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This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1102/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
maftools 2.16.0  (landing page)
Anand Mayakonda
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/maftools
git_branch: RELEASE_3_17
git_last_commit: 39bddc8
git_last_commit_date: 2023-04-25 10:48:19 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for maftools on kjohnson2


To the developers/maintainers of the maftools package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: maftools
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maftools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maftools_2.16.0.tar.gz
StartedAt: 2023-10-18 04:25:10 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 04:28:40 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 209.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: maftools.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:maftools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings maftools_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/maftools.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maftools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maftools’ version ‘2.16.0’
* 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 ... WARNING
Found the following significant warnings:
  snpcounts.c:56:26: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/maftools.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  7.9Mb
  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 ... NOTE
Namespace in Imports field not imported from: ‘Rhtslib’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.dnaCopy_plotter: no visible binding for global variable ‘contig’
.dnaCopy_plotter: no visible binding for global variable ‘Chromosome’
.dnaCopy_plotter: no visible global function definition for ‘par’
.dnaCopy_plotter: no visible global function definition for ‘abline’
.dnaCopy_plotter: no visible global function definition for ‘segments’
.dnaCopy_plotter: no visible global function definition for ‘axis’
.mafSetKeys: no visible binding for global variable ‘Chromosome’
.mafSetKeys: no visible binding for global variable ‘Start_Position’
.mafSetKeys: no visible binding for global variable ‘End_Position’
OncogenicPathways: no visible binding for global variable
  ‘n_affected_genes’
OncogenicPathways: no visible binding for global variable ‘ID’
OncogenicPathways: no visible global function definition for ‘layout’
OncogenicPathways: no visible global function definition for ‘par’
OncogenicPathways: no visible global function definition for ‘text’
OncogenicPathways: no visible global function definition for ‘title’
OncogenicPathways: no visible global function definition for ‘rect’
OncogenicPathways: no visible global function definition for ‘axis’
PlotOncogenicPathways: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
PlotOncogenicPathways: no visible global function definition for ‘par’
PlotOncogenicPathways: no visible global function definition for
  ‘image’
PlotOncogenicPathways: no visible global function definition for
  ‘abline’
PlotOncogenicPathways: no visible global function definition for
  ‘points’
PlotOncogenicPathways: no visible global function definition for
  ‘mtext’
PlotOncogenicPathways: no visible global function definition for ‘text’
PlotOncogenicPathways: no visible global function definition for
  ‘title’
add_legend: no visible global function definition for ‘par’
add_legend: no visible global function definition for ‘legend’
add_oncoprint: no visible global function definition for ‘unit’
add_oncoprint: no visible binding for global variable ‘bg’
add_oncoprint2: no visible global function definition for ‘unit’
annovarToMaf: no visible binding for global variable ‘Hugo_Symbol’
annovarToMaf: no visible binding for global variable ‘Gene.refGene’
annovarToMaf: no visible binding for global variable ‘Func.refGene’
annovarToMaf: no visible binding for global variable
  ‘Variant_Classification’
annovarToMaf: no visible binding for global variable
  ‘ExonicFunc.refGene’
annovarToMaf: no visible binding for global variable ‘ref_alt_diff’
annovarToMaf: no visible binding for global variable ‘Ref’
annovarToMaf: no visible binding for global variable ‘Alt’
annovarToMaf: no visible binding for global variable ‘Variant_Type’
annovarToMaf : <anonymous>: no visible binding for global variable
  ‘Variant_Classification’
annovarToMaf : <anonymous>: no visible binding for global variable
  ‘ref_alt_diff’
annovarToMaf: no visible binding for global variable ‘ens_id’
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’
binconf : bc: no visible global function definition for ‘qf’
binconf : bc: no visible global function definition for ‘qnorm’
bubble_plot: no visible global function definition for ‘layout’
bubble_plot: no visible global function definition for ‘symbols’
bubble_plot: no visible global function definition for ‘axis’
bubble_plot: no visible global function definition for ‘abline’
bubble_plot: no visible global function definition for ‘mtext’
bubble_plot: no visible global function definition for ‘text’
bubble_plot: no visible global function definition for ‘par’
cancerhotspots: no visible global function definition for ‘browseURL’
cancerhotspotsAggr : <anonymous>: no visible global function definition
  for ‘.’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘A’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘G’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘C’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘Ins’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘Del’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘t_depth’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘VAF’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘End_Position’
cancerhotspotsAggr : <anonymous>: no visible binding for global
  variable ‘Start_Position’
cancerhotspotsAggr: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
clinicalEnrichment : pairwise.fisher.test : compare.levels: no visible
  global function definition for ‘fisher.test’
clinicalEnrichment : pairwise.fisher.test: no visible global function
  definition for ‘pairwise.table’
clinicalEnrichment : <anonymous>: no visible binding for global
  variable ‘Gene’
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 global
  function definition for ‘fisher.test’
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’
clinicalEnrichment: no visible binding for global variable ‘OR_low’
clinicalEnrichment: no visible binding for global variable ‘OR_high’
clinicalEnrichment: no visible global function definition for
  ‘p.adjust’
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’
coBarplot: no visible binding for global variable ‘Hugo_Symbol’
coBarplot: no visible binding for global variable ‘ID’
coBarplot: no visible global function definition for ‘.’
coBarplot: no visible binding for global variable ‘AlteredSamples’
coBarplot: no visible global function definition for ‘par’
coBarplot: no visible global function definition for ‘barplot’
coBarplot: no visible global function definition for ‘text’
coBarplot: no visible global function definition for ‘axis’
coBarplot: no visible global function definition for ‘mtext’
coBarplot: no visible global function definition for ‘title’
coBarplot: no visible global function definition for ‘legend’
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’
coOncoplot: no visible global function definition for ‘plot.new’
coOncoplot: no visible global function definition for ‘par’
coOncoplot: no visible global function definition for ‘image’
coOncoplot: no visible global function definition for ‘text’
coOncoplot: no visible global function definition for ‘legend’
createOncoMatrix: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
createOncoMatrix: no visible binding for global variable ‘Hugo_Symbol’
createOncoMatrix: no visible binding for global variable ‘Variant_Type’
createOncoMatrix: no visible binding for global variable
  ‘Variant_Classification’
createOncoMatrix: no visible binding for global variable
  ‘Variant_Classification_temp’
createOncoMatrix: no visible global function definition for ‘.’
dashboard: no visible binding for global variable ‘statFontSize’
dashboard: no visible binding for global variable ‘fs’
dashboard: no visible binding for global variable ‘pie’
dashboard: no visible global function definition for ‘par’
dashboard: no visible global function definition for ‘barplot’
dashboard: no visible global function definition for ‘abline’
dashboard: no visible global function definition for ‘axis’
dashboard: no visible global function definition for ‘title’
dashboard: no visible binding for global variable ‘value’
dashboard: no visible binding for global variable ‘variable’
dashboard: no visible global function definition for ‘text’
dashboard: no visible global function definition for ‘mtext’
dashboard: no visible binding for global variable ‘ID’
dashboard: no visible binding for global variable ‘Mean’
dashboard: no visible global function definition for ‘lines’
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 global function definition for ‘boxplot’
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 global function definition for
  ‘write.table’
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 ‘par’
drugInteractions: no visible global function definition for ‘pie’
drugInteractions: no visible global function definition for
  ‘heat.colors’
drugInteractions: no visible global function definition for ‘barplot’
drugInteractions: no visible global function definition for ‘text’
drugInteractions: no visible global function definition for ‘axis’
drugInteractions: no visible global function definition for ‘mtext’
drugInteractions: no visible global function definition for ‘title’
estimateSignatures: no visible global function definition for ‘png’
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’
filterMaf: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
filterMaf: no visible binding for global variable ‘Hugo_Symbol’
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 ‘pos’
forestPlot: no visible global function definition for ‘par’
forestPlot: no visible global function definition for ‘.’
forestPlot: no visible binding for global variable ‘or’
forestPlot: no visible binding for global variable ‘ci.up’
forestPlot: no visible binding for global variable ‘ci.low’
forestPlot: no visible binding for global variable ‘or_new’
forestPlot: no visible binding for global variable ‘upper’
forestPlot: no visible binding for global variable ‘lower’
forestPlot : <anonymous>: no visible global function definition for
  ‘points’
forestPlot : <anonymous>: no visible global function definition for
  ‘segments’
forestPlot: no visible global function definition for ‘abline’
forestPlot: no visible global function definition for ‘axis’
forestPlot: no visible global function definition for ‘mtext’
forestPlot: no visible global function definition for ‘title’
forestPlot: no visible global function definition for ‘text’
genesToBarcodes: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
genesToBarcodes : <anonymous>: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
genotypeMatrix: no visible binding for global variable ‘id’
genotypeMatrix: no visible binding for global variable ‘Chromosome’
genotypeMatrix: no visible binding for global variable ‘Start_Position’
genotypeMatrix: no visible binding for global variable ‘t_vaf’
get_anno_cols: no visible global function definition for
  ‘colorRampPalette’
get_col_df: no visible binding for global variable ‘Hugo_Symbol’
get_col_df: no visible binding for global variable ‘Var1’
get_col_df: no visible binding for global variable ‘Freq’
get_col_df: no visible global function definition for ‘.’
get_col_df: no visible binding for global variable ‘Gene’
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’
get_pw_summary: no visible binding for global variable ‘Pathway’
get_pw_summary: no visible binding for global variable
  ‘fraction_affected’
get_pw_summary: no visible binding for global variable
  ‘n_affected_genes’
get_pw_summary: no visible binding for global variable ‘N’
get_pw_summary: no visible binding for global variable ‘ID’
get_pw_summary: no visible binding for global variable
  ‘Fraction_mutated_samples’
get_pw_summary: no visible binding for global variable
  ‘Mutated_samples’
get_threshold : <anonymous>: no visible global function definition for
  ‘dbinom’
gisticBubblePlot: no visible binding for global variable ‘qvalues’
gisticBubblePlot: no visible binding for global variable ‘Chromosome’
gisticBubblePlot: no visible binding for global variable ‘loc’
gisticBubblePlot: no visible binding for global variable
  ‘Start_Position’
gisticBubblePlot: no visible binding for global variable ‘End_Position’
gisticBubblePlot: no visible global function definition for ‘.’
gisticBubblePlot: no visible binding for global variable ‘Cytoband’
gisticBubblePlot: no visible binding for global variable
  ‘Variant_Classification’
gisticBubblePlot: no visible binding for global variable ‘nGenes’
gisticBubblePlot: no visible binding for global variable ‘log_q’
gisticBubblePlot: no visible global function definition for ‘par’
gisticChromPlot: no visible binding for global variable ‘qvalues’
gisticChromPlot: no visible binding for global variable ‘Chromosome’
gisticChromPlot: no visible binding for global variable ‘loc’
gisticChromPlot: no visible binding for global variable
  ‘Start_Position’
gisticChromPlot: no visible binding for global variable ‘End_Position’
gisticChromPlot: no visible global function definition for ‘.’
gisticChromPlot: no visible binding for global variable ‘Cytoband’
gisticChromPlot: no visible binding for global variable
  ‘Variant_Classification’
gisticChromPlot: no visible binding for global variable ‘amp’
gisticChromPlot: no visible global function definition for ‘layout’
gisticChromPlot: no visible global function definition for ‘par’
gisticChromPlot: no visible global function definition for ‘abline’
gisticChromPlot: no visible global function definition for ‘axis’
gisticChromPlot: no visible global function definition for ‘mtext’
gisticChromPlot: no visible global function definition for ‘segments’
gisticChromPlot: no visible global function definition for ‘rect’
gisticChromPlot: no visible global function definition for ‘text’
gisticChromPlot: no visible binding for global variable
  ‘Start_Position_updated’
gisticChromPlot: no visible binding for global variable
  ‘End_Position_updated’
gisticChromPlot: no visible global function definition for
  ‘complete.cases’
gisticChromPlot: no visible binding for global variable ‘Hugo_Symbol’
gisticChromPlot: no visible binding for global variable ‘G_Score’
gisticChromPlot: no visible binding for global variable ‘fdr’
gisticMap: no visible binding for global variable ‘Cytoband’
gisticMap: no visible binding for global variable
  ‘Variant_Classification’
gisticOncoPlot: no visible global function definition for ‘par’
gisticOncoPlot: no visible global function definition for ‘image’
gisticOncoPlot: no visible global function definition for ‘abline’
gisticOncoPlot: no visible global function definition for ‘mtext’
gisticOncoPlot: no visible global function definition for ‘text’
gisticOncoPlot: no visible global function definition for ‘legend’
gtMarkers: no visible global function definition for ‘download.file’
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 global function definition for
  ‘write.table’
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’
inferHeterogeneity: no visible global function definition for ‘median’
intersectMAF: no visible binding for global variable ‘Chromosome’
intersectMAF: no visible binding for global variable ‘Start_Position’
intersectMAF: no visible binding for global variable ‘End_Position’
intersectMAF: no visible global function definition for ‘.’
intersectMAF: no visible binding for global variable ‘Reference_Allele’
intersectMAF: no visible binding for global variable
  ‘Tumor_Seq_Allele2’
intersectMAF: no visible binding for global variable ‘variant_ID’
intersectMAF: no visible binding for global variable ‘maf_slot’
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 ‘domain_lenght’
lollipopPlot: no visible binding for global variable ‘End’
lollipopPlot: no visible binding for global variable ‘Start’
lollipopPlot: no visible binding for global variable ‘ID’
lollipopPlot: no visible binding for global variable ‘MutatedSamples’
lollipopPlot: no visible binding for global variable ‘conv’
lollipopPlot: no visible binding for global variable ‘count2’
lollipopPlot: no visible binding for global variable ‘count’
lollipopPlot: no visible binding for global variable ‘posRounded’
lollipopPlot: no visible binding for global variable ‘lab’
lollipopPlot: no visible binding for global variable ‘labThis’
lollipopPlot: no visible binding for global variable ‘pos2’
lollipopPlot: no visible binding for global variable ‘Label’
lollipopPlot: no visible global function definition for ‘par’
lollipopPlot: no visible global function definition for ‘rect’
lollipopPlot: no visible global function definition for ‘axis’
lollipopPlot: no visible global function definition for ‘segments’
lollipopPlot: no visible global function definition for ‘points’
lollipopPlot: no visible binding for global variable ‘domainCol’
lollipopPlot: no visible global function definition for ‘title’
lollipopPlot: no visible global function definition for ‘text’
lollipopPlot: no visible global function definition for ‘legend’
lollipopPlot2: no visible binding for global variable ‘Label’
lollipopPlot2: no visible binding for global variable
  ‘Variant_Classification’
lollipopPlot2: no visible global function definition for ‘par’
lollipopPlot2: no visible global function definition for ‘rect’
lollipopPlot2: no visible global function definition for ‘axis’
lollipopPlot2: no visible global function definition for ‘segments’
lollipopPlot2: no visible binding for global variable ‘pos2’
lollipopPlot2: no visible binding for global variable ‘count2’
lollipopPlot2: no visible global function definition for ‘points’
lollipopPlot2: no visible binding for global variable ‘domainCol’
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 global function definition for ‘text’
lollipopPlot2: no visible global function definition for ‘mtext’
lollipopPlot2: no visible binding for global variable ‘refseq.ID’
lollipopPlot2: no visible binding for global variable ‘conv’
lollipopPlot2: no visible global function definition for ‘legend’
mafCompare: no visible global function definition for ‘.’
mafCompare: no visible binding for global variable ‘Pathway’
mafCompare: no visible binding for global variable ‘Mutated_samples’
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 : <anonymous>: no visible global function definition for
  ‘fisher.test’
mafCompare: no visible binding for global variable ‘pval’
mafCompare: no visible binding for global variable ‘adjPval’
mafCompare: no visible global function definition for ‘p.adjust’
mafSurvGroup: no visible binding for global variable ‘Time’
mafSurvGroup: no visible global function definition for ‘.’
mafSurvGroup: no visible global function definition for ‘median’
mafSurvGroup: no visible binding for global variable ‘Group’
mafSurvGroup: no visible global function definition for ‘pchisq’
mafSurvGroup: no visible global function definition for ‘par’
mafSurvGroup: no visible global function definition for ‘abline’
mafSurvGroup: no visible global function definition for ‘points’
mafSurvGroup: no visible binding for global variable ‘survProb’
mafSurvGroup: no visible global function definition for ‘lines’
mafSurvGroup: no visible global function definition for ‘axis’
mafSurvGroup: no visible global function definition for ‘mtext’
mafSurvGroup: no visible global function definition for ‘legend’
mafSurvGroup: no visible global function definition for ‘title’
mafSurvival: no visible binding for global variable ‘Time’
mafSurvival: no visible global function definition for ‘.’
mafSurvival: no visible global function definition for ‘median’
mafSurvival: no visible binding for global variable ‘Group’
mafSurvival: no visible global function definition for ‘pchisq’
mafSurvival: no visible global function definition for ‘par’
mafSurvival: no visible global function definition for ‘abline’
mafSurvival: no visible global function definition for ‘points’
mafSurvival: no visible binding for global variable ‘survProb’
mafSurvival: no visible global function definition for ‘lines’
mafSurvival: no visible global function definition for ‘axis’
mafSurvival: no visible global function definition for ‘mtext’
mafSurvival: no visible global function definition for ‘legend’
mafSurvival: no visible global function definition for ‘title’
mafbarplot: no visible binding for global variable ‘ID’
mafbarplot: no visible global function definition for ‘.’
mafbarplot: no visible binding for global variable ‘Hugo_Symbol’
mafbarplot: no visible binding for global variable ‘AlteredSamples’
mafbarplot: no visible global function definition for ‘par’
mafbarplot: no visible global function definition for ‘barplot’
mafbarplot: no visible global function definition for ‘axis’
mafbarplot: no visible global function definition for ‘text’
mafbarplot: no visible global function definition for ‘abline’
mafbarplot: no visible global function definition for ‘mtext’
mafbarplot: no visible global function definition for ‘legend’
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_ref_count’
math.score: no visible binding for global variable ‘t_alt_count’
math.score: no visible binding for global variable ‘t_vaf’
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’
math.score : <anonymous>: no visible global function definition for
  ‘median’
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 global function definition for ‘read.csv’
oncodrive: no visible global function definition for ‘sd’
oncodrive: no visible binding for global variable ‘Hugo_Symbol’
oncodrive: no visible global function definition for ‘pnorm’
oncodrive: no visible global function definition for ‘p.adjust’
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 global function definition for ‘glm’
oncodrive: no visible global function definition for ‘poisson’
oncodrive : <anonymous>: no visible global function definition for
  ‘poisson.test’
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 ‘Gene’
oncoplot: no visible global function definition for ‘.’
oncoplot: no visible binding for global variable ‘Pathway’
oncoplot: no visible binding for global variable ‘AlteredSamples’
oncoplot: no visible binding for global variable ‘Hugo_Symbol’
oncoplot: no visible binding for global variable ‘MutatedSamples’
oncoplot: no visible binding for global variable ‘fractMutated’
oncoplot: no visible binding for global variable ‘mutload’
oncoplot: no visible binding for global variable ‘Tumor_Sample_Barcode’
oncoplot: no visible binding for global variable ‘total’
oncoplot: no visible binding for global variable
  ‘Variant_Classification_temp’
oncoplot: no visible binding for global variable
  ‘Variant_Classification’
oncoplot: no visible binding for global variable ‘value’
oncoplot: no visible binding for global variable ‘CNV_total’
oncoplot: no visible binding for global variable ‘Amp’
oncoplot: no visible binding for global variable ‘Del’
oncoplot: no visible binding for global variable ‘max_alt’
oncoplot: no visible binding for global variable ‘n’
oncoplot : <anonymous>: no visible binding for global variable
  ‘pct_alt’
oncoplot: no visible global function definition for ‘par’
oncoplot: no visible global function definition for ‘axis’
oncoplot: no visible global function definition for ‘rect’
oncoplot: no visible global function definition for ‘mtext’
oncoplot: no visible global function definition for ‘title’
oncoplot: no visible global function definition for ‘image’
oncoplot: no visible global function definition for ‘write.table’
oncoplot: no visible global function definition for ‘abline’
oncoplot: no visible binding for global variable ‘row_id’
oncoplot : <anonymous>: no visible global function definition for
  ‘rect’
oncoplot: no visible binding for global variable ‘temp_af’
oncoplot : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
oncoplot: no visible global function definition for ‘box’
oncoplot: no visible global function definition for ‘text’
oncoplot: no visible global function definition for ‘plot.new’
oncoplot: no visible global function definition for ‘legend’
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 global function definition for ‘txtProgressBar’
parse_prot: no visible binding for global variable ‘th’
parse_prot: no visible global function definition for
  ‘setTxtProgressBar’
pathway_load: no visible binding for global variable ‘Gene’
pathway_load: no visible global function definition for ‘.’
pathway_load: no visible binding for global variable ‘Pathway’
pathway_load: no visible binding for global variable
  ‘fraction_affected’
pathway_load: no visible binding for global variable ‘n_affected_genes’
pathway_load: no visible binding for global variable ‘N’
pathway_load: no visible binding for global variable ‘ID’
pathway_load: no visible binding for global variable
  ‘Fraction_mutated_samples’
pathway_load: no visible binding for global variable ‘Mutated_samples’
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 global function definition for ‘complete.cases’
pfamDomains: no visible binding for global variable ‘nMuts’
pfamDomains: no visible global function definition for ‘write.table’
pfamDomains: no visible global function definition for ‘par’
pfamDomains: no visible global function definition for ‘mtext’
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 ‘title’
plotApobecDiff: no visible binding for global variable ‘variable’
plotApobecDiff: no visible binding for global variable ‘value’
plotApobecDiff: no visible global function definition for ‘par’
plotApobecDiff: no visible binding for global variable ‘n_mutations’
plotApobecDiff: no visible global function definition for ‘boxplot’
plotApobecDiff: no visible global function definition for ‘title’
plotApobecDiff: no visible global function definition for ‘axis’
plotApobecDiff: no visible global function definition for ‘na.omit’
plotApobecDiff: no visible binding for global variable ‘N’
plotApobecDiff: no visible global function definition for ‘mtext’
plotApobecDiff: no visible global function definition for ‘wilcox.test’
plotApobecDiff: no visible global function definition for ‘text’
plotApobecDiff: no visible global function definition for ‘segments’
plotApobecDiff: no visible global function definition for ‘pie’
plotApobecDiff: no visible global function definition for ‘symbols’
plotApobecDiff: no visible global function definition for ‘barplot’
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 global function definition for ‘par’
plotCBS: no visible global function definition for ‘axis’
plotCBS: no visible global function definition for ‘abline’
plotCBS: no visible global function definition for ‘rect’
plotCBS: no visible global function definition for ‘title’
plotCBS: no visible global function definition for ‘mtext’
plotCBSchr: no visible binding for global variable ‘Sample’
plotCBSchr: no visible binding for global variable ‘Chromosome’
plotCBSsegments: no visible binding for global variable ‘Chromosome’
plotCBSsegments: no visible binding for global variable
  ‘Start_Position’
plotCBSsegments: no visible binding for global variable ‘End_Position’
plotCBSsegments: no visible binding for global variable ‘Sample’
plotCBSsegments: no visible global function definition for
  ‘write.table’
plotCBSsegments: no visible global function definition for ‘.’
plotCBSsegments: no visible binding for global variable ‘Hugo_Symbol’
plotCBSsegments: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
plotCBSsegments: no visible binding for global variable ‘Segment_Start’
plotCBSsegments: no visible binding for global variable ‘Segment_End’
plotCBSsegments: no visible binding for global variable ‘Segment_Mean’
plotCBSsegments: no visible binding for global variable ‘CN’
plotCBSsegments: no visible global function definition for ‘text’
plotCBSsegments: no visible global function definition for ‘segments’
plotClusters: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
plotClusters: no visible global function definition for ‘par’
plotClusters: no visible global function definition for ‘boxplot’
plotClusters: no visible binding for global variable ‘t_vaf’
plotClusters: no visible global function definition for ‘density’
plotClusters: no visible global function definition for ‘lines’
plotClusters: no visible global function definition for ‘abline’
plotClusters: no visible global function definition for ‘axis’
plotClusters: no visible global function definition for ‘points’
plotClusters: no visible global function definition for ‘title’
plotClusters: no visible binding for global variable ‘MATH’
plotClusters: no visible global function definition for ‘segments’
plotClusters: no visible global function definition for ‘text’
plotClusters: no visible binding for global variable ‘Hugo_Symbol’
plotClusters: no visible global function definition for ‘legend’
plotClusters: no visible global function definition for ‘mtext’
plotCophenetic: no visible global function definition for ‘par’
plotCophenetic: no visible global function definition for ‘axis’
plotCophenetic: no visible global function definition for ‘lines’
plotCophenetic: no visible global function definition for ‘points’
plotCophenetic: no visible global function definition for ‘segments’
plotCophenetic: no visible binding for global variable ‘cophenetic’
plotCophenetic: no visible global function definition for ‘title’
plotEnrichmentResults: no visible binding for global variable ‘P_value’
plotEnrichmentResults: no visible binding for global variable ‘OR’
plotEnrichmentResults: no visible binding for global variable ‘Group1’
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 : add_legend: no visible global function
  definition for ‘par’
plotEnrichmentResults : add_legend: no visible global function
  definition for ‘legend’
plotEnrichmentResults: no visible global function definition for ‘par’
plotEnrichmentResults: no visible global function definition for
  ‘barplot’
plotEnrichmentResults: no visible global function definition for ‘axis’
plotEnrichmentResults: no visible global function definition for
  ‘segments’
plotEnrichmentResults: no visible global function definition for ‘text’
plotEnrichmentResults: no visible global function definition for
  ‘legend’
plotEnrichmentResults: no visible global function definition for
  ‘title’
plotMosdepth : <anonymous>: no visible binding for global variable
  ‘chr’
plotMosdepth : <anonymous>: no visible binding for global variable
  ‘Chromosome’
plotMosdepth: no visible binding for global variable ‘Chromosome’
plotMosdepth: no visible binding for global variable ‘Start_Position’
plotMosdepth: no visible binding for global variable ‘End_Position’
plotMosdepth: no visible global function definition for ‘.’
plotMosdepth: no visible binding for global variable ‘logR’
plotMosdepth: no visible binding for global variable ‘doc_t’
plotMosdepth: no visible binding for global variable ‘doc_n’
plotMosdepth: no visible global function definition for ‘par’
plotMosdepth : <anonymous>: no visible global function definition for
  ‘points’
plotMosdepth : <anonymous>: no visible global function definition for
  ‘rect’
plotMosdepth: no visible global function definition for ‘abline’
plotMosdepth: no visible global function definition for ‘axis’
plotMosdepth: no visible global function definition for ‘mtext’
plotMosdepth: no visible global function definition for ‘title’
plotMosdepth_t: no visible binding for global variable ‘chr’
plotMosdepth_t: no visible binding for global variable ‘start’
plotMosdepth_t: no visible global function definition for ‘median’
plotMosdepth_t: no visible binding for global variable ‘doc’
plotMosdepth_t: no visible binding for global variable ‘End_Position’
plotMosdepth_t: no visible global function definition for ‘.’
plotMosdepth_t: no visible binding for global variable ‘Chromosome’
plotMosdepth_t: no visible binding for global variable ‘doc_norm’
plotMosdepth_t: no visible binding for global variable ‘Start_Position’
plotMosdepth_t: no visible global function definition for ‘par’
plotMosdepth_t : <anonymous>: no visible global function definition for
  ‘points’
plotMosdepth_t : <anonymous>: no visible global function definition for
  ‘rect’
plotMosdepth_t : <anonymous>: no visible binding for global variable
  ‘Start_Position_updated’
plotMosdepth_t : <anonymous>: no visible binding for global variable
  ‘End_Position_updated’
plotMosdepth_t: no visible global function definition for ‘abline’
plotMosdepth_t: no visible global function definition for ‘axis’
plotMosdepth_t: no visible global function definition for ‘title’
plotOncodrive: no visible binding for global variable ‘log_fdr’
plotOncodrive: no visible binding for global variable ‘fdr’
plotOncodrive: no visible global function definition for ‘par’
plotOncodrive: no visible binding for global variable ‘significant’
plotOncodrive: no visible global function definition for ‘mtext’
plotProtein: no visible binding for global variable ‘HGNC’
plotProtein: no visible binding for global variable ‘refseq.ID’
plotProtein: no visible binding for global variable ‘protein.ID’
plotProtein: no visible global function definition for ‘.’
plotProtein: no visible binding for global variable ‘aa.length’
plotProtein: no visible binding for global variable ‘domain_lenght’
plotProtein: no visible binding for global variable ‘End’
plotProtein: no visible binding for global variable ‘Start’
plotProtein: no visible binding for global variable ‘Label’
plotProtein: no visible global function definition for ‘par’
plotProtein: no visible global function definition for ‘rect’
plotProtein: no visible binding for global variable ‘domainCol’
plotProtein: no visible global function definition for ‘text’
plotProtein: no visible global function definition for ‘title’
plotProtein: no visible global function definition for ‘legend’
plotSignatures: no visible global function definition for ‘par’
plotSignatures: no visible global function definition for ‘barplot’
plotSignatures: no visible global function definition for ‘axis’
plotSignatures: no visible global function definition for ‘mtext’
plotSignatures: no visible global function definition for ‘plot.new’
plotSignatures: no visible global function definition for ‘legend’
plotSignatures: no visible global function definition for ‘title’
plotSignatures: no visible global function definition for ‘rect’
plotSignatures: no visible global function definition for ‘text’
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’
plotTiTv: no visible global function definition for ‘par’
plotTiTv: no visible global function definition for ‘barplot’
plotTiTv: no visible global function definition for ‘axis’
plotTiTv: no visible global function definition for ‘mtext’
plotTiTv: no visible global function definition for ‘boxplot’
plotTiTv: no visible global function definition for ‘abline’
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 global function definition for ‘median’
plotVaf: no visible binding for global variable ‘V1’
plotVaf: no visible global function definition for ‘par’
plotVaf: no visible global function definition for ‘boxplot’
plotVaf: no visible global function definition for ‘axis’
plotVaf: no visible global function definition for ‘abline’
plotVaf: no visible global function definition for ‘stripchart’
plotmafSummary: no visible binding for global variable ‘statFontSize’
plotmafSummary: no visible global function definition for ‘par’
plotmafSummary: no visible global function definition for ‘barplot’
plotmafSummary: no visible global function definition for ‘axis’
plotmafSummary: no visible global function definition for ‘title’
plotmafSummary: no visible binding for global variable ‘Mean’
plotmafSummary: no visible binding for global variable ‘Median’
plotmafSummary: no visible global function definition for ‘lines’
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 global function definition for ‘boxplot’
plotmafSummary: no visible binding for global variable ‘boxStat’
plotmafSummary: no visible global function definition for ‘plot.new’
plotmafSummary: no visible global function definition for ‘legend’
prepAscat : <anonymous>: no visible binding for global variable ‘loci’
prepAscat : <anonymous>: no visible binding for global variable
  ‘tot_depth’
prepAscat : <anonymous>: no visible global function definition for ‘.’
prepAscat : <anonymous>: no visible binding for global variable ‘A’
prepAscat : <anonymous>: no visible binding for global variable ‘G’
prepAscat : <anonymous>: no visible binding for global variable ‘C’
prepAscat : <anonymous>: no visible binding for global variable ‘baf’
prepAscat : <anonymous>: no visible global function definition for
  ‘runif’
prepAscat_t : <anonymous>: no visible binding for global variable
  ‘loci’
prepAscat_t : <anonymous>: no visible binding for global variable
  ‘tot_depth’
prepAscat_t : <anonymous>: no visible global function definition for
  ‘.’
prepAscat_t : <anonymous>: no visible binding for global variable ‘A’
prepAscat_t : <anonymous>: no visible binding for global variable ‘G’
prepAscat_t : <anonymous>: no visible binding for global variable ‘C’
prepAscat_t : <anonymous>: no visible binding for global variable ‘baf’
prepAscat_t : <anonymous>: no visible global function definition for
  ‘runif’
prepAscat_t: no visible global function definition for ‘median’
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’
prepareMutSig: no visible global function definition for ‘write.table’
print_mat: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
print_mat: no visible global function definition for ‘par’
print_mat: no visible global function definition for ‘image’
print_mat: no visible global function definition for ‘rect’
print_mat : <anonymous>: no visible binding for global variable
  ‘temp_af’
print_mat : <anonymous> : <anonymous> : <anonymous>: no visible global
  function definition for ‘points’
print_mat: no visible global function definition for ‘abline’
print_mat: no visible global function definition for ‘mtext’
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 global function definition for
  ‘complete.cases’
rainfallPlot: no visible global function definition for ‘par’
rainfallPlot: no visible global function definition for ‘segments’
rainfallPlot: no visible global function definition for ‘points’
rainfallPlot: no visible global function definition for ‘axis’
rainfallPlot: no visible global function definition for ‘mtext’
rainfallPlot: no visible global function definition for ‘arrows’
rainfallPlot: no visible global function definition for ‘title’
rainfallPlot: no visible global function definition for ‘legend’
rainfallPlot: no visible global function definition for ‘dev.copy’
read.maf: no visible binding for global variable ‘Mutation_Status’
read.maf: no visible binding for global variable ‘Hugo_Symbol’
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 ‘Unique_Name’
read.maf: no visible binding for global variable ‘Wide_Peak_Limits’
read.maf: no visible binding for global variable ‘id’
readGistic: no visible binding for global variable ‘Unique_Name’
readGistic: no visible binding for global variable ‘Wide_Peak_Limits’
readGistic: no visible binding for global variable ‘cytoband’
readGistic: no visible binding for global variable ‘value’
readGistic: no visible global function definition for ‘.’
readGistic: no visible binding for global variable ‘variable’
readGistic : <anonymous>: no visible binding for global variable
  ‘variable’
readGistic : <anonymous>: no visible binding for global variable
  ‘cytoband’
readGistic : <anonymous>: no visible binding for global variable
  ‘TumorSampleBarcode’
readGistic: no visible binding for global variable ‘CN’
readGistic: no visible binding for global variable ‘TumorSampleBarcode’
readGistic: no visible binding for global variable ‘Variant_Type’
readGistic: no visible binding for global variable ‘Cytoband’
readGistic: no visible binding for global variable ‘peakID’
readGistic: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
readGistic: no visible binding for global variable ‘qvalues’
readSegs: no visible binding for global variable ‘Chromosome’
readSegs: no visible binding for global variable ‘Start_Position’
readSegs: no visible binding for global variable ‘End_Position’
refineClusters: no visible binding for global variable ‘t_vaf’
repelPoints: no visible binding for global variable ‘pos’
repelPoints: no visible binding for global variable ‘distance’
repelPoints: no visible global function definition for ‘.’
run_surv: no visible binding for global variable ‘Group’
run_surv: no visible global function definition for ‘pchisq’
run_surv: no visible global function definition for ‘par’
run_surv: no visible global function definition for ‘abline’
run_surv: no visible global function definition for ‘points’
run_surv: no visible binding for global variable ‘Time’
run_surv: no visible binding for global variable ‘survProb’
run_surv: no visible global function definition for ‘lines’
run_surv: no visible global function definition for ‘axis’
run_surv: no visible global function definition for ‘mtext’
run_surv: no visible global function definition for ‘legend’
run_surv: no visible global function definition for ‘title’
sampleSwaps: no visible binding for global variable ‘id’
sampleSwaps: no visible binding for global variable ‘chr’
sampleSwaps: no visible binding for global variable ‘start’
sampleSwaps : <anonymous>: no visible global function definition for
  ‘.’
sampleSwaps : <anonymous>: no visible binding for global variable ‘id’
sampleSwaps : <anonymous>: no visible binding for global variable ‘ref’
sampleSwaps : <anonymous>: no visible binding for global variable ‘alt’
sampleSwaps : <anonymous> : <anonymous>: no visible binding for global
  variable ‘vaf’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘loci’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘ref_rc’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘alt_rc’
sampleSwaps : <anonymous>: no visible binding for global variable ‘vaf’
sampleSwaps: no visible binding for global variable ‘vaf’
sampleSwaps: no visible binding for global variable ‘total’
sampleSwaps: no visible binding for global variable ‘ref_rc’
sampleSwaps: no visible binding for global variable ‘alt_rc’
sampleSwaps: no visible global function definition for ‘complete.cases’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for ‘fisher.test’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable ‘ref_rc’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
  binding for global variable ‘alt_rc’
sampleSwaps : <anonymous> : <anonymous>: no visible global function
  definition for ‘cor.test’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘XY_possibly_paired’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘fract_concordant_snps’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘cor_coef’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘X_bam’
sampleSwaps : <anonymous>: no visible binding for global variable
  ‘Y_bam’
sampleSwaps: no visible binding for global variable
  ‘XY_possibly_paired’
segmentLogR: no visible binding for global variable ‘contig’
segmentLogR: no visible binding for global variable ‘logR’
segmentLogR: no visible binding for global variable ‘pos’
segmentLogR: no visible global function definition for ‘write.table’
segmentLogR: no visible global function definition for ‘png’
setdiffMAF: no visible binding for global variable ‘Chromosome’
setdiffMAF: no visible binding for global variable ‘Start_Position’
setdiffMAF: no visible binding for global variable ‘End_Position’
setdiffMAF: no visible global function definition for ‘.’
setdiffMAF: no visible binding for global variable ‘Reference_Allele’
setdiffMAF: no visible binding for global variable ‘Tumor_Seq_Allele2’
setdiffMAF: no visible binding for global variable ‘variant_ID’
setdiffMAF: no visible binding for global variable ‘maf_slot’
shiftPoints: no visible binding for global variable ‘pos’
signatureEnrichment: no visible global function definition for ‘kmeans’
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 ‘sd’
signatureEnrichment : <anonymous>: no visible binding for global
  variable ‘N’
signatureEnrichment : add_legend: no visible global function definition
  for ‘par’
signatureEnrichment : add_legend: no visible global function definition
  for ‘legend’
signatureEnrichment: no visible global function definition for ‘par’
signatureEnrichment: no visible global function definition for
  ‘barplot’
signatureEnrichment: no visible global function definition for
  ‘segments’
signatureEnrichment: no visible global function definition for ‘axis’
signatureEnrichment: no visible global function definition for ‘mtext’
signatureEnrichment: no visible global function definition for ‘title’
signatureEnrichment: no visible global function definition for
  ‘boxplot’
signatureEnrichment: no visible global function definition for ‘.’
signatureEnrichment: no visible global function definition for ‘median’
signatureEnrichment: no visible binding for global variable ‘N’
signatureEnrichment: no visible global function definition for
  ‘write.table’
somaticInteractions: no visible binding for global variable
  ‘Hugo_Symbol’
somaticInteractions: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
somaticInteractions : <anonymous> : <anonymous>: no visible global
  function definition for ‘fisher.test’
somaticInteractions: no visible binding for global variable ‘pAdj’
somaticInteractions: no visible global function definition for
  ‘p.adjust’
somaticInteractions: no visible binding for global variable ‘pValue’
somaticInteractions: no visible global function definition for ‘.’
somaticInteractions: no visible binding for global variable ‘gene1’
somaticInteractions: no visible binding for global variable ‘gene2’
somaticInteractions: no visible binding for global variable
  ‘event_ratio’
somaticInteractions: no visible binding for global variable ‘01’
somaticInteractions: no visible binding for global variable ‘10’
somaticInteractions: no visible binding for global variable ‘11’
somaticInteractions: no visible binding for global variable ‘pair’
somaticInteractions: no visible binding for global variable
  ‘AlteredSamples’
somaticInteractions: no visible global function definition for ‘par’
somaticInteractions: no visible global function definition for ‘image’
somaticInteractions: no visible global function definition for ‘abline’
somaticInteractions: no visible global function definition for ‘mtext’
somaticInteractions: no visible binding for global variable ‘Event’
somaticInteractions: no visible global function definition for ‘text’
somaticInteractions: no visible global function definition for ‘points’
somaticInteractions: no visible global function definition for ‘axis’
sortByMutation: no visible binding for global variable ‘MutatedSamples’
sortByMutation: no visible binding for global variable ‘Hugo_Symbol’
subsetMaf: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
subsetMaf: no visible binding for global variable ‘Variant_Type’
subsetMaf: no visible binding for global variable ‘Hugo_Symbol’
subsetMaf: no visible binding for global variable ‘Chromosome’
subsetMaf: no visible binding for global variable ‘Start_Position’
subsetMaf: no visible binding for global variable ‘End_Position’
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 ‘median’
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 ‘median’
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’
survGroup: no visible binding for global variable ‘Hugo_Symbol’
survGroup: no visible global function definition for ‘combn’
survGroup: no visible binding for global variable ‘Time’
survGroup: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
survGroup: no visible binding for global variable ‘P_value’
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 : <anonymous>: no visible global function definition for
  ‘.’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘Tumor_Sample_Barcode’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘total’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘cohort’
tcgaCompare: no visible global function definition for
  ‘pairwise.t.test’
tcgaCompare: no visible binding for global variable ‘plot_total’
tcgaCompare: no visible binding for global variable ‘total_perMB’
tcgaCompare: no visible global function definition for ‘median’
tcgaCompare: no visible binding for global variable ‘V2’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘plot_total’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘TCGA’
tcgaCompare: no visible global function definition for ‘rect’
tcgaCompare: no visible global function definition for ‘par’
tcgaCompare: no visible global function definition for ‘abline’
tcgaCompare : <anonymous>: no visible binding for global variable ‘V3’
tcgaCompare : <anonymous>: no visible global function definition for
  ‘points’
tcgaCompare: no visible global function definition for ‘axis’
tcgaCompare: no visible binding for global variable
  ‘Median_Mutations_log10’
tcgaCompare: no visible binding for global variable ‘Median_Mutations’
tcgaCompare: no visible global function definition for ‘mtext’
tcgaCompare : <anonymous>: no visible global function definition for
  ‘segments’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘Median_Mutations_log10’
tcgaCompare : <anonymous>: no visible binding for global variable
  ‘Median_Mutations’
tcgaCompare: no visible binding for global variable ‘TCGA’
tcgaCompare: no visible binding for global variable ‘Pval’
tcgaDriverBP: no visible binding for global variable ‘Hugo_Symbol’
tcgaDriverBP: no visible global function definition for ‘.’
tcgaDriverBP: no visible binding for global variable ‘AlteredSamples’
tcgaDriverBP: no visible global function definition for ‘par’
tcgaDriverBP: no visible global function definition for ‘image’
tcgaDriverBP: no visible global function definition for ‘abline’
tcgaDriverBP: no visible global function definition for ‘points’
tcgaDriverBP: no visible global function definition for ‘mtext’
tcgaDriverBP: no visible global function definition for ‘text’
tcgaDriverBP: no visible global function definition for ‘title’
tcgaDriverBP : <anonymous>: no visible binding for global variable
  ‘Gene’
tcgaDriverBP: no visible binding for global variable ‘Cancer_type’
tcgaDriverBP: no visible binding for global variable ‘Pathway’
tcgaDriverBP: no visible binding for global variable ‘ID’
tcgaDriverBP: no visible binding for global variable ‘pctAltered’
tcgaDriverBP: no visible binding for global variable ‘tcga_driver’
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 ‘con’
titv: no visible global function definition for ‘.’
titv: no visible binding for global variable ‘Tumor_Sample_Barcode’
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’
titv: no visible global function definition for ‘write.table’
tmb: no visible global function definition for ‘.’
tmb: no visible binding for global variable ‘Tumor_Sample_Barcode’
tmb: no visible binding for global variable ‘total’
tmb: no visible binding for global variable ‘total_perMB’
tmb: no visible binding for global variable ‘total_perMB_log’
tmb: no visible global function definition for ‘median’
tmb: no visible global function definition for ‘par’
tmb: no visible global function definition for ‘abline’
tmb: no visible global function definition for ‘points’
tmb: no visible global function definition for ‘title’
tmb: no visible global function definition for ‘axis’
tmb: no visible global function definition for ‘mtext’
transformSegments: no visible binding for global variable
  ‘Start_Position’
transformSegments: no visible binding for global variable
  ‘End_Position’
transformSegments: no visible binding for global variable ‘Chromosome’
trinucleotideMatrix: no visible binding for global variable ‘pkgname’
trinucleotideMatrix: no visible binding for global variable
  ‘Chromosome’
trinucleotideMatrix: no visible binding for global variable
  ‘Start_Position’
trinucleotideMatrix: no visible binding for global variable
  ‘End_Position’
trinucleotideMatrix: no visible binding for global variable ‘N’
trinucleotideMatrix: no visible binding for global variable ‘Start’
trinucleotideMatrix: no visible binding for global variable ‘End’
trinucleotideMatrix: no visible binding for global variable ‘upstream’
trinucleotideMatrix: no visible binding for global variable
  ‘downstream’
trinucleotideMatrix: no visible global function definition for ‘.’
trinucleotideMatrix: no visible binding for global variable ‘A’
trinucleotideMatrix: no visible binding for global variable ‘C’
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 : <anonymous>: no visible global function
  definition for ‘fisher.test’
trinucleotideMatrix: no visible binding for global variable
  ‘fisher_pvalue’
trinucleotideMatrix: no visible binding for global variable ‘fdr’
trinucleotideMatrix: no visible global function definition for
  ‘p.adjust’
trinucleotideMatrix: no visible binding for global variable
  ‘APOBEC_Enriched’
trinucleotideMatrix: no visible binding for global variable
  ‘SubstitutionTypeMotif’
trinucleotideMatrix: no visible global function definition for
  ‘write.table’
vafCompare: no visible binding for global variable ‘Hugo_Symbol’
vafCompare: no visible binding for global variable ‘t_vaf’
vafCompare: no visible binding for global variable ‘t_alt_count’
vafCompare: no visible binding for global variable ‘t_ref_count’
vafCompare: no visible global function definition for ‘.’
vafCompare: no visible binding for global variable ‘Cohort’
vafCompare: no visible global function definition for ‘layout’
vafCompare: no visible global function definition for ‘par’
vafCompare: no visible global function definition for ‘boxplot’
vafCompare: no visible global function definition for ‘stripchart’
vafCompare: no visible global function definition for ‘axis’
vafCompare: no visible global function definition for ‘title’
vafCompare: no visible global function definition for ‘abline’
vafCompare: no visible global function definition for ‘t.test’
vafCompare: no visible global function definition for ‘text’
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 ‘Reference_Allele’
validateMaf: no visible binding for global variable ‘Tumor_Seq_Allele2’
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’
validateMaf: no visible binding for global variable ‘End_Position’
write.GisticSummary: no visible global function definition for
  ‘write.table’
write.mafSummary: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  . 01 10 11 A A>C A>G A>T AAChange AAChange_ AGA APOBEC_Enriched
  APOBEC_Enrichment A[G>A]A A[G>C]A A[G>T]A Alt AlteredSamples Amp
  Analysis C C>A C>G C>T CN CNV CNV_total Cancer_type Chromosome
  Cluster Cohort Cytoband Del Description DomainLabel End End_Position
  End_Position_updated Entrez Entrez_Gene_Id Event ExonicFunc.refGene
  Feature_1 Feature_2 Fraction_mutated_samples Freq Func.refGene G G>A
  G>C G>T G_Score Gene Gene.refGene Genotype Group Group1 Group2 HGNC
  Hugo_Symbol ID Ins Label MATH Mean Median Median_Mutations
  Median_Mutations_log10 MutSig_Synonym MutatedSamples MutatedSamples.x
  MutatedSamples.y Mutated_samples Mutation_Status N N.x N.y
  OG_Hugo_Symbol OR OR_high OR_low P_value Pathway Pval Ref
  Reference_Allele Sample SampleSize Segment_End Segment_Mean
  Segment_Start Signature Size Start Start_Position
  Start_Position_updated Substitution SubstitutionMotif
  SubstitutionType SubstitutionTypeMotif T>A T>C T>G TCA TCGA TCT TGA
  T[C>A]A T[C>A]T T[C>G]A T[C>G]T T[C>T]A T[C>T]T T[G>A]A T[G>C]A
  T[G>T]A TiTv Time TumorSampleBarcode Tumor_Sample_Barcode
  Tumor_Seq_Allele2 Unique_Name V1 V2 V3 VAF Var1 Var2
  Variant_Classification Variant_Classification_temp Variant_Type
  Wide_Peak_Limits XY_possibly_paired X_bam Y_bam aa.length abline
  adjPval alt alt_rc amp arrows assembly_version axis baf barplot bg
  box boxStat boxplot browseURL category cf chr chromosome
  chromosome_end chromosome_start ci.low ci.up cohort colorRampPalette
  combn complete.cases con con.class consequence_type contig conv
  cophenetic cor.test cor_coef count count2 cytoband dbinom density
  dev.copy distance doc doc_n doc_norm doc_t domainCol domain_lenght
  download.file downstream dp endDist ens_id event_ratio fdr
  fisher.test fisher_pvalue fract fractMutated fract_concordant_snps
  fract_muts_in_clusters fraction fraction_APOBEC_mutations
  fraction_affected fs g1_muts g1_title g1_tot g2_muts g2_title g2_tot
  gene1 gene2 gene_affected glm heat.colors hgnc_symbol i.End_Position
  i.Start_Position icgc_sample_id id idx image kmeans lab labThis label
  layout legend lines loc loci logR log_fdr log_q lower maf_slot
  max_alt median mtext mutated_from_allele mutated_to_allele mutload
  muts_in_clusters n nGenes nMut nMuts nVars n_A n_C n_C>G_and_C>T n_G
  n_T n_affected_genes n_mutated_Feature n_mutated_Feature1
  n_mutated_Feature2 n_mutated_group1 n_mutated_group2 n_mutations
  na.omit nonApobec non_APOBEC_mutations or or_new p.adjust pAdj pValue
  p_value pair pairwise.t.test pairwise.table par pchisq pctAltered
  pct_alt peakID pfam pie pkgname plot.new plot_total png pnorm points
  poisson poisson.test poissonFdr pos pos2 posRounded protein.ID pval
  qf qnorm qvalues read.csv rect ref ref_alt_diff ref_rc
  reference_genome_allele refseq.ID row_id row_idx runif sd segments
  sequencing_strategy setTxtProgressBar significant site start
  startDist statFontSize stripchart survProb symbols t.test tCw
  tCw_to_A tCw_to_G tCw_to_G+tCw_to_T tCw_to_T tFdr t_alt_count t_depth
  t_ref_count t_vaf tcga_driver tcw temp_af text th title tot tot_depth
  total total_perMB total_perMB_log trinucleotide txtProgressBar unit
  updown upper upstream vaf value variable variantId variant_ID
  verification_platform verification_status wGa wGa_to_A wGa_to_C
  wGa_to_T wga wilcox.test write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.copy", "heat.colors",
             "png")
  importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
             "boxplot", "image", "layout", "legend", "lines", "mtext",
             "par", "pie", "plot.new", "points", "rect", "segments",
             "stripchart", "symbols", "text", "title")
  importFrom("stats", "C", "complete.cases", "cophenetic", "cor.test",
             "dbinom", "density", "fisher.test", "glm", "kmeans",
             "median", "na.omit", "p.adjust", "pairwise.t.test",
             "pairwise.table", "pchisq", "pnorm", "poisson",
             "poisson.test", "qf", "qnorm", "runif", "sd", "start",
             "t.test", "wilcox.test")
  importFrom("utils", "browseURL", "combn", "download.file", "read.csv",
             "setTxtProgressBar", "txtProgressBar", "write.table")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/maftools/libs/maftools.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
maf2mae 16.254  0.395  25.233
* 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 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/maftools.Rcheck/00check.log’
for details.

Installation output

maftools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maftools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘maftools’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ntcounts.c -o ntcounts.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c snpcounts.c -o snpcounts.o
snpcounts.c:56:26: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  int nloci = countlines(bedfile);
                         ^~~~~~~
snpcounts.c:13:22: note: passing argument to parameter 'filename' here
int countlines(char *filename){
                     ^
snpcounts.c:56:7: warning: unused variable 'nloci' [-Wunused-variable]
  int nloci = countlines(bedfile);
      ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c somaticfreq.c -o somaticfreq.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o maftools.so ntcounts.o snpcounts.o somaticfreq.o /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-maftools/00new/maftools/libs
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maftools)

Tests output

Example timings

maftools.Rcheck/maftools-Ex.timings

nameusersystemelapsed
MAF0.2100.0280.374
OncogenicPathways0.8150.0431.200
PlotOncogenicPathways0.3340.0230.507
annovarToMaf0.1790.0200.304
clinicalEnrichment000
coBarplot0.3460.0220.560
coOncoplot0.3450.0210.561
drugInteractions0.5050.0350.829
estimateSignatures000
extractSignatures0.0000.0000.001
filterMaf0.8340.0291.251
forestPlot0.2880.0200.391
genesToBarcodes0.3620.0170.482
genotypeMatrix0.3660.0180.487
getClinicalData0.3390.0170.458
getCytobandSummary0.6340.0190.847
getFields0.3390.0170.446
getGeneSummary0.3510.0180.468
getSampleSummary0.3460.0200.471
gisticBubblePlot0.6340.0170.832
gisticChromPlot0.7330.0170.959
gisticOncoPlot0.7580.0210.996
icgcSimpleMutationToMAF0.0920.0130.129
inferHeterogeneity000
lollipopPlot0.8400.0391.223
lollipopPlot21.2160.0361.803
maf2mae16.254 0.39525.233
mafCompare0.2620.0220.434
mafSummary0.5950.0450.977
mafSurvGroup0.4430.0270.716
mafSurvival0.3590.0170.577
mafbarplot0.3300.0180.530
math.score0.3330.0190.536
mutCountMatrix0.5140.4901.526
oncodrive1.3500.0472.158
oncoplot1.0280.0301.633
oncostrip0.3320.0260.488
pfamDomains1.5030.0372.307
plotApobecDiff000
plotCBSsegments0.0360.0020.061
plotClusters000
plotOncodrive1.4070.0472.243
plotProtein0.9520.0171.466
plotTiTv0.4000.0200.647
plotVaf0.3690.0180.598
plotmafSummary0.4000.0190.639
prepareMutSig0.3980.0260.649
read.maf0.3110.0150.501
readGistic0.6050.0130.946
setMaf0.4500.0180.721
somaticInteractions0.5370.0220.843
subsetMaf0.6670.0271.047
survGroup0.6560.0251.030
tcgaAvailable0.0340.0190.387
tcgaCompare0.6470.0471.058
tcgaDriverBP0.7820.0331.246
tcgaLoad0.1070.0161.848
titv0.3700.0170.493
tmb0.3240.0170.499
trinucleotideMatrix000
write.GisticSummary0.7050.0251.110
write.mafSummary0.3320.0190.538