Anand Mayakonda
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/maftools |
| Branch: RELEASE_3_8 |
| Last Commit: 9fedc12 |
| Last Changed Date: 2019-04-14 10:38:30 -0400 (Sun, 14 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:47 -0400 (Tue, 16 Apr 2019).
| Package 866/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| maftools 1.8.10 Anand Mayakonda
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: maftools |
| Version: 1.8.10 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:maftools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings maftools_1.8.10.tar.gz |
| StartedAt: 2019-04-16 00:58:13 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:03:16 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 302.6 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 --install=check:maftools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings maftools_1.8.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/maftools.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.10’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maftools’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.8Mb
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
* 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 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’
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 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 ‘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’
forestPlot: no visible binding for global variable ‘gg.fp’
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’
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 ‘nSamples’
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’
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 ‘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’
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 ‘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’
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
‘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’
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’
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’
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 ‘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’
signatureEnrichment: no visible binding for global variable
‘mut.load.p’
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 ‘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 ‘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 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 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
SampleFraction 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 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 clusters
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 gg.fp heat.colors hgnc_symbol
i.End_Position i.Start_Position icgc_sample_id id idx lab labPos
labThis label loc log10OR log10OR_high log10OR_low minDiff mut.load.p
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_affected_genes n_mutated_Feature n_mutated_Feature1
n_mutated_Feature2 n_mutated_group1 n_mutated_group2 n_mutations
nonApobec non_APOBEC_mutations numMat or pValue p_value pair peakID
pfam pkgname poissonFdr pos2 posRounded protein.ID pval qvalues
reference_genome_allele refseq.ID row_idx sampleId
sequencing_strategy significant site 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 tot total trinucleotide uid
updown upstream value variable variantId verification_platform
verification_status wGa wGa_to_A wGa_to_C wGa_to_T wga ybig ysmall
ystart
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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotOncodrive 14.913 11.693 4.053
oncodrive 11.717 13.693 3.121
pfamDomains 7.830 7.009 2.396
coOncoplot 9.015 5.363 4.094
OncogenicPathways 7.640 6.160 1.989
lollipopPlot 5.555 5.953 2.171
oncoplot 6.590 4.157 2.034
gisticChromPlot 5.721 4.385 1.719
lollipopPlot2 4.709 4.653 1.909
mafSummary 4.054 4.846 1.172
mutCountMatrix 3.718 4.629 1.760
gisticOncoPlot 4.780 3.155 3.265
mafSurvival 4.788 2.614 1.084
oncostrip 3.622 3.527 1.396
annovarToMaf 2.301 4.255 0.865
PlotOncogenicPathways 4.104 2.315 1.361
tcgaCompare 3.910 2.400 1.805
titv 4.043 2.227 0.930
plotTiTv 3.946 2.256 0.745
geneCloud 2.423 3.398 0.719
drugInteractions 3.392 2.358 0.718
gisticBubblePlot 2.909 2.774 1.020
genotypeMatrix 3.814 1.851 0.676
pancanComparison 2.094 3.464 1.009
somaticInteractions 2.972 2.502 0.795
getGeneSummary 3.551 1.604 0.546
genesToBarcodes 2.263 2.818 0.642
* 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
‘/Users/biocbuild/bbs-3.8-bioc/meat/maftools.Rcheck/00check.log’
for details.
maftools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL maftools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘maftools’ ... ** R ** inst ** byte-compile and prepare 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 | |
| OncogenicPathways | 7.640 | 6.160 | 1.989 | |
| PlotOncogenicPathways | 4.104 | 2.315 | 1.361 | |
| annovarToMaf | 2.301 | 4.255 | 0.865 | |
| clinicalEnrichment | 0.002 | 0.002 | 0.001 | |
| coOncoplot | 9.015 | 5.363 | 4.094 | |
| drugInteractions | 3.392 | 2.358 | 0.718 | |
| extractSignatures | 0 | 0 | 0 | |
| forestPlot | 1.967 | 1.605 | 0.410 | |
| geneCloud | 2.423 | 3.398 | 0.719 | |
| genesToBarcodes | 2.263 | 2.818 | 0.642 | |
| genotypeMatrix | 3.814 | 1.851 | 0.676 | |
| getClinicalData | 1.844 | 2.652 | 0.558 | |
| getCytobandSummary | 1.799 | 2.487 | 0.524 | |
| getFields | 1.974 | 2.481 | 0.547 | |
| getGeneSummary | 3.551 | 1.604 | 0.546 | |
| getSampleSummary | 1.967 | 2.520 | 0.546 | |
| gisticBubblePlot | 2.909 | 2.774 | 1.020 | |
| gisticChromPlot | 5.721 | 4.385 | 1.719 | |
| gisticOncoPlot | 4.780 | 3.155 | 3.265 | |
| icgcSimpleMutationToMAF | 0.180 | 0.240 | 0.073 | |
| inferHeterogeneity | 0.000 | 0.002 | 0.000 | |
| lollipopPlot | 5.555 | 5.953 | 2.171 | |
| lollipopPlot2 | 4.709 | 4.653 | 1.909 | |
| mafCompare | 2.297 | 1.152 | 0.381 | |
| mafSummary | 4.054 | 4.846 | 1.172 | |
| mafSurvival | 4.788 | 2.614 | 1.084 | |
| math.score | 1.782 | 2.594 | 0.568 | |
| mutCountMatrix | 3.718 | 4.629 | 1.760 | |
| oncodrive | 11.717 | 13.693 | 3.121 | |
| oncoplot | 6.590 | 4.157 | 2.034 | |
| oncostrip | 3.622 | 3.527 | 1.396 | |
| oncotate | 0.003 | 0.001 | 0.003 | |
| pancanComparison | 2.094 | 3.464 | 1.009 | |
| pfamDomains | 7.830 | 7.009 | 2.396 | |
| plotApobecDiff | 0.001 | 0.001 | 0.001 | |
| plotCBSsegments | 0.879 | 1.071 | 0.311 | |
| plotClusters | 0.000 | 0.000 | 0.001 | |
| plotOncodrive | 14.913 | 11.693 | 4.053 | |
| plotTiTv | 3.946 | 2.256 | 0.745 | |
| plotVaf | 2.044 | 1.743 | 0.757 | |
| plotmafSummary | 2.386 | 2.047 | 0.643 | |
| prepareMutSig | 2.880 | 1.554 | 0.578 | |
| read.maf | 2.813 | 1.410 | 0.534 | |
| readGistic | 1.523 | 1.205 | 0.408 | |
| somaticInteractions | 2.972 | 2.502 | 0.795 | |
| subsetMaf | 3.592 | 1.157 | 0.559 | |
| tcgaCompare | 3.910 | 2.400 | 1.805 | |
| titv | 4.043 | 2.227 | 0.930 | |
| trinucleotideMatrix | 0.001 | 0.002 | 0.000 | |
| write.GisticSummary | 1.966 | 2.049 | 0.586 | |
| write.mafSummary | 1.859 | 1.501 | 0.514 | |