Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-19 12:12 -0400 (Wed, 19 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4687 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4402 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4351 |
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 1114/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maftools 2.21.0 (landing page) Anand Mayakonda
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the maftools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maftools.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
Package: maftools |
Version: 2.21.0 |
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_2.21.0.tar.gz |
StartedAt: 2024-06-18 21:54:15 -0400 (Tue, 18 Jun 2024) |
EndedAt: 2024-06-18 21:55:03 -0400 (Tue, 18 Jun 2024) |
EllapsedTime: 48.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: maftools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/maftools.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘maftools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘maftools’ version ‘2.21.0’ * 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 ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: extdata 6.0Mb * 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’ .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’ 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 : <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’ 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 : <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 ‘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 : <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 ‘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’ 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’ 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’ 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 ‘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 : <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’ 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 : <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’ 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’ 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’ 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’ 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’ 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’ 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[G>A]A A[G>C]A A[G>T]A A>C A>G A>T aa.length AAChange AAChange_ AAChange.refGene abline adjPval AGA alt Alt alt_rc AlteredSamples amp Amp Analysis anno_Position APOBEC_Enriched APOBEC_Enrichment arrows assembly_version axis baf barplot bg box boxplot boxStat browseURL C C>A C>G C>T Cancer_type category cf chr chromosome Chromosome chromosome_end chromosome_start ci.low ci.up Cluster CN CNV CNV_total cohort Cohort colorRampPalette combn complete.cases con con.class consequence_type contig conv cophenetic cor_coef cor.test count count2 cytoband Cytoband dbinom Del density Description dev.copy distance doc doc_n doc_norm doc_t domain_lenght domainCol DomainLabel download.file downstream dp End End_Position End_Position_updated endDist ens_id Entrez Entrez_Gene_Id Event event_ratio ExonicFunc.refGene fdr Feature_1 Feature_2 fisher_pvalue fisher.test fract fract_concordant_snps fract_muts_in_clusters fraction fraction_affected fraction_APOBEC_mutations Fraction_mutated_samples fractMutated Freq fs Func.refGene G G_Score G>A G>C G>T g1_muts g1_title g1_tot g2_muts g2_title g2_tot Gene gene_affected Gene.refGene gene1 gene2 Genotype gistic glm Group Group1 Group2 head heat.colors HGNC hgnc_symbol Hugo_Symbol i.End_Position i.Start_Position icgc_sample_id id ID idx image Ins kmeans lab label Label labThis layout legend lines loc loci log_fdr log_q logR lower maf_slot MATH max_alt Mean median Median Median_Mutations Median_Mutations_log10 mtext mutated_from_allele Mutated_samples mutated_to_allele MutatedSamples MutatedSamples_m1 MutatedSamples_m2 Mutation_Status mutload muts_in_clusters MutSig_Synonym n N n_A n_affected_genes n_C n_C>G_and_C>T n_G n_mutated_Feature n_mutated_Feature1 n_mutated_Feature2 n_mutated_group1 n_mutated_group2 n_mutations n_T N.x N.y na.omit nGenes nMut nMuts non_APOBEC_mutations nonApobec nVars OG_Hugo_Symbol or OR OR_high OR_low or_new p_value P_value p.adjust pAdj pair pairwise.t.test pairwise.table par Pathway pchisq pct_alt pctAltered peakID pfam pie pkgname plot_total plot.new png pnorm points poisson poisson.test poissonFdr pos pos2 posRounded protein.ID pval Pval pValue qf qnorm qvalues read.csv rect ref Ref ref_alt ref_alt_diff ref_alt_len ref_rc Reference_Allele reference_genome_allele refseq.ID row_id row_idx rug runif Sample SampleSize sd Segment_End Segment_Mean Segment_Start segments sequencing_strategy setTxtProgressBar Signature significant site Size start Start Start_Position Start_Position_updated startDist statFontSize stripchart Substitution SubstitutionMotif SubstitutionType SubstitutionTypeMotif survProb symbols t_alt_count t_depth t_ref_count t_vaf t.test 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 T>A T>C T>G TCA TCGA tcga_driver TCT tcw tCw tCw_to_A tCw_to_G tCw_to_G+tCw_to_T tCw_to_T temp_af text tFdr TGA th Time title TiTv tot tot_depth total total_perMB total_perMB_log trinucleotide Tumor_Sample_Barcode Tumor_Seq_Allele2 TumorSampleBarcode txtProgressBar Unique_Name unit updown upper upstream V1 V2 V3 vaf VAF value Var1 Var2 variable Variant_Classification Variant_Classification_temp variant_ID Variant_Type variantId VC verification_platform verification_status wga wGa wGa_to_A wGa_to_C wGa_to_T Wide_Peak_Limits wilcox.test write.table X_bam XY_possibly_paired Y_bam ystart Consider adding importFrom("graphics", "abline", "arrows", "axis", "barplot", "box", "boxplot", "image", "layout", "legend", "lines", "mtext", "par", "pie", "plot.new", "points", "rect", "rug", "segments", "stripchart", "symbols", "text", "title") importFrom("grDevices", "colorRampPalette", "dev.copy", "heat.colors", "png") 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", "head", "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 ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 * 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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/maftools.Rcheck/00check.log’ for details.
maftools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL maftools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘maftools’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ 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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c snpcounts.c -o snpcounts.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 -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/4.4-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-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)
maftools.Rcheck/maftools-Ex.timings
name | user | system | elapsed | |
MAF | 0.062 | 0.008 | 0.071 | |
annovarToMaf | 0.046 | 0.004 | 0.049 | |
clinicalEnrichment | 0 | 0 | 0 | |
coBarplot | 0.091 | 0.006 | 0.096 | |
coGisticChromPlot | 0 | 0 | 0 | |
coOncoplot | 0.087 | 0.005 | 0.092 | |
drugInteractions | 0.118 | 0.011 | 0.129 | |
estimateSignatures | 0 | 0 | 0 | |
extractSignatures | 0 | 0 | 0 | |
filterMaf | 0.239 | 0.019 | 0.259 | |
forestPlot | 0.064 | 0.004 | 0.068 | |
genesToBarcodes | 0.096 | 0.008 | 0.105 | |
genotypeMatrix | 0.088 | 0.008 | 0.095 | |
getClinicalData | 0.085 | 0.006 | 0.091 | |
getCytobandSummary | 0.158 | 0.006 | 0.165 | |
getFields | 0.081 | 0.005 | 0.086 | |
getGeneSummary | 0.089 | 0.005 | 0.094 | |
getSampleSummary | 0.095 | 0.010 | 0.103 | |
gisticBubblePlot | 0.165 | 0.010 | 0.175 | |
gisticChromPlot | 0.190 | 0.006 | 0.197 | |
gisticOncoPlot | 0.166 | 0.008 | 0.174 | |
icgcSimpleMutationToMAF | 0.028 | 0.003 | 0.031 | |
inferHeterogeneity | 0 | 0 | 0 | |
lollipopPlot | 0.294 | 0.008 | 0.303 | |
lollipopPlot2 | 0.535 | 0.014 | 0.549 | |
maf2mae | 4.281 | 0.089 | 4.370 | |
mafCompare | 0.060 | 0.004 | 0.064 | |
mafSummary | 0.422 | 0.009 | 0.431 | |
mafSurvGroup | 0.103 | 0.006 | 0.108 | |
mafSurvival | 0.102 | 0.005 | 0.107 | |
mafbarplot | 0.084 | 0.005 | 0.088 | |
math.score | 0.083 | 0.004 | 0.087 | |
mutCountMatrix | 0.149 | 0.175 | 0.326 | |
oncodrive | 0.343 | 0.014 | 0.364 | |
oncoplot | 0.167 | 0.010 | 0.178 | |
oncostrip | 0.108 | 0.011 | 0.119 | |
pathways | 0.174 | 0.009 | 0.186 | |
pfamDomains | 0.332 | 0.013 | 0.344 | |
plotApobecDiff | 0 | 0 | 0 | |
plotCBSsegments | 0.013 | 0.001 | 0.013 | |
plotClusters | 0 | 0 | 0 | |
plotOncodrive | 0.346 | 0.034 | 0.381 | |
plotPathways | 0.182 | 0.009 | 0.191 | |
plotProtein | 0.333 | 0.005 | 0.338 | |
plotTiTv | 0.140 | 0.011 | 0.150 | |
plotVaf | 0.102 | 0.006 | 0.107 | |
plotmafSummary | 0.110 | 0.005 | 0.115 | |
prepareMutSig | 0.119 | 0.009 | 0.129 | |
read.maf | 0.088 | 0.005 | 0.093 | |
readGistic | 0.155 | 0.009 | 0.163 | |
setMaf | 0.127 | 0.010 | 0.137 | |
somaticInteractions | 0.152 | 0.008 | 0.159 | |
subsetMaf | 0.175 | 0.007 | 0.183 | |
survGroup | 0.180 | 0.014 | 0.193 | |
tcgaAvailable | 0.008 | 0.004 | 0.367 | |
tcgaCompare | 0.199 | 0.016 | 0.216 | |
tcgaLoad | 0.063 | 0.007 | 1.194 | |
titv | 0.186 | 0.005 | 0.190 | |
tmb | 0.094 | 0.006 | 0.099 | |
trinucleotideMatrix | 0 | 0 | 0 | |
write.GisticSummary | 0.425 | 0.007 | 0.433 | |
write.mafSummary | 0.081 | 0.016 | 0.100 | |