maftools 1.2.30
Anand Mayakonda
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/maftools | | Branch: RELEASE_3_5 | | Last Commit: 5873a10 | | Last Changed Date: 2017-05-22 23:26:26 -0400 (Mon, 22 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings maftools_1.2.30.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/maftools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maftools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maftools’ version ‘1.2.30’
* 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 6.4Mb
sub-directories of 1Mb or more:
doc 1.8Mb
extdata 4.2Mb
* 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’
dashboard: no visible binding for global variable ‘statFontSize’
dashboard: no visible binding for global variable ‘fs’
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 ‘ymax’
dashboard: no visible binding for global variable ‘ymin’
dashboard: no visible binding for global variable ‘dat’
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’
dirichletClusters: no visible binding for global variable ‘t_vaf’
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 ‘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 ‘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’
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 ‘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 binding for global variable
‘Tumor_Sample_Barcode’
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 ‘MutatedSamples’
mafCompare: no visible binding for global variable ‘Hugo_Symbol’
mafCompare: no visible global function definition for ‘.’
mafSurvival : <anonymous>: no visible binding for global variable
‘Tumor_Sample_Barcode’
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’
oncodrive: no visible binding for global variable
‘Variant_Classification’
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’
oncostrip: no visible binding for global variable ‘sort_by_anno’
pancanComparision: no visible binding for global variable ‘gene’
pancanComparision: no visible global function definition for ‘.’
pancanComparision: no visible binding for global variable ‘nMut’
pancanComparision: 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_Classification’
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 ‘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’
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 ‘Hugo_Symbol’
plotGisticResults: no visible binding for global variable ‘qvalues’
plotGisticResults: no visible binding for global variable ‘Chromosome’
plotGisticResults: no visible binding for global variable ‘loc’
plotGisticResults: no visible binding for global variable
‘Start_Position’
plotGisticResults: no visible binding for global variable
‘End_Position’
plotGisticResults: no visible global function definition for ‘.’
plotGisticResults: no visible binding for global variable ‘Cytoband’
plotGisticResults: no visible binding for global variable
‘Variant_Classification’
plotGisticResults: no visible binding for global variable
‘Start_Position_updated’
plotGisticResults: no visible binding for global variable
‘End_Position_updated’
plotGisticResults: no visible binding for global variable ‘ystart’
plotGisticResults: no visible binding for global variable ‘amp’
plotGisticResults: no visible binding for global variable ‘nSamples’
plotGisticResults: no visible binding for global variable ‘pos’
plotGisticResults: no visible binding for global variable ‘lab’
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 ‘n_mutations’
plotSignatures: no visible binding for global variable
‘APOBEC_Enriched’
plotSignatures: no visible binding for global variable
‘fraction_APOBEC_mutations’
plotSignatures: no visible binding for global variable ‘nonApobec’
plotSignatures: no visible binding for global variable ‘V1’
plotSignatures: no visible binding for global variable ‘variable’
plotSignatures: no visible binding for global variable ‘value’
plotSignatures: no visible binding for global variable ‘N’
plotSignatures: no visible binding for global variable ‘Var2’
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 ‘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 binding for global variable ‘Hugo_Symbol’
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
‘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 ‘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’
sortByAnnotation: no visible binding for global variable ‘Hugo_Symbol’
sortByMutation: no visible binding for global variable ‘Hugo_Symbol’
subsetMaf: no visible binding for global variable
‘Variant_Classification’
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_Classification’
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
‘Variant_Classification’
trinucleotideMatrix: no visible binding for global variable
‘Variant_Type’
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
‘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’
write.mafSummary: 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 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 ExonicFunc.refGene G G>A
G>C G>T Group HGNC Hugo_Symbol ID Label 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
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 amp assembly_version bg
chromosome chromosome_end chromosome_start ci.low ci.up clusters
cohort con con.class consequence_type conv count count2 cytoband dat
distance downstream endDist ens_id fdr fisher_pvalue flow fract
fract_muts_in_clusters fraction fraction_APOBEC_mutations fs gene
gene_affected hgnc_symbol i.End_Position i.Start_Position
icgc_sample_id id idx lab labThis label loc log10OR
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 or peakID pfam poissonFdr
pos pos2 posRounded protein.ID pval qvalues reference_genome_allele
refseq.ID sequencing_strategy significant site sort_by_anno startDist
statFontSize 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
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 ymax ymin ystart
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘corrplot’
'library' or 'require' call not declared from: ‘corrplot’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/maftools.Rcheck/00check.log’
for details.