############################################################################## ############################################################################## ### ### 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_2.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/maftools.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘maftools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘maftools’ version ‘2.23.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘maftools’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... INFO installed size is 8.4Mb sub-directories of 1Mb or more: extdata 6.2Mb libs 1.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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’ .getAmpDelCounts: no visible binding for global variable ‘Variant_Classification’ .getdomains: no visible binding for global variable ‘HGNC’ .getdomains: no visible binding for global variable ‘refseq.ID’ .getdomains: no visible binding for global variable ‘protein.ID’ .getdomains: no visible global function definition for ‘.’ .getdomains: no visible binding for global variable ‘aa.length’ .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’ .seg2arm: no visible binding for global variable ‘Chromosome’ .seg2arm: no visible binding for global variable ‘Start’ .seg2arm: no visible binding for global variable ‘End’ .seg2arm: no visible global function definition for ‘median’ .seg2arm: no visible binding for global variable ‘Segment_Mean’ .seg2arm: no visible global function definition for ‘.’ .seg2arm: no visible binding for global variable ‘name’ .seg2arm: no visible binding for global variable ‘cn’ .seg2arm: no visible binding for global variable ‘logR’ .seg2arm: no visible binding for global variable ‘chromosome’ .seg2arm: no visible binding for global variable ‘arm’ 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 ‘ExonicFunc.refGene’ annovarToMaf: no visible binding for global variable ‘AAChange.refGene’ annovarToMaf: no visible binding for global variable ‘ref_alt_len’ annovarToMaf: no visible binding for global variable ‘Ref’ annovarToMaf: no visible binding for global variable ‘Alt’ annovarToMaf: no visible binding for global variable ‘ref_alt_diff’ annovarToMaf: no visible binding for global variable ‘Variant_Type’ annovarToMaf: no visible binding for global variable ‘ref_alt’ 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 : : no visible global function definition for ‘.’ cancerhotspotsAggr : : no visible binding for global variable ‘A’ cancerhotspotsAggr : : no visible binding for global variable ‘G’ cancerhotspotsAggr : : no visible binding for global variable ‘C’ cancerhotspotsAggr : : no visible binding for global variable ‘Ins’ cancerhotspotsAggr : : no visible binding for global variable ‘Del’ cancerhotspotsAggr : : no visible binding for global variable ‘t_depth’ cancerhotspotsAggr : : no visible binding for global variable ‘VAF’ cancerhotspotsAggr : : no visible binding for global variable ‘End_Position’ cancerhotspotsAggr : : 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 : : 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 : : : no visible global function definition for ‘fisher.test’ clinicalEnrichment : : : no visible binding for global variable ‘Group’ clinicalEnrichment : : : no visible binding for global variable ‘Genotype’ clinicalEnrichment : : no visible binding for global variable ‘Hugo_Symbol’ clinicalEnrichment : : no visible binding for global variable ‘Analysis’ clinicalEnrichment : : no visible global function definition for ‘.’ clinicalEnrichment : : no visible binding for global variable ‘Var1’ clinicalEnrichment : : no visible binding for global variable ‘Var2’ clinicalEnrichment : : no visible binding for global variable ‘value’ clinicalEnrichment : : no visible binding for global variable ‘fdr’ clinicalEnrichment : : no visible binding for global variable ‘cf’ clinicalEnrichment : : no visible binding for global variable ‘Genotype’ clinicalEnrichment : : no visible binding for global variable ‘N’ clinicalEnrichment : : no visible binding for global variable ‘n_mutated_Feature’ clinicalEnrichment : : no visible binding for global variable ‘N.x’ clinicalEnrichment : : no visible binding for global variable ‘N.y’ 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 ‘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 : : 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’ coGisticChromPlot: no visible binding for global variable ‘Chromosome’ coGisticChromPlot: no visible binding for global variable ‘loc’ coGisticChromPlot: no visible binding for global variable ‘Start_Position’ coGisticChromPlot: no visible binding for global variable ‘End_Position’ coGisticChromPlot: no visible global function definition for ‘.’ coGisticChromPlot: no visible binding for global variable ‘qvalues’ coGisticChromPlot: no visible binding for global variable ‘Cytoband’ coGisticChromPlot: no visible binding for global variable ‘Variant_Classification’ coGisticChromPlot: no visible binding for global variable ‘value’ coGisticChromPlot: no visible global function definition for ‘layout’ coGisticChromPlot: no visible global function definition for ‘par’ coGisticChromPlot: no visible global function definition for ‘text’ coGisticChromPlot: no visible global function definition for ‘segments’ coGisticChromPlot: no visible global function definition for ‘axis’ coGisticChromPlot: no visible global function definition for ‘mtext’ coGisticChromPlot: no visible global function definition for ‘rect’ coGisticChromPlot: no visible global function definition for ‘lines’ coGisticChromPlot: no visible global function definition for ‘head’ coGisticChromPlot: no visible binding for global variable ‘gistic’ coGisticChromPlot: no visible binding for global variable ‘Start_Position_updated’ coGisticChromPlot: no visible binding for global variable ‘End_Position_updated’ coGisticChromPlot: no visible binding for global variable ‘ystart’ coGisticChromPlot: no visible global function definition for ‘complete.cases’ coGisticChromPlot: no visible global function definition for ‘rug’ coGisticChromPlot: no visible binding for global variable ‘Hugo_Symbol’ coGisticChromPlot: no visible binding for global variable ‘VC’ coGisticChromPlot: no visible binding for global variable ‘G_Score’ coGisticChromPlot: no visible binding for global variable ‘anno_Position’ coOncoplot: no visible binding for global variable ‘Hugo_Symbol’ coOncoplot: no visible global function definition for ‘.’ coOncoplot: no visible binding for global variable ‘MutatedSamples’ coOncoplot: no visible binding for global variable ‘MutatedSamples_m1’ coOncoplot: no visible binding for global variable ‘MutatedSamples_m2’ 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 : : no visible global function definition for ‘points’ forestPlot : : 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 : : 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 ‘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_lp_data: no visible binding for global variable ‘Label’ 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_pw_summary: no visible global function definition for ‘.’ get_threshold : : 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’ gisticCompare: no visible binding for global variable ‘ID’ gisticCompare: no visible binding for global variable ‘Variant_Classification’ gisticCompare: no visible global function definition for ‘.’ gisticCompare: no visible binding for global variable ‘Cytoband’ gisticCompare: no visible binding for global variable ‘G1_wt’ gisticCompare: no visible binding for global variable ‘G1’ gisticCompare: no visible binding for global variable ‘G2_wt’ gisticCompare: no visible binding for global variable ‘G2’ gisticCompare : : no visible binding for global variable ‘G1’ gisticCompare : : no visible binding for global variable ‘G1_wt’ gisticCompare : : no visible binding for global variable ‘G2’ gisticCompare : : no visible binding for global variable ‘G2_wt’ gisticCompare : : no visible global function definition for ‘fisher.test’ gisticCompare: no visible binding for global variable ‘pval’ gisticCompare: no visible binding for global variable ‘adjPval’ gisticCompare: no visible global function definition for ‘p.adjust’ 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 ‘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 ‘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 ‘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 binding for global variable ‘refseq.ID’ 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 : : 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 : : no visible binding for global variable ‘Tumor_Sample_Barcode’ math.score : : 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 : : 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 global function definition for ‘.’ oncoplot: no visible binding for global variable ‘Pathway’ oncoplot: no visible binding for global variable ‘Gene’ oncoplot: no visible global function definition for ‘setNames’ 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 : : 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 ‘abline’ 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 binding for global variable ‘row_id’ oncoplot : : no visible global function definition for ‘rect’ oncoplot: no visible binding for global variable ‘temp_af’ oncoplot : : : 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 ‘colorRampPalette’ oncoplot: no visible global function definition for ‘plot.new’ oncoplot: no visible global function definition for ‘complete.cases’ 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’ pathways: no visible global function definition for ‘.’ pathways: no visible binding for global variable ‘Pathway’ pathways: no visible binding for global variable ‘Gene’ pathways: no visible binding for global variable ‘n_affected_genes’ pathways: no visible binding for global variable ‘Fraction_mutated_samples’ pathways : draw_rect: no visible global function definition for ‘rect’ pathways : draw_text: no visible global function definition for ‘text’ pathways : draw_text_sub: no visible global function definition for ‘text’ pathways: no visible binding for global variable ‘ID’ pathways: no visible global function definition for ‘layout’ pathways: no visible global function definition for ‘par’ pathways: no visible global function definition for ‘text’ pathways: no visible global function definition for ‘title’ pathways: no visible global function definition for ‘rect’ pathways: no visible global function definition for ‘axis’ 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 : : 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_muts’ plotEnrichmentResults : : 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 ‘title’ plotMosdepth : : no visible binding for global variable ‘chr’ plotMosdepth : : 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 : : no visible global function definition for ‘points’ plotMosdepth : : 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 : : no visible global function definition for ‘points’ plotMosdepth_t : : no visible global function definition for ‘rect’ plotMosdepth_t : : no visible binding for global variable ‘Start_Position_updated’ plotMosdepth_t : : 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’ plotPathways: no visible binding for global variable ‘Tumor_Sample_Barcode’ plotPathways: no visible global function definition for ‘par’ plotPathways: no visible global function definition for ‘image’ plotPathways: no visible global function definition for ‘abline’ plotPathways: no visible global function definition for ‘mtext’ plotPathways: no visible global function definition for ‘text’ 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 : : no visible binding for global variable ‘loci’ prepAscat : : no visible binding for global variable ‘tot_depth’ prepAscat : : no visible global function definition for ‘.’ prepAscat : : no visible binding for global variable ‘A’ prepAscat : : no visible binding for global variable ‘G’ prepAscat : : no visible binding for global variable ‘C’ prepAscat : : no visible binding for global variable ‘baf’ prepAscat : : no visible global function definition for ‘runif’ prepAscat_t : : no visible binding for global variable ‘loci’ prepAscat_t : : no visible binding for global variable ‘tot_depth’ prepAscat_t : : no visible global function definition for ‘.’ prepAscat_t : : no visible binding for global variable ‘A’ prepAscat_t : : no visible binding for global variable ‘G’ prepAscat_t : : no visible binding for global variable ‘C’ prepAscat_t : : no visible binding for global variable ‘baf’ prepAscat_t : : 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 : : no visible binding for global variable ‘temp_af’ print_mat : : : : 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 : : no visible binding for global variable ‘variable’ readGistic : : no visible binding for global variable ‘cytoband’ readGistic : : 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 : : no visible global function definition for ‘.’ sampleSwaps : : no visible binding for global variable ‘id’ sampleSwaps : : no visible binding for global variable ‘ref’ sampleSwaps : : no visible binding for global variable ‘alt’ sampleSwaps : : : no visible binding for global variable ‘vaf’ sampleSwaps : : no visible binding for global variable ‘loci’ sampleSwaps : : no visible binding for global variable ‘ref_rc’ sampleSwaps : : no visible binding for global variable ‘alt_rc’ sampleSwaps : : 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 : : : : no visible global function definition for ‘fisher.test’ 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 ‘cor.test’ sampleSwaps : : no visible binding for global variable ‘XY_possibly_paired’ sampleSwaps : : no visible binding for global variable ‘fract_concordant_snps’ sampleSwaps : : no visible binding for global variable ‘cor_coef’ sampleSwaps : : no visible binding for global variable ‘X_bam’ sampleSwaps : : no visible binding for global variable ‘Y_bam’ sampleSwaps: no visible binding for global variable ‘XY_possibly_paired’ segSummarize: no visible binding for global variable ‘Chromosome’ segSummarize: no visible binding for global variable ‘Start’ segSummarize: no visible binding for global variable ‘End’ segSummarize: no visible binding for global variable ‘Sample’ segSummarize: no visible binding for global variable ‘id’ segSummarize: no visible binding for global variable ‘name’ segSummarize: no visible binding for global variable ‘arm’ segSummarize: no visible binding for global variable ‘chromosome’ segSummarize: no visible global function definition for ‘complete.cases’ segSummarize: no visible global function definition for ‘setNames’ segSummarize : : no visible global function definition for ‘setNames’ segSummarize: no visible binding for global variable ‘Variant_Classification’ segSummarize: no visible global function definition for ‘.’ segSummarize: no visible binding for global variable ‘N’ 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 : : no visible binding for global variable ‘Signature’ signatureEnrichment : : no visible binding for global variable ‘Tumor_Sample_Barcode’ signatureEnrichment : : no visible binding for global variable ‘sd’ signatureEnrichment : : 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 : : : 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 : : 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 ‘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 binding for global variable ‘total_perMB’ tcgaCompare: no visible global function definition for ‘median’ tcgaCompare: no visible binding for global variable ‘V2’ tcgaCompare : : no visible binding for global variable ‘plot_total’ tcgaCompare : : 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 : : no visible binding for global variable ‘V3’ tcgaCompare : : 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 : : no visible global function definition for ‘segments’ tcgaCompare : : no visible binding for global variable ‘Median_Mutations_log10’ tcgaCompare : : 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 : : 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 binding for global variable ‘size’ tmb: no visible binding for global variable ‘end’ tmb: no visible binding for global variable ‘start’ 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 ‘grid’ tmb: no visible global function definition for ‘abline’ tmb: no visible global function definition for ‘points’ tmb: no visible global function definition for ‘adjustcolor’ tmb: no visible global function definition for ‘title’ tmb: no visible global function definition for ‘axis’ tmb: no visible global function definition for ‘mtext’ tmb: no visible global function definition for ‘boxplot’ tmb: no visible global function definition for ‘stripchart’ 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 : : 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.refGene 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 G1 G1_wt G2 G2_wt 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_m1 MutatedSamples_m2 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 VC Var1 Var2 Variant_Classification Variant_Classification_temp Variant_Type Wide_Peak_Limits XY_possibly_paired X_bam Y_bam aa.length abline adjPval adjustcolor alt alt_rc amp anno_Position arm arrows assembly_version axis baf barplot bg box boxStat boxplot browseURL category cf chr chromosome chromosome_end chromosome_start ci.low ci.up cn 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 end 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 gistic glm grid head 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 name 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 ref_alt_diff ref_alt_len ref_rc reference_genome_allele refseq.ID row_id row_idx rug runif sd segments sequencing_strategy setNames setTxtProgressBar significant site size 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 ystart Consider adding importFrom("grDevices", "adjustcolor", "colorRampPalette", "dev.copy", "heat.colors", "png") importFrom("graphics", "abline", "arrows", "axis", "barplot", "box", "boxplot", "grid", "image", "layout", "legend", "lines", "mtext", "par", "pie", "plot.new", "points", "rect", "rug", "segments", "stripchart", "symbols", "text", "title") importFrom("stats", "C", "complete.cases", "cophenetic", "cor.test", "dbinom", "density", "end", "fisher.test", "glm", "kmeans", "median", "na.omit", "p.adjust", "pairwise.t.test", "pairwise.table", "pchisq", "pnorm", "poisson", "poisson.test", "qf", "qnorm", "runif", "sd", "setNames", "start", "t.test", "wilcox.test") importFrom("utils", "browseURL", "combn", "download.file", "head", "read.csv", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plotMosdepth.Rd: DNAcopy plotMosdepth_t.Rd: DNAcopy segSummarize.Rd: segment segmentLogR.Rd: DNAcopy subsetMaf.Rd: foverlaps Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... INFO 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 ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/maftools/libs/maftools.so’: Found ‘___assert_rtn’, possibly from ‘assert’ (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) 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 10.106 0.193 10.330 segSummarize 5.726 0.909 6.662 tcgaAvailable 0.016 0.011 6.106 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/maftools.Rcheck/00check.log’ for details.