‘End_Position_updated’
rainfallPlot: no visible binding for global variable ‘pos’
read.maf: no visible binding for global variable ‘Mutation_Status’
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 ‘id’
read.maf: no visible binding for global variable ‘Hugo_Symbol’
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 ‘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 ‘.’
shiftPoints: no visible binding for global variable ‘pos’
somaticInteractions: no visible binding for global variable
  ‘Hugo_Symbol’
somaticInteractions: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
somaticInteractions: no visible binding for global variable ‘gene1’
somaticInteractions: no visible binding for global variable ‘gene2’
somaticInteractions: no visible global function definition for ‘.’
somaticInteractions: no visible binding for global variable ‘pValue’
somaticInteractions: no visible binding for global variable ‘pair’
somaticInteractions: no visible binding for global variable ‘Event’
sortByMutation: no visible binding for global variable ‘MutatedSamples’
sortByMutation: no visible binding for global variable ‘Hugo_Symbol’
subsetMaf: no visible binding for global variable ‘Variant_Type’
subsetMaf: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
subsetMaf: no visible binding for global variable ‘Hugo_Symbol’
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 ‘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 ‘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’
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: no visible binding for global variable ‘V2’
tcgaCompare: no visible binding for global variable ‘TCGA’
tcgaCompare: no visible binding for global variable ‘Median_Mutations’
tcgaCompare: no visible binding for global variable ‘Cohort’
titv: no visible binding for global variable ‘Variant_Type’
titv: no visible global function definition for ‘.’
titv: no visible binding for global variable ‘Hugo_Symbol’
titv: no visible binding for global variable ‘Start_Position’
titv: no visible binding for global variable ‘End_Position’
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 ‘Tumor_Sample_Barcode’
titv: no visible binding for global variable ‘con’
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’
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
  ‘Chromosome’
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 ‘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
  ‘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: no visible binding for global variable
  ‘fisher_pvalue’
trinucleotideMatrix: no visible binding for global variable ‘fdr’
trinucleotideMatrix: no visible binding for global variable
  ‘APOBEC_Enriched’
trinucleotideMatrix: no visible binding for global variable
  ‘SubstitutionTypeMotif’
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 ‘Hugo_Symbol’
validateMaf: no visible binding for global variable
  ‘Variant_Classification’
validateMaf: no visible binding for global variable ‘Variant_Type’
Undefined global functions or variables:
  . A A>C A>G A>T AAChange AGA APOBEC_Enriched APOBEC_Enrichment
  A[G>A]A A[G>C]A A[G>T]A AlteredSamples Avg_intermutation_dist C>A C>G
  C>T CN CNV CNV_total Chromosome Cohort Cytoband Description
  DomainLabel End End_Position End_Position_updated Entrez
  Entrez_Gene_Id Event ExonicFunc.refGene FDR G G>A G>C G>T Group HGNC
  Hugo_Symbol ID Label MATH Mean Median Median_Mutations MutSig_Synonym
  MutatedSamples MutatedSamples.x MutatedSamples.y Mutation_Status N
  OG_Hugo_Symbol Reference_Allele Sample SampleFraction SampleSize
  Segment_End Segment_Mean Segment_Start Size Start Start_Position
  Start_Position_updated Substitution SubstitutionMotif
  SubstitutionTypeMotif T>A T>C T>G TCA TCGA TCT TGA 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 TiTv Time
  TumorSampleBarcode Tumor_Sample_Barcode Tumor_Seq_Allele2 Unique_Name
  V1 V2 Var1 Var2 Variant_Classification Variant_Type Wide_Peak_Limits
  aa.length adjPval amp anno.df assembly_version bg chromosome
  chromosome_end chromosome_start ci.low ci.up clusters cohort con
  con.class consequence_type conv count count2 cytoband distance
  downstream dp endDist ens_id fdr fisher_pvalue flow fract
  fract_muts_in_clusters fraction fraction_APOBEC_mutations fs gene
  gene1 gene2 gene_affected hgnc_symbol i.End_Position i.Start_Position
  icgc_sample_id id idx lab labPos labThis label loc log10OR minDiff
  mutated_from_allele mutated_to_allele mutations muts_in_clusters
  nGenes nMut nMuts nSamples nVars n_A n_C n_C>G_and_C>T n_G n_T
  n_mutations nonApobec non_APOBEC_mutations numMat or pValue pair
  peakID pfam poissonFdr pos pos2 posRounded protein.ID pval qvalues
  reference_genome_allele refseq.ID sampleId sequencing_strategy
  significant site startDist statFontSize statLeft statRight survLower
  survProb survUp tCw tCw_to_A tCw_to_G tCw_to_G+tCw_to_T tCw_to_T tFdr
  t_alt_count t_ref_count t_vaf tcw th tot total trinucleotide uid
  updown upstream value variable variantId verification_platform
  verification_status wGa wGa_to_A wGa_to_C wGa_to_T wga x y ybig
  ysmall ystart
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘pheatmap’
'library' or 'require' calls not declared from:
  ‘ggfortify’ ‘pheatmap’
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/maftools.Rcheck/00check.log’
for details.

* installing *source* package ‘maftools’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (maftools)

name	user	system	elapsed
annovarToMaf	0.388	0.044	0.259
coOncoplot	4.588	0.172	4.716
extractSignatures	0.004	0.000	0.001
forestPlot	2.768	0.136	2.803
geneCloud	0.496	0.052	0.486
genesToBarcodes	0.544	0.060	0.548
genotypeMatrix	0.416	0.028	0.396
getClinicalData	0.444	0.048	0.430
getCytobandSummary	0.372	0.012	0.343
getFields	0.464	0.048	0.451
getGeneSummary	0.448	0.036	0.416
getSampleSummary	0.428	0.044	0.415
gisticBubblePlot	1.456	0.020	1.410
gisticChromPlot	1.012	0.004	0.963
gisticOncoPlot	2.388	0.012	2.351
icgcSimpleMutationToMAF	0.028	0.032	0.066
inferHeterogeneity	0.496	0.052	0.499
lollipopPlot	2.100	0.256	2.320
mafCompare	0.436	0.088	0.429
mafSummary	0.928	0.076	0.878
mafSurvival	1.040	0.080	1.075
math.score	0.436	0.080	0.469
mutCountMatrix	0.844	0.252	1.044
oncodrive	2.432	0.148	2.278
oncoplot	1.400	0.068	1.410
oncostrip	1.084	0.104	1.143
oncotate	0.000	0.000	0.003
pancanComparison	1.300	0.160	1.463
pfamDomains	1.156	0.124	1.172
plotApobecDiff	0.000	0.000	0.001
plotCBSsegments	0.240	0.024	0.229
plotClusters	1.260	0.072	1.240
plotOncodrive	1.904	0.140	1.774
plotTiTv	2.648	0.140	2.728
plotVaf	0.996	0.060	1.004
plotmafSummary	1.596	0.068	1.628
prepareMutSig	0.424	0.084	0.463
read.maf	0.476	0.068	0.488
readGistic	0.464	0.016	0.431
somaticInteractions	0.700	0.068	0.712
subsetMaf	0.440	0.060	0.445
tcgaCompare	1.380	0.112	1.444
titv	1.684	0.096	1.736
trinucleotideMatrix	0	0	0
write.GisticSummary	0.424	0.012	0.391
write.mafSummary	0.436	0.044	0.425