Multiple platform build/check report for BioC 3.9 - CHECK report for maftools on tokay2

Package: maftools

Version: 1.9.30

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maftools.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings maftools_1.9.30.tar.gz

StartedAt: 2019-04-09 03:56:21 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:00:01 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 220.7 seconds

RetCode: 0

Status: OK

CheckDir: maftools.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:maftools.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings maftools_1.9.30.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/maftools.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'maftools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'maftools' version '1.9.30'
* 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 whether package 'maftools' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
OncogenicPathways: no visible binding for global variable 'Pathway'
OncogenicPathways: no visible binding for global variable
  'fraction_affected'
OncogenicPathways: no visible binding for global variable
  'n_affected_genes'
OncogenicPathways: no visible binding for global variable 'N'
PlotOncogenicPathways: no visible binding for global variable
  'Tumor_Sample_Barcode'
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
  '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'
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 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_low'
clinicalEnrichment: no visible binding for global variable 'OR_high'
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'
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 binding for global variable
  'Tumor_Sample_Barcode'
createOncoMatrix: no visible binding for global variable 'Hugo_Symbol'
createOncoMatrix: no visible global function definition for '.'
createOncoMatrix: no visible binding for global variable
  'Variant_Classification'
dashboard: no visible binding for global variable 'statFontSize'
dashboard: no visible binding for global variable 'fs'
dashboard: no visible binding for global variable 'value'
dashboard: no visible binding for global variable 'variable'
dashboard: no visible binding for global variable 'ID'
dashboard: no visible binding for global variable 'Mean'
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 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 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
  'heat.colors'
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 binding for global variable 'log10OR_high'
forestPlot: no visible binding for global variable 'ci.up'
forestPlot: no visible binding for global variable 'log10OR_low'
forestPlot: no visible binding for global variable 'ci.low'
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'
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 'Label'
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'
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'
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 binding for global variable
  'Start_Position_updated'
gisticChromPlot: no visible binding for global variable
  'End_Position_updated'
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'
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 '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 '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 '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'
lollipopPlot2: no visible binding for global variable 'Label'
lollipopPlot2: no visible binding for global variable
  'Variant_Classification'
lollipopPlot2: no visible binding for global variable 'pos2'
lollipopPlot2: no visible binding for global variable 'count2'
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 binding for global variable 'refseq.ID'
lollipopPlot2: no visible binding for global variable 'conv'
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 'pval'
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'
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: no visible binding for global variable 'total'
oncoplot: no visible binding for global variable 'CNV_total'
oncoplot: no visible binding for global variable 'temp_af'
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 'log_q_pancan'
pancanComparison: no visible binding for global variable 'log_q'
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 'N'
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 '.'
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'
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'
plotEnrichmentResults: no visible binding for global variable 'P_value'
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: no visible binding for global variable 'Group1'
plotOncodrive: no visible binding for global variable 'log_fdr'
plotOncodrive: no visible binding for global variable 'fdr'
plotOncodrive: no visible binding for global variable 'significant'
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'
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 'statFontSize'
plotmafSummary: no visible binding for global variable 'Mean'
plotmafSummary: no visible binding for global variable 'Median'
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 binding for global variable 'boxStat'
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'
print_mat: no visible binding for global variable
  'Tumor_Sample_Barcode'
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 'id'
rainfallPlot: no visible binding for global variable 'minDiff'
rainfallPlot: no visible binding for global variable
  'Start_Position_updated'
rainfallPlot: no visible binding for global variable
  'End_Position_updated'
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
  '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 'distance'
repelPoints: no visible global function definition for '.'
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 'N'
signatureEnrichment: no visible global function definition for '.'
signatureEnrichment: no visible binding for global variable 'N'
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 : <anonymous>: no visible binding for global variable
  'total'
tcgaCompare : <anonymous>: no visible binding for global variable
  'TCGA'
tcgaCompare : <anonymous>: no visible binding for global variable 'V2'
tcgaCompare : <anonymous>: no visible binding for global variable 'V3'
tcgaCompare: no visible binding for global variable
  'Median_Mutations_log10'
tcgaCompare: no visible binding for global variable 'Median_Mutations'
tcgaCompare : <anonymous>: no visible binding for global variable
  'Median_Mutations_log10'
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 '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 '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: 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 AAChange_ AGA APOBEC_Enriched
  APOBEC_Enrichment A[G>A]A A[G>C]A A[G>T]A AlteredSamples Analysis C>A
  C>G C>T CN CNV CNV_total Chromosome Cluster Cohort Cytoband
  Description DomainLabel End End_Position End_Position_updated Entrez
  Entrez_Gene_Id Event ExonicFunc.refGene FDR Feature_1 Feature_2 G G>A
  G>C G>T Gene Genotype Group Group1 Group2 HGNC Hugo_Symbol ID Label
  MATH Mean Median Median_Mutations Median_Mutations_log10
  MutSig_Synonym MutatedSamples MutatedSamples.x MutatedSamples.y
  Mutation_Status N N.x N.y OG_Hugo_Symbol OR_high OR_low P_value
  Pathway Reference_Allele Sample SampleSize Segment_End Segment_Mean
  Segment_Start Signature Size Start Start_Position
  Start_Position_updated Substitution SubstitutionMotif
  SubstitutionType 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 V3 Var1 Var2
  Variant_Classification Variant_Type Wide_Peak_Limits aa.length
  adjPval amp anno.df assembly_version bg boxStat category cf
  chromosome chromosome_end chromosome_start ci.low ci.up cohort con
  con.class consequence_type conv count count2 cytoband distance
  domain_lenght downstream dp endDist ens_id fdr fisher_pvalue fract
  fract_muts_in_clusters fraction fraction_APOBEC_mutations
  fraction_affected fs g1_muts g1_title g1_tot g2_muts g2_title g2_tot
  gene gene1 gene2 gene_affected heat.colors hgnc_symbol i.End_Position
  i.Start_Position icgc_sample_id id idx lab labThis label loc log10OR
  log10OR_high log10OR_low log_fdr log_q log_q_pancan minDiff
  mutated_from_allele mutated_to_allele muts_in_clusters nGenes nMut
  nMuts nVars n_A n_C n_C>G_and_C>T n_G n_T n_affected_genes
  n_mutated_Feature n_mutated_Feature1 n_mutated_Feature2
  n_mutated_group1 n_mutated_group2 n_mutations nonApobec
  non_APOBEC_mutations or pValue p_value pair peakID pfam pkgname
  poissonFdr pos2 posRounded protein.ID pval qvalues
  reference_genome_allele refseq.ID row_idx sequencing_strategy
  significant site startDist statFontSize survProb 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 temp_af th tot total trinucleotide uid unit updown upstream
  value variable variantId verification_platform verification_status
  wGa wGa_to_A wGa_to_C wGa_to_T wga
Consider adding
  importFrom("grDevices", "heat.colors")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/maftools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/maftools_1.9.30.tar.gz && rm -rf maftools.buildbin-libdir && mkdir maftools.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=maftools.buildbin-libdir maftools_1.9.30.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL maftools_1.9.30.zip && rm maftools_1.9.30.tar.gz maftools_1.9.30.zip
###
##############################################################################
##############################################################################


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100 6295k  100 6295k    0     0  24.3M      0 --:--:-- --:--:-- --:--:-- 25.0M

install for i386

* installing *source* package 'maftools' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'maftools'
    finding HTML links ... done
    GISTIC-class                            html  
    MAF-class                               html  
    OncogenicPathways                       html  
    PlotOncogenicPathways                   html  
    annovarToMaf                            html  
    clinicalEnrichment                      html  
    coOncoplot                              html  
    drugInteractions                        html  
    extractSignatures                       html  
    finding level-2 HTML links ... done

    forestPlot                              html  
    geneCloud                               html  
    genesToBarcodes                         html  
    genotypeMatrix                          html  
    getClinicalData                         html  
    getCytobandSummary                      html  
    getFields                               html  
    getGeneSummary                          html  
    getSampleSummary                        html  
    gisticBubblePlot                        html  
    gisticChromPlot                         html  
    gisticOncoPlot                          html  
    icgcSimpleMutationToMAF                 html  
    inferHeterogeneity                      html  
    lollipopPlot                            html  
    lollipopPlot2                           html  
    mafCompare                              html  
    mafSummary                              html  
    mafSurvival                             html  
    math.score                              html  
    merge_mafs                              html  
    mutCountMatrix                          html  
    oncodrive                               html  
    oncoplot                                html  
    oncostrip                               html  
    oncotate                                html  
    pancanComparison                        html  
    pfamDomains                             html  
    plotApobecDiff                          html  
    plotCBSsegments                         html  
    plotClusters                            html  
    plotEnrichmentResults                   html  
    plotOncodrive                           html  
    plotSignatures                          html  
    plotTiTv                                html  
    plotVaf                                 html  
    plotmafSummary                          html  
    prepareMutSig                           html  
    rainfallPlot                            html  
    read.maf                                html  
    readGistic                              html  
    signatureEnrichment                     html  
    somaticInteractions                     html  
    subsetMaf                               html  
    tcgaCompare                             html  
    titv                                    html  
    trinucleotideMatrix                     html  
    write.GisticSummary                     html  
    write.mafSummary                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'maftools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maftools' as maftools_1.9.30.zip
* DONE (maftools)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'maftools' successfully unpacked and MD5 sums checked

CHECK report for maftools on tokay2

Summary

Command output

Installation output

Tests output

Example timings