Anand Mayakonda
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/maftools |
| Branch: RELEASE_3_6 |
| Last Commit: 3816106 |
| Last Changed Date: 2018-04-10 05:41:34 -0400 (Tue, 10 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:43:18 -0400 (Thu, 12 Apr 2018).
| Package 774/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| maftools 1.4.28 Anand Mayakonda
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: maftools |
| Version: 1.4.28 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maftools_1.4.28.tar.gz |
| StartedAt: 2018-04-12 05:47:07 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 05:52:20 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 312.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: maftools.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maftools_1.4.28.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/maftools.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 11.8Mb
sub-directories of 1Mb or more:
doc 6.8Mb
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
Examples with CPU or elapsed time > 5s
user system elapsed
coOncoplot 6.47 0.332 6.083
* 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
‘/Users/biocbuild/bbs-3.6-bioc/meat/maftools.Rcheck/00check.log’
for details.
maftools.Rcheck/00install.out
* 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)
maftools.Rcheck/maftools-Ex.timings
| name | user | system | elapsed | |
| annovarToMaf | 0.254 | 0.044 | 0.177 | |
| coOncoplot | 6.470 | 0.332 | 6.083 | |
| extractSignatures | 0.001 | 0.000 | 0.001 | |
| forestPlot | 3.637 | 0.112 | 3.510 | |
| geneCloud | 0.613 | 0.056 | 0.543 | |
| genesToBarcodes | 0.468 | 0.052 | 0.384 | |
| genotypeMatrix | 0.577 | 0.098 | 0.410 | |
| getClinicalData | 1.031 | 0.059 | 0.963 | |
| getCytobandSummary | 0.531 | 0.044 | 0.425 | |
| getFields | 0.425 | 0.023 | 0.419 | |
| getGeneSummary | 0.510 | 0.060 | 0.393 | |
| getSampleSummary | 0.517 | 0.054 | 0.386 | |
| gisticBubblePlot | 2.151 | 0.200 | 1.737 | |
| gisticChromPlot | 1.271 | 0.066 | 1.168 | |
| gisticOncoPlot | 3.065 | 0.061 | 2.992 | |
| icgcSimpleMutationToMAF | 0.043 | 0.004 | 0.048 | |
| inferHeterogeneity | 0.506 | 0.027 | 0.475 | |
| lollipopPlot | 1.874 | 0.126 | 1.729 | |
| mafCompare | 0.900 | 0.059 | 0.781 | |
| mafSummary | 1.153 | 0.126 | 0.895 | |
| mafSurvival | 1.588 | 0.158 | 1.284 | |
| math.score | 0.404 | 0.017 | 0.392 | |
| mutCountMatrix | 1.401 | 0.464 | 1.567 | |
| oncodrive | 2.115 | 0.308 | 1.491 | |
| oncoplot | 2.478 | 0.251 | 2.051 | |
| oncostrip | 1.143 | 0.091 | 1.011 | |
| oncotate | 0.004 | 0.000 | 0.006 | |
| pancanComparison | 0.994 | 0.109 | 0.767 | |
| pfamDomains | 1.764 | 0.341 | 1.186 | |
| plotApobecDiff | 0.001 | 0.000 | 0.001 | |
| plotCBSsegments | 0.565 | 0.125 | 0.329 | |
| plotClusters | 1.683 | 0.210 | 1.296 | |
| plotOncodrive | 2.459 | 0.260 | 1.889 | |
| plotTiTv | 3.495 | 0.070 | 3.452 | |
| plotVaf | 1.326 | 0.060 | 1.229 | |
| plotmafSummary | 2.247 | 0.119 | 2.066 | |
| prepareMutSig | 0.520 | 0.034 | 0.483 | |
| read.maf | 0.467 | 0.042 | 0.392 | |
| readGistic | 0.571 | 0.061 | 0.458 | |
| somaticInteractions | 0.948 | 0.110 | 0.709 | |
| subsetMaf | 0.470 | 0.024 | 0.454 | |
| tcgaCompare | 1.763 | 0.152 | 1.540 | |
| titv | 1.979 | 0.063 | 1.911 | |
| trinucleotideMatrix | 0.001 | 0.000 | 0.000 | |
| write.GisticSummary | 0.996 | 0.023 | 1.007 | |
| write.mafSummary | 0.518 | 0.056 | 0.402 | |