| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:34 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1085/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| maftools 2.17.0 (landing page) Anand Mayakonda
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: maftools |
| Version: 2.17.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maftools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings maftools_2.17.0.tar.gz |
| StartedAt: 2023-05-09 20:01:27 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 20:07:47 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 380.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: maftools.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maftools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings maftools_2.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/maftools.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘maftools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘maftools’ version ‘2.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘maftools’ can be installed ... WARNING
Found the following significant warnings:
snpcounts.c:89:47: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.17-bioc/meat/maftools.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 10.1Mb
sub-directories of 1Mb or more:
extdata 6.0Mb
libs 2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Rhtslib’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.dnaCopy_plotter: no visible binding for global variable ‘contig’
.dnaCopy_plotter: no visible binding for global variable ‘Chromosome’
.dnaCopy_plotter: no visible global function definition for ‘par’
.dnaCopy_plotter: no visible global function definition for ‘abline’
.dnaCopy_plotter: no visible global function definition for ‘segments’
.dnaCopy_plotter: no visible global function definition for ‘axis’
.mafSetKeys: no visible binding for global variable ‘Chromosome’
.mafSetKeys: no visible binding for global variable ‘Start_Position’
.mafSetKeys: no visible binding for global variable ‘End_Position’
OncogenicPathways: no visible binding for global variable
‘n_affected_genes’
OncogenicPathways: no visible binding for global variable ‘ID’
OncogenicPathways: no visible global function definition for ‘layout’
OncogenicPathways: no visible global function definition for ‘par’
OncogenicPathways: no visible global function definition for ‘text’
OncogenicPathways: no visible global function definition for ‘title’
OncogenicPathways: no visible global function definition for ‘rect’
OncogenicPathways: no visible global function definition for ‘axis’
PlotOncogenicPathways: no visible binding for global variable
‘Tumor_Sample_Barcode’
PlotOncogenicPathways: no visible global function definition for ‘par’
PlotOncogenicPathways: no visible global function definition for
‘image’
PlotOncogenicPathways: no visible global function definition for
‘abline’
PlotOncogenicPathways: no visible global function definition for
‘points’
PlotOncogenicPathways: no visible global function definition for
‘mtext’
PlotOncogenicPathways: no visible global function definition for ‘text’
PlotOncogenicPathways: no visible global function definition for
‘title’
add_legend: no visible global function definition for ‘par’
add_legend: no visible global function definition for ‘legend’
add_oncoprint: no visible global function definition for ‘unit’
add_oncoprint: no visible binding for global variable ‘bg’
add_oncoprint2: no visible global function definition for ‘unit’
annovarToMaf: no visible binding for global variable ‘Hugo_Symbol’
annovarToMaf: no visible binding for global variable ‘Gene.refGene’
annovarToMaf: no visible binding for global variable ‘Func.refGene’
annovarToMaf: no visible binding for global variable
‘Variant_Classification’
annovarToMaf: no visible binding for global variable
‘ExonicFunc.refGene’
annovarToMaf: no visible binding for global variable ‘ref_alt_diff’
annovarToMaf: no visible binding for global variable ‘Ref’
annovarToMaf: no visible binding for global variable ‘Alt’
annovarToMaf: no visible binding for global variable ‘Variant_Type’
annovarToMaf : <anonymous>: no visible binding for global variable
‘Variant_Classification’
annovarToMaf : <anonymous>: no visible binding for global variable
‘ref_alt_diff’
annovarToMaf: no visible binding for global variable ‘ens_id’
annovarToMaf: no visible binding for global variable ‘hgnc_symbol’
annovarToMaf: no visible binding for global variable ‘Entrez_Gene_Id’
annovarToMaf: no visible binding for global variable ‘Entrez’
binconf : bc: no visible global function definition for ‘qf’
binconf : bc: no visible global function definition for ‘qnorm’
bubble_plot: no visible global function definition for ‘layout’
bubble_plot: no visible global function definition for ‘symbols’
bubble_plot: no visible global function definition for ‘axis’
bubble_plot: no visible global function definition for ‘abline’
bubble_plot: no visible global function definition for ‘mtext’
bubble_plot: no visible global function definition for ‘text’
bubble_plot: no visible global function definition for ‘par’
cancerhotspots: no visible global function definition for ‘browseURL’
cancerhotspotsAggr : <anonymous>: no visible global function definition
for ‘.’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘A’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘G’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘C’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘Ins’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘Del’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘t_depth’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘VAF’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘End_Position’
cancerhotspotsAggr : <anonymous>: no visible binding for global
variable ‘Start_Position’
cancerhotspotsAggr: no visible binding for global variable
‘Tumor_Sample_Barcode’
clinicalEnrichment : pairwise.fisher.test : compare.levels: no visible
global function definition for ‘fisher.test’
clinicalEnrichment : pairwise.fisher.test: no visible global function
definition for ‘pairwise.table’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘Gene’
clinicalEnrichment: no visible binding for global variable
‘AlteredSamples’
clinicalEnrichment: no visible binding for global variable
‘Hugo_Symbol’
clinicalEnrichment: no visible binding for global variable
‘MutatedSamples’
clinicalEnrichment : <anonymous> : <anonymous>: no visible global
function definition for ‘fisher.test’
clinicalEnrichment : <anonymous> : <anonymous>: no visible binding for
global variable ‘Group’
clinicalEnrichment : <anonymous> : <anonymous>: no visible binding for
global variable ‘Genotype’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘Hugo_Symbol’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘Analysis’
clinicalEnrichment : <anonymous>: no visible global function definition
for ‘.’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘Var1’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘Var2’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘value’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘fdr’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘cf’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘Genotype’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘N’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘n_mutated_Feature’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘N.x’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘N.y’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘Feature_1’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘Feature_2’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘n_mutated_Feature1’
clinicalEnrichment : <anonymous>: no visible binding for global
variable ‘n_mutated_Feature2’
clinicalEnrichment: no visible binding for global variable ‘Analysis’
clinicalEnrichment: no visible global function definition for ‘.’
clinicalEnrichment: no visible binding for global variable ‘Feature_1’
clinicalEnrichment: no visible binding for global variable ‘Feature_2’
clinicalEnrichment: no visible binding for global variable
‘n_mutated_Feature1’
clinicalEnrichment: no visible binding for global variable
‘n_mutated_Feature2’
clinicalEnrichment: no visible binding for global variable ‘fdr’
clinicalEnrichment: no visible binding for global variable ‘Group1’
clinicalEnrichment: no visible binding for global variable ‘Group2’
clinicalEnrichment: no visible binding for global variable
‘n_mutated_group1’
clinicalEnrichment: no visible binding for global variable
‘n_mutated_group2’
clinicalEnrichment: no visible binding for global variable ‘p_value’
clinicalEnrichment: no visible binding for global variable ‘OR’
clinicalEnrichment: no visible binding for global variable ‘OR_low’
clinicalEnrichment: no visible binding for global variable ‘OR_high’
clinicalEnrichment: no visible global function definition for
‘p.adjust’
clinicalEnrichment: no visible binding for global variable ‘cf’
cluster_prot: no visible binding for global variable ‘N’
cluster_prot: no visible binding for global variable ‘distance’
cluster_prot: no visible binding for global variable ‘startDist’
cluster_prot: no visible binding for global variable ‘endDist’
cluster_prot: no visible binding for global variable ‘fraction’
cluster_prot : <anonymous>: no visible binding for global variable
‘fraction’
coBarplot: no visible binding for global variable ‘Hugo_Symbol’
coBarplot: no visible binding for global variable ‘ID’
coBarplot: no visible global function definition for ‘.’
coBarplot: no visible binding for global variable ‘AlteredSamples’
coBarplot: no visible global function definition for ‘par’
coBarplot: no visible global function definition for ‘barplot’
coBarplot: no visible global function definition for ‘text’
coBarplot: no visible global function definition for ‘axis’
coBarplot: no visible global function definition for ‘mtext’
coBarplot: no visible global function definition for ‘title’
coBarplot: no visible global function definition for ‘legend’
coOncoplot: no visible global function definition for ‘.’
coOncoplot: no visible binding for global variable ‘Hugo_Symbol’
coOncoplot: no visible binding for global variable ‘MutatedSamples’
coOncoplot: no visible binding for global variable ‘MutatedSamples.x’
coOncoplot: no visible binding for global variable ‘MutatedSamples.y’
coOncoplot: no visible global function definition for ‘plot.new’
coOncoplot: no visible global function definition for ‘par’
coOncoplot: no visible global function definition for ‘image’
coOncoplot: no visible global function definition for ‘text’
coOncoplot: no visible global function definition for ‘legend’
createOncoMatrix: no visible binding for global variable
‘Tumor_Sample_Barcode’
createOncoMatrix: no visible binding for global variable ‘Hugo_Symbol’
createOncoMatrix: no visible binding for global variable ‘Variant_Type’
createOncoMatrix: no visible binding for global variable
‘Variant_Classification’
createOncoMatrix: no visible binding for global variable
‘Variant_Classification_temp’
createOncoMatrix: no visible global function definition for ‘.’
dashboard: no visible binding for global variable ‘statFontSize’
dashboard: no visible binding for global variable ‘fs’
dashboard: no visible binding for global variable ‘pie’
dashboard: no visible global function definition for ‘par’
dashboard: no visible global function definition for ‘barplot’
dashboard: no visible global function definition for ‘abline’
dashboard: no visible global function definition for ‘axis’
dashboard: no visible global function definition for ‘title’
dashboard: no visible binding for global variable ‘value’
dashboard: no visible binding for global variable ‘variable’
dashboard: no visible global function definition for ‘text’
dashboard: no visible global function definition for ‘mtext’
dashboard: no visible binding for global variable ‘ID’
dashboard: no visible binding for global variable ‘Mean’
dashboard: no visible global function definition for ‘lines’
dashboard: no visible binding for global variable ‘Median’
dashboard: no visible binding for global variable ‘N’
dashboard: no visible global function definition for ‘.’
dashboard: no visible binding for global variable
‘Variant_Classification’
dashboard: no visible global function definition for ‘boxplot’
dashboard: no visible binding for global variable ‘boxStat’
dashboard: no visible binding for global variable ‘Hugo_Symbol’
dashboard: no visible binding for global variable ‘AlteredSamples’
detect_kataegis: no visible global function definition for
‘write.table’
detect_kataegis: no visible binding for global variable
‘Tumor_Sample_Barcode’
detect_kataegis_chr: no visible binding for global variable ‘row_idx’
detect_kataegis_chr: no visible binding for global variable
‘Start_Position’
detect_kataegis_chr: no visible binding for global variable
‘Chromosome’
detect_kataegis_chr: no visible binding for global variable ‘Size’
detect_kataegis_chr: no visible binding for global variable
‘End_Position’
detect_kataegis_chr: no visible global function definition for ‘.’
detect_kataegis_chr: no visible binding for global variable ‘con.class’
detect_kataegis_chr: no visible binding for global variable
‘Tumor_Sample_Barcode’
dirichletClusters: no visible binding for global variable ‘dp’
drugInteractions: no visible binding for global variable ‘Hugo_Symbol’
drugInteractions: no visible binding for global variable ‘Gene’
drugInteractions: no visible binding for global variable ‘N’
drugInteractions: no visible binding for global variable ‘category’
drugInteractions: no visible global function definition for ‘.’
drugInteractions: no visible binding for global variable ‘V1’
drugInteractions: no visible binding for global variable ‘label’
drugInteractions: no visible global function definition for ‘par’
drugInteractions: no visible global function definition for ‘pie’
drugInteractions: no visible global function definition for
‘heat.colors’
drugInteractions: no visible global function definition for ‘barplot’
drugInteractions: no visible global function definition for ‘text’
drugInteractions: no visible global function definition for ‘axis’
drugInteractions: no visible global function definition for ‘mtext’
drugInteractions: no visible global function definition for ‘title’
estimateSignatures: no visible global function definition for ‘png’
filterCopyNumber: no visible global function definition for ‘.’
filterCopyNumber: no visible binding for global variable ‘Hugo_Symbol’
filterCopyNumber: no visible binding for global variable ‘Chromosome’
filterCopyNumber: no visible binding for global variable
‘i.Start_Position’
filterCopyNumber: no visible binding for global variable
‘i.End_Position’
filterCopyNumber: no visible binding for global variable
‘Tumor_Sample_Barcode’
filterCopyNumber: no visible binding for global variable ‘t_vaf’
filterCopyNumber: no visible binding for global variable
‘Start_Position’
filterCopyNumber: no visible binding for global variable ‘End_Position’
filterCopyNumber: no visible binding for global variable ‘Segment_Mean’
filterCopyNumber: no visible binding for global variable ‘CN’
filterMaf: no visible binding for global variable
‘Tumor_Sample_Barcode’
filterMaf: no visible binding for global variable ‘Hugo_Symbol’
forestPlot: no visible binding for global variable ‘pval’
forestPlot: no visible binding for global variable ‘adjPval’
forestPlot: no visible binding for global variable ‘Cohort’
forestPlot: no visible binding for global variable ‘SampleSize’
forestPlot: no visible binding for global variable ‘pos’
forestPlot: no visible global function definition for ‘par’
forestPlot: no visible global function definition for ‘.’
forestPlot: no visible binding for global variable ‘or’
forestPlot: no visible binding for global variable ‘ci.up’
forestPlot: no visible binding for global variable ‘ci.low’
forestPlot: no visible binding for global variable ‘or_new’
forestPlot: no visible binding for global variable ‘upper’
forestPlot: no visible binding for global variable ‘lower’
forestPlot : <anonymous>: no visible global function definition for
‘points’
forestPlot : <anonymous>: no visible global function definition for
‘segments’
forestPlot: no visible global function definition for ‘abline’
forestPlot: no visible global function definition for ‘axis’
forestPlot: no visible global function definition for ‘mtext’
forestPlot: no visible global function definition for ‘title’
forestPlot: no visible global function definition for ‘text’
genesToBarcodes: no visible binding for global variable
‘Tumor_Sample_Barcode’
genesToBarcodes : <anonymous>: no visible binding for global variable
‘Tumor_Sample_Barcode’
genotypeMatrix: no visible binding for global variable ‘id’
genotypeMatrix: no visible binding for global variable ‘Chromosome’
genotypeMatrix: no visible binding for global variable ‘Start_Position’
genotypeMatrix: no visible binding for global variable ‘t_vaf’
get_anno_cols: no visible global function definition for
‘colorRampPalette’
get_col_df: no visible binding for global variable ‘Hugo_Symbol’
get_col_df: no visible binding for global variable ‘Var1’
get_col_df: no visible binding for global variable ‘Freq’
get_col_df: no visible global function definition for ‘.’
get_col_df: no visible binding for global variable ‘Gene’
get_lp_data: no visible binding for global variable ‘Hugo_Symbol’
get_lp_data: no visible global function definition for ‘.’
get_lp_data: no visible binding for global variable ‘Variant_Type’
get_lp_data: no visible binding for global variable
‘Variant_Classification’
get_lp_data: no visible binding for global variable ‘AAChange’
get_lp_data: no visible binding for global variable ‘HGNC’
get_lp_data: no visible binding for global variable ‘refseq.ID’
get_lp_data: no visible binding for global variable ‘protein.ID’
get_lp_data: no visible binding for global variable ‘aa.length’
get_lp_data: no visible binding for global variable ‘Label’
get_lp_data: no visible binding for global variable ‘domain_lenght’
get_lp_data: no visible binding for global variable ‘End’
get_lp_data: no visible binding for global variable ‘Start’
get_lp_data: no visible binding for global variable ‘ID’
get_lp_data: no visible binding for global variable ‘MutatedSamples’
get_lp_data: no visible binding for global variable ‘conv’
get_lp_data: no visible binding for global variable ‘count2’
get_lp_data: no visible binding for global variable ‘count’
get_lp_data: no visible binding for global variable ‘posRounded’
get_lp_data: no visible binding for global variable ‘lab’
get_pw_summary: no visible binding for global variable ‘Pathway’
get_pw_summary: no visible binding for global variable
‘fraction_affected’
get_pw_summary: no visible binding for global variable
‘n_affected_genes’
get_pw_summary: no visible binding for global variable ‘N’
get_pw_summary: no visible binding for global variable ‘ID’
get_pw_summary: no visible binding for global variable
‘Fraction_mutated_samples’
get_pw_summary: no visible binding for global variable
‘Mutated_samples’
get_threshold : <anonymous>: no visible global function definition for
‘dbinom’
gisticBubblePlot: no visible binding for global variable ‘qvalues’
gisticBubblePlot: no visible binding for global variable ‘Chromosome’
gisticBubblePlot: no visible binding for global variable ‘loc’
gisticBubblePlot: no visible binding for global variable
‘Start_Position’
gisticBubblePlot: no visible binding for global variable ‘End_Position’
gisticBubblePlot: no visible global function definition for ‘.’
gisticBubblePlot: no visible binding for global variable ‘Cytoband’
gisticBubblePlot: no visible binding for global variable
‘Variant_Classification’
gisticBubblePlot: no visible binding for global variable ‘nGenes’
gisticBubblePlot: no visible binding for global variable ‘log_q’
gisticBubblePlot: no visible global function definition for ‘par’
gisticChromPlot: no visible binding for global variable ‘qvalues’
gisticChromPlot: no visible binding for global variable ‘Chromosome’
gisticChromPlot: no visible binding for global variable ‘loc’
gisticChromPlot: no visible binding for global variable
‘Start_Position’
gisticChromPlot: no visible binding for global variable ‘End_Position’
gisticChromPlot: no visible global function definition for ‘.’
gisticChromPlot: no visible binding for global variable ‘Cytoband’
gisticChromPlot: no visible binding for global variable
‘Variant_Classification’
gisticChromPlot: no visible binding for global variable ‘amp’
gisticChromPlot: no visible global function definition for ‘layout’
gisticChromPlot: no visible global function definition for ‘par’
gisticChromPlot: no visible global function definition for ‘abline’
gisticChromPlot: no visible global function definition for ‘axis’
gisticChromPlot: no visible global function definition for ‘mtext’
gisticChromPlot: no visible global function definition for ‘segments’
gisticChromPlot: no visible global function definition for ‘rect’
gisticChromPlot: no visible global function definition for ‘text’
gisticChromPlot: no visible binding for global variable
‘Start_Position_updated’
gisticChromPlot: no visible binding for global variable
‘End_Position_updated’
gisticChromPlot: no visible global function definition for
‘complete.cases’
gisticChromPlot: no visible binding for global variable ‘Hugo_Symbol’
gisticChromPlot: no visible binding for global variable ‘G_Score’
gisticChromPlot: no visible binding for global variable ‘fdr’
gisticMap: no visible binding for global variable ‘Cytoband’
gisticMap: no visible binding for global variable
‘Variant_Classification’
gisticOncoPlot: no visible global function definition for ‘par’
gisticOncoPlot: no visible global function definition for ‘image’
gisticOncoPlot: no visible global function definition for ‘abline’
gisticOncoPlot: no visible global function definition for ‘mtext’
gisticOncoPlot: no visible global function definition for ‘text’
gisticOncoPlot: no visible global function definition for ‘legend’
gtMarkers: no visible global function definition for ‘download.file’
icgcSimpleMutationToMAF: no visible binding for global variable
‘consequence_type’
icgcSimpleMutationToMAF: no visible binding for global variable
‘gene_affected’
icgcSimpleMutationToMAF: no visible binding for global variable
‘assembly_version’
icgcSimpleMutationToMAF: no visible binding for global variable
‘chromosome’
icgcSimpleMutationToMAF: no visible binding for global variable
‘chromosome_start’
icgcSimpleMutationToMAF: no visible binding for global variable
‘chromosome_end’
icgcSimpleMutationToMAF: no visible binding for global variable
‘Variant_Classification’
icgcSimpleMutationToMAF: no visible binding for global variable
‘Variant_Type’
icgcSimpleMutationToMAF: no visible binding for global variable
‘reference_genome_allele’
icgcSimpleMutationToMAF: no visible binding for global variable
‘mutated_from_allele’
icgcSimpleMutationToMAF: no visible binding for global variable
‘mutated_to_allele’
icgcSimpleMutationToMAF: no visible binding for global variable
‘icgc_sample_id’
icgcSimpleMutationToMAF: no visible binding for global variable
‘verification_status’
icgcSimpleMutationToMAF: no visible binding for global variable
‘sequencing_strategy’
icgcSimpleMutationToMAF: no visible binding for global variable
‘verification_platform’
icgcSimpleMutationToMAF: no visible binding for global variable
‘ens_id’
icgcSimpleMutationToMAF: no visible binding for global variable
‘Hugo_Symbol’
icgcSimpleMutationToMAF: no visible binding for global variable
‘hgnc_symbol’
icgcSimpleMutationToMAF: no visible binding for global variable
‘Entrez_Gene_Id’
icgcSimpleMutationToMAF: no visible binding for global variable
‘Entrez’
icgcSimpleMutationToMAF: no visible global function definition for
‘write.table’
icgcSimpleMutationToMAF: no visible binding for global variable
‘Tumor_Sample_Barcode’
inferHeterogeneity: no visible binding for global variable
‘Tumor_Sample_Barcode’
inferHeterogeneity: no visible binding for global variable ‘t_vaf’
inferHeterogeneity: no visible binding for global variable
‘t_alt_count’
inferHeterogeneity: no visible binding for global variable
‘t_ref_count’
inferHeterogeneity: no visible binding for global variable ‘Chromosome’
inferHeterogeneity: no visible binding for global variable
‘Start_Position’
inferHeterogeneity: no visible binding for global variable
‘End_Position’
inferHeterogeneity: no visible binding for global variable ‘Sample’
inferHeterogeneity: no visible global function definition for ‘.’
inferHeterogeneity: no visible binding for global variable
‘Hugo_Symbol’
inferHeterogeneity: no visible global function definition for ‘median’
intersectMAF: no visible binding for global variable ‘Chromosome’
intersectMAF: no visible binding for global variable ‘Start_Position’
intersectMAF: no visible binding for global variable ‘End_Position’
intersectMAF: no visible global function definition for ‘.’
intersectMAF: no visible binding for global variable ‘Reference_Allele’
intersectMAF: no visible binding for global variable
‘Tumor_Seq_Allele2’
intersectMAF: no visible binding for global variable ‘variant_ID’
intersectMAF: no visible binding for global variable ‘maf_slot’
label_pos: no visible binding for global variable ‘labThis’
label_pos: no visible binding for global variable ‘pos2’
label_pos: no visible binding for global variable ‘count2’
label_pos: no visible binding for global variable ‘conv’
lollipopPlot: no visible binding for global variable ‘Hugo_Symbol’
lollipopPlot: no visible global function definition for ‘.’
lollipopPlot: no visible binding for global variable ‘Variant_Type’
lollipopPlot: no visible binding for global variable
‘Variant_Classification’
lollipopPlot: no visible binding for global variable ‘AAChange_’
lollipopPlot: no visible binding for global variable ‘HGNC’
lollipopPlot: no visible binding for global variable ‘refseq.ID’
lollipopPlot: no visible binding for global variable ‘protein.ID’
lollipopPlot: no visible binding for global variable ‘aa.length’
lollipopPlot: no visible binding for global variable ‘domain_lenght’
lollipopPlot: no visible binding for global variable ‘End’
lollipopPlot: no visible binding for global variable ‘Start’
lollipopPlot: no visible binding for global variable ‘ID’
lollipopPlot: no visible binding for global variable ‘MutatedSamples’
lollipopPlot: no visible binding for global variable ‘conv’
lollipopPlot: no visible binding for global variable ‘count2’
lollipopPlot: no visible binding for global variable ‘count’
lollipopPlot: no visible binding for global variable ‘posRounded’
lollipopPlot: no visible binding for global variable ‘lab’
lollipopPlot: no visible binding for global variable ‘labThis’
lollipopPlot: no visible binding for global variable ‘pos2’
lollipopPlot: no visible binding for global variable ‘Label’
lollipopPlot: no visible global function definition for ‘par’
lollipopPlot: no visible global function definition for ‘rect’
lollipopPlot: no visible global function definition for ‘axis’
lollipopPlot: no visible global function definition for ‘segments’
lollipopPlot: no visible global function definition for ‘points’
lollipopPlot: no visible binding for global variable ‘domainCol’
lollipopPlot: no visible global function definition for ‘title’
lollipopPlot: no visible global function definition for ‘text’
lollipopPlot: no visible global function definition for ‘legend’
lollipopPlot2: no visible binding for global variable ‘Label’
lollipopPlot2: no visible binding for global variable
‘Variant_Classification’
lollipopPlot2: no visible global function definition for ‘par’
lollipopPlot2: no visible global function definition for ‘rect’
lollipopPlot2: no visible global function definition for ‘axis’
lollipopPlot2: no visible global function definition for ‘segments’
lollipopPlot2: no visible binding for global variable ‘pos2’
lollipopPlot2: no visible binding for global variable ‘count2’
lollipopPlot2: no visible global function definition for ‘points’
lollipopPlot2: no visible binding for global variable ‘domainCol’
lollipopPlot2: no visible binding for global variable ‘Start’
lollipopPlot2: no visible binding for global variable ‘End’
lollipopPlot2: no visible global function definition for ‘.’
lollipopPlot2: no visible global function definition for ‘text’
lollipopPlot2: no visible global function definition for ‘mtext’
lollipopPlot2: no visible binding for global variable ‘refseq.ID’
lollipopPlot2: no visible binding for global variable ‘conv’
lollipopPlot2: no visible global function definition for ‘legend’
mafCompare: no visible global function definition for ‘.’
mafCompare: no visible binding for global variable ‘Pathway’
mafCompare: no visible binding for global variable ‘Mutated_samples’
mafCompare: no visible binding for global variable ‘AlteredSamples’
mafCompare: no visible binding for global variable ‘Hugo_Symbol’
mafCompare: no visible binding for global variable ‘MutatedSamples’
mafCompare : <anonymous>: no visible global function definition for
‘fisher.test’
mafCompare: no visible binding for global variable ‘pval’
mafCompare: no visible binding for global variable ‘adjPval’
mafCompare: no visible global function definition for ‘p.adjust’
mafSurvGroup: no visible binding for global variable ‘Time’
mafSurvGroup: no visible global function definition for ‘.’
mafSurvGroup: no visible global function definition for ‘median’
mafSurvGroup: no visible binding for global variable ‘Group’
mafSurvGroup: no visible global function definition for ‘pchisq’
mafSurvGroup: no visible global function definition for ‘par’
mafSurvGroup: no visible global function definition for ‘abline’
mafSurvGroup: no visible global function definition for ‘points’
mafSurvGroup: no visible binding for global variable ‘survProb’
mafSurvGroup: no visible global function definition for ‘lines’
mafSurvGroup: no visible global function definition for ‘axis’
mafSurvGroup: no visible global function definition for ‘mtext’
mafSurvGroup: no visible global function definition for ‘legend’
mafSurvGroup: no visible global function definition for ‘title’
mafSurvival: no visible binding for global variable ‘Time’
mafSurvival: no visible global function definition for ‘.’
mafSurvival: no visible global function definition for ‘median’
mafSurvival: no visible binding for global variable ‘Group’
mafSurvival: no visible global function definition for ‘pchisq’
mafSurvival: no visible global function definition for ‘par’
mafSurvival: no visible global function definition for ‘abline’
mafSurvival: no visible global function definition for ‘points’
mafSurvival: no visible binding for global variable ‘survProb’
mafSurvival: no visible global function definition for ‘lines’
mafSurvival: no visible global function definition for ‘axis’
mafSurvival: no visible global function definition for ‘mtext’
mafSurvival: no visible global function definition for ‘legend’
mafSurvival: no visible global function definition for ‘title’
mafbarplot: no visible binding for global variable ‘ID’
mafbarplot: no visible global function definition for ‘.’
mafbarplot: no visible binding for global variable ‘Hugo_Symbol’
mafbarplot: no visible binding for global variable ‘AlteredSamples’
mafbarplot: no visible global function definition for ‘par’
mafbarplot: no visible global function definition for ‘barplot’
mafbarplot: no visible global function definition for ‘axis’
mafbarplot: no visible global function definition for ‘text’
mafbarplot: no visible global function definition for ‘abline’
mafbarplot: no visible global function definition for ‘mtext’
mafbarplot: no visible global function definition for ‘legend’
mapMutsToSegs: no visible binding for global variable ‘Sample’
mapMutsToSegs: no visible binding for global variable ‘Chromosome’
mapMutsToSegs: no visible binding for global variable ‘Start_Position’
mapMutsToSegs: no visible binding for global variable ‘End_Position’
mapMutsToSegs: no visible binding for global variable ‘Variant_Type’
mapMutsToSegs: no visible global function definition for ‘.’
mapMutsToSegs: no visible binding for global variable ‘Hugo_Symbol’
mapMutsToSegs: no visible binding for global variable
‘Tumor_Sample_Barcode’
mapMutsToSegs: no visible binding for global variable
‘i.Start_Position’
mapMutsToSegs: no visible binding for global variable ‘i.End_Position’
mapMutsToSegs: no visible binding for global variable ‘Segment_Mean’
mapMutsToSegs: no visible binding for global variable
‘Start_Position_updated’
mapMutsToSegs: no visible binding for global variable
‘End_Position_updated’
mapMutsToSegs: no visible binding for global variable ‘CN’
math.score: no visible binding for global variable
‘Tumor_Sample_Barcode’
math.score: no visible binding for global variable ‘t_ref_count’
math.score: no visible binding for global variable ‘t_alt_count’
math.score: no visible binding for global variable ‘t_vaf’
math.score: no visible global function definition for ‘.’
math.score: no visible binding for global variable ‘Hugo_Symbol’
math.score : <anonymous>: no visible binding for global variable
‘Tumor_Sample_Barcode’
math.score : <anonymous>: no visible global function definition for
‘median’
mutCountMatrix: no visible binding for global variable
‘Variant_Classification’
mutCountMatrix: no visible global function definition for ‘.’
mutCountMatrix: no visible binding for global variable ‘Hugo_Symbol’
mutCountMatrix: no visible binding for global variable
‘Tumor_Sample_Barcode’
mutCountMatrix: no visible binding for global variable ‘tot’
oncodrive: no visible global function definition for ‘read.csv’
oncodrive: no visible global function definition for ‘sd’
oncodrive: no visible binding for global variable ‘Hugo_Symbol’
oncodrive: no visible global function definition for ‘pnorm’
oncodrive: no visible global function definition for ‘p.adjust’
oncodrive: no visible binding for global variable
‘fract_muts_in_clusters’
oncodrive: no visible binding for global variable ‘muts_in_clusters’
oncodrive: no visible binding for global variable ‘total’
oncodrive: no visible global function definition for ‘glm’
oncodrive: no visible global function definition for ‘poisson’
oncodrive : <anonymous>: no visible global function definition for
‘poisson.test’
oncodrive: no visible binding for global variable ‘poissonFdr’
oncodrive: no visible global function definition for ‘.’
oncodrive: no visible binding for global variable ‘tFdr’
oncodrive: no visible binding for global variable ‘fdr’
oncoplot: no visible binding for global variable ‘Gene’
oncoplot: no visible global function definition for ‘.’
oncoplot: no visible binding for global variable ‘Pathway’
oncoplot: no visible binding for global variable ‘AlteredSamples’
oncoplot: no visible binding for global variable ‘Hugo_Symbol’
oncoplot: no visible binding for global variable ‘MutatedSamples’
oncoplot: no visible binding for global variable ‘fractMutated’
oncoplot: no visible binding for global variable ‘mutload’
oncoplot: no visible binding for global variable ‘Tumor_Sample_Barcode’
oncoplot: no visible binding for global variable ‘total’
oncoplot: no visible binding for global variable
‘Variant_Classification_temp’
oncoplot: no visible binding for global variable
‘Variant_Classification’
oncoplot: no visible binding for global variable ‘value’
oncoplot: no visible binding for global variable ‘CNV_total’
oncoplot: no visible binding for global variable ‘Amp’
oncoplot: no visible binding for global variable ‘Del’
oncoplot: no visible binding for global variable ‘max_alt’
oncoplot: no visible binding for global variable ‘n’
oncoplot : <anonymous>: no visible binding for global variable
‘pct_alt’
oncoplot: no visible global function definition for ‘par’
oncoplot: no visible global function definition for ‘axis’
oncoplot: no visible global function definition for ‘rect’
oncoplot: no visible global function definition for ‘mtext’
oncoplot: no visible global function definition for ‘title’
oncoplot: no visible global function definition for ‘image’
oncoplot: no visible global function definition for ‘write.table’
oncoplot: no visible global function definition for ‘abline’
oncoplot: no visible binding for global variable ‘row_id’
oncoplot : <anonymous>: no visible global function definition for
‘rect’
oncoplot: no visible binding for global variable ‘temp_af’
oncoplot : <anonymous> : <anonymous>: no visible global function
definition for ‘points’
oncoplot: no visible global function definition for ‘box’
oncoplot: no visible global function definition for ‘text’
oncoplot: no visible global function definition for ‘plot.new’
oncoplot: no visible global function definition for ‘legend’
parse_prot: no visible global function definition for ‘.’
parse_prot: no visible binding for global variable ‘Hugo_Symbol’
parse_prot: no visible binding for global variable
‘Variant_Classification’
parse_prot: no visible binding for global variable ‘AAChange’
parse_prot: no visible binding for global variable ‘conv’
parse_prot: no visible binding for global variable ‘aa.length’
parse_prot: no visible binding for global variable ‘total’
parse_prot: no visible global function definition for ‘txtProgressBar’
parse_prot: no visible binding for global variable ‘th’
parse_prot: no visible global function definition for
‘setTxtProgressBar’
pathway_load: no visible binding for global variable ‘Gene’
pathway_load: no visible global function definition for ‘.’
pathway_load: no visible binding for global variable ‘Pathway’
pathway_load: no visible binding for global variable
‘fraction_affected’
pathway_load: no visible binding for global variable ‘n_affected_genes’
pathway_load: no visible binding for global variable ‘N’
pathway_load: no visible binding for global variable ‘ID’
pathway_load: no visible binding for global variable
‘Fraction_mutated_samples’
pathway_load: no visible binding for global variable ‘Mutated_samples’
pfamDomains: no visible binding for global variable ‘Variant_Type’
pfamDomains: no visible global function definition for ‘.’
pfamDomains: no visible binding for global variable ‘Hugo_Symbol’
pfamDomains: no visible binding for global variable
‘Variant_Classification’
pfamDomains: no visible binding for global variable ‘AAChange’
pfamDomains: no visible binding for global variable ‘conv’
pfamDomains: no visible binding for global variable ‘total’
pfamDomains: no visible binding for global variable ‘N’
pfamDomains: no visible binding for global variable ‘fraction’
pfamDomains: no visible binding for global variable ‘HGNC’
pfamDomains: no visible binding for global variable ‘Start’
pfamDomains: no visible binding for global variable ‘End’
pfamDomains: no visible binding for global variable ‘Label’
pfamDomains: no visible binding for global variable ‘pfam’
pfamDomains: no visible binding for global variable ‘Description’
pfamDomains: no visible binding for global variable ‘idx’
pfamDomains: no visible binding for global variable ‘DomainLabel’
pfamDomains: no visible binding for global variable ‘nMut’
pfamDomains: no visible binding for global variable ‘nGenes’
pfamDomains: no visible global function definition for ‘complete.cases’
pfamDomains: no visible binding for global variable ‘nMuts’
pfamDomains: no visible global function definition for ‘write.table’
pfamDomains: no visible global function definition for ‘par’
pfamDomains: no visible global function definition for ‘mtext’
plotApobecDiff: no visible binding for global variable
‘APOBEC_Enriched’
plotApobecDiff: no visible binding for global variable
‘fraction_APOBEC_mutations’
plotApobecDiff: no visible binding for global variable
‘Tumor_Sample_Barcode’
plotApobecDiff: no visible binding for global variable ‘ID’
plotApobecDiff: no visible global function definition for ‘.’
plotApobecDiff: no visible binding for global variable ‘Mean’
plotApobecDiff: no visible binding for global variable ‘Median’
plotApobecDiff: no visible binding for global variable ‘Cohort’
plotApobecDiff: no visible binding for global variable ‘pval’
plotApobecDiff: no visible binding for global variable ‘Hugo_Symbol’
plotApobecDiff: no visible binding for global variable ‘MutatedSamples’
plotApobecDiff: no visible binding for global variable ‘SampleSize’
plotApobecDiff: no visible binding for global variable ‘nonApobec’
plotApobecDiff: no visible binding for global variable ‘V1’
plotApobecDiff: no visible binding for global variable ‘title’
plotApobecDiff: no visible binding for global variable ‘variable’
plotApobecDiff: no visible binding for global variable ‘value’
plotApobecDiff: no visible global function definition for ‘par’
plotApobecDiff: no visible binding for global variable ‘n_mutations’
plotApobecDiff: no visible global function definition for ‘boxplot’
plotApobecDiff: no visible global function definition for ‘title’
plotApobecDiff: no visible global function definition for ‘axis’
plotApobecDiff: no visible global function definition for ‘na.omit’
plotApobecDiff: no visible binding for global variable ‘N’
plotApobecDiff: no visible global function definition for ‘mtext’
plotApobecDiff: no visible global function definition for ‘wilcox.test’
plotApobecDiff: no visible global function definition for ‘text’
plotApobecDiff: no visible global function definition for ‘segments’
plotApobecDiff: no visible global function definition for ‘pie’
plotApobecDiff: no visible global function definition for ‘symbols’
plotApobecDiff: no visible global function definition for ‘barplot’
plotCBS: no visible binding for global variable ‘Sample’
plotCBS: no visible binding for global variable ‘Chromosome’
plotCBS: no visible binding for global variable ‘Start_Position’
plotCBS: no visible global function definition for ‘par’
plotCBS: no visible global function definition for ‘axis’
plotCBS: no visible global function definition for ‘abline’
plotCBS: no visible global function definition for ‘rect’
plotCBS: no visible global function definition for ‘title’
plotCBS: no visible global function definition for ‘mtext’
plotCBSchr: no visible binding for global variable ‘Sample’
plotCBSchr: no visible binding for global variable ‘Chromosome’
plotCBSsegments: no visible binding for global variable ‘Chromosome’
plotCBSsegments: no visible binding for global variable
‘Start_Position’
plotCBSsegments: no visible binding for global variable ‘End_Position’
plotCBSsegments: no visible binding for global variable ‘Sample’
plotCBSsegments: no visible global function definition for
‘write.table’
plotCBSsegments: no visible global function definition for ‘.’
plotCBSsegments: no visible binding for global variable ‘Hugo_Symbol’
plotCBSsegments: no visible binding for global variable
‘Tumor_Sample_Barcode’
plotCBSsegments: no visible binding for global variable ‘Segment_Start’
plotCBSsegments: no visible binding for global variable ‘Segment_End’
plotCBSsegments: no visible binding for global variable ‘Segment_Mean’
plotCBSsegments: no visible binding for global variable ‘CN’
plotCBSsegments: no visible global function definition for ‘text’
plotCBSsegments: no visible global function definition for ‘segments’
plotClusters: no visible binding for global variable
‘Tumor_Sample_Barcode’
plotClusters: no visible global function definition for ‘par’
plotClusters: no visible global function definition for ‘boxplot’
plotClusters: no visible binding for global variable ‘t_vaf’
plotClusters: no visible global function definition for ‘density’
plotClusters: no visible global function definition for ‘lines’
plotClusters: no visible global function definition for ‘abline’
plotClusters: no visible global function definition for ‘axis’
plotClusters: no visible global function definition for ‘points’
plotClusters: no visible global function definition for ‘title’
plotClusters: no visible binding for global variable ‘MATH’
plotClusters: no visible global function definition for ‘segments’
plotClusters: no visible global function definition for ‘text’
plotClusters: no visible binding for global variable ‘Hugo_Symbol’
plotClusters: no visible global function definition for ‘legend’
plotClusters: no visible global function definition for ‘mtext’
plotCophenetic: no visible global function definition for ‘par’
plotCophenetic: no visible global function definition for ‘axis’
plotCophenetic: no visible global function definition for ‘lines’
plotCophenetic: no visible global function definition for ‘points’
plotCophenetic: no visible global function definition for ‘segments’
plotCophenetic: no visible binding for global variable ‘cophenetic’
plotCophenetic: no visible global function definition for ‘title’
plotEnrichmentResults: no visible binding for global variable ‘P_value’
plotEnrichmentResults: no visible binding for global variable ‘OR’
plotEnrichmentResults: no visible binding for global variable ‘Group1’
plotEnrichmentResults : <anonymous>: no visible binding for global
variable ‘g1_muts’
plotEnrichmentResults : <anonymous>: no visible binding for global
variable ‘g1_tot’
plotEnrichmentResults : <anonymous>: no visible binding for global
variable ‘g2_muts’
plotEnrichmentResults : <anonymous>: no visible binding for global
variable ‘g2_tot’
plotEnrichmentResults: no visible binding for global variable
‘g1_title’
plotEnrichmentResults: no visible binding for global variable ‘g1_muts’
plotEnrichmentResults: no visible binding for global variable ‘g1_tot’
plotEnrichmentResults: no visible binding for global variable
‘g2_title’
plotEnrichmentResults: no visible binding for global variable ‘g2_muts’
plotEnrichmentResults: no visible binding for global variable ‘g2_tot’
plotEnrichmentResults : add_legend: no visible global function
definition for ‘par’
plotEnrichmentResults : add_legend: no visible global function
definition for ‘legend’
plotEnrichmentResults: no visible global function definition for ‘par’
plotEnrichmentResults: no visible global function definition for
‘barplot’
plotEnrichmentResults: no visible global function definition for ‘axis’
plotEnrichmentResults: no visible global function definition for
‘segments’
plotEnrichmentResults: no visible global function definition for ‘text’
plotEnrichmentResults: no visible global function definition for
‘legend’
plotEnrichmentResults: no visible global function definition for
‘title’
plotMosdepth : <anonymous>: no visible binding for global variable
‘chr’
plotMosdepth : <anonymous>: no visible binding for global variable
‘Chromosome’
plotMosdepth: no visible binding for global variable ‘Chromosome’
plotMosdepth: no visible binding for global variable ‘Start_Position’
plotMosdepth: no visible binding for global variable ‘End_Position’
plotMosdepth: no visible global function definition for ‘.’
plotMosdepth: no visible binding for global variable ‘logR’
plotMosdepth: no visible binding for global variable ‘doc_t’
plotMosdepth: no visible binding for global variable ‘doc_n’
plotMosdepth: no visible global function definition for ‘par’
plotMosdepth : <anonymous>: no visible global function definition for
‘points’
plotMosdepth : <anonymous>: no visible global function definition for
‘rect’
plotMosdepth: no visible global function definition for ‘abline’
plotMosdepth: no visible global function definition for ‘axis’
plotMosdepth: no visible global function definition for ‘mtext’
plotMosdepth: no visible global function definition for ‘title’
plotMosdepth_t: no visible binding for global variable ‘chr’
plotMosdepth_t: no visible binding for global variable ‘start’
plotMosdepth_t: no visible global function definition for ‘median’
plotMosdepth_t: no visible binding for global variable ‘doc’
plotMosdepth_t: no visible binding for global variable ‘End_Position’
plotMosdepth_t: no visible global function definition for ‘.’
plotMosdepth_t: no visible binding for global variable ‘Chromosome’
plotMosdepth_t: no visible binding for global variable ‘doc_norm’
plotMosdepth_t: no visible binding for global variable ‘Start_Position’
plotMosdepth_t: no visible global function definition for ‘par’
plotMosdepth_t : <anonymous>: no visible global function definition for
‘points’
plotMosdepth_t : <anonymous>: no visible global function definition for
‘rect’
plotMosdepth_t : <anonymous>: no visible binding for global variable
‘Start_Position_updated’
plotMosdepth_t : <anonymous>: no visible binding for global variable
‘End_Position_updated’
plotMosdepth_t: no visible global function definition for ‘abline’
plotMosdepth_t: no visible global function definition for ‘axis’
plotMosdepth_t: no visible global function definition for ‘title’
plotOncodrive: no visible binding for global variable ‘log_fdr’
plotOncodrive: no visible binding for global variable ‘fdr’
plotOncodrive: no visible global function definition for ‘par’
plotOncodrive: no visible binding for global variable ‘significant’
plotOncodrive: no visible global function definition for ‘mtext’
plotProtein: no visible binding for global variable ‘HGNC’
plotProtein: no visible binding for global variable ‘refseq.ID’
plotProtein: no visible binding for global variable ‘protein.ID’
plotProtein: no visible global function definition for ‘.’
plotProtein: no visible binding for global variable ‘aa.length’
plotProtein: no visible binding for global variable ‘domain_lenght’
plotProtein: no visible binding for global variable ‘End’
plotProtein: no visible binding for global variable ‘Start’
plotProtein: no visible binding for global variable ‘Label’
plotProtein: no visible global function definition for ‘par’
plotProtein: no visible global function definition for ‘rect’
plotProtein: no visible binding for global variable ‘domainCol’
plotProtein: no visible global function definition for ‘text’
plotProtein: no visible global function definition for ‘title’
plotProtein: no visible global function definition for ‘legend’
plotSignatures: no visible global function definition for ‘par’
plotSignatures: no visible global function definition for ‘barplot’
plotSignatures: no visible global function definition for ‘axis’
plotSignatures: no visible global function definition for ‘mtext’
plotSignatures: no visible global function definition for ‘plot.new’
plotSignatures: no visible global function definition for ‘legend’
plotSignatures: no visible global function definition for ‘title’
plotSignatures: no visible global function definition for ‘rect’
plotSignatures: no visible global function definition for ‘text’
plotTiTv: no visible binding for global variable ‘value’
plotTiTv: no visible global function definition for ‘.’
plotTiTv: no visible binding for global variable ‘variable’
plotTiTv: no visible binding for global variable ‘V1’
plotTiTv: no visible global function definition for ‘par’
plotTiTv: no visible global function definition for ‘barplot’
plotTiTv: no visible global function definition for ‘axis’
plotTiTv: no visible global function definition for ‘mtext’
plotTiTv: no visible global function definition for ‘boxplot’
plotTiTv: no visible global function definition for ‘abline’
plotVaf: no visible binding for global variable ‘Hugo_Symbol’
plotVaf: no visible binding for global variable ‘t_vaf’
plotVaf: no visible binding for global variable ‘t_alt_count’
plotVaf: no visible binding for global variable ‘t_ref_count’
plotVaf: no visible global function definition for ‘.’
plotVaf: no visible binding for global variable ‘value’
plotVaf: no visible global function definition for ‘median’
plotVaf: no visible binding for global variable ‘V1’
plotVaf: no visible global function definition for ‘par’
plotVaf: no visible global function definition for ‘boxplot’
plotVaf: no visible global function definition for ‘axis’
plotVaf: no visible global function definition for ‘abline’
plotVaf: no visible global function definition for ‘stripchart’
plotmafSummary: no visible binding for global variable ‘statFontSize’
plotmafSummary: no visible global function definition for ‘par’
plotmafSummary: no visible global function definition for ‘barplot’
plotmafSummary: no visible global function definition for ‘axis’
plotmafSummary: no visible global function definition for ‘title’
plotmafSummary: no visible binding for global variable ‘Mean’
plotmafSummary: no visible binding for global variable ‘Median’
plotmafSummary: no visible global function definition for ‘lines’
plotmafSummary: no visible binding for global variable ‘N’
plotmafSummary: no visible global function definition for ‘.’
plotmafSummary: no visible binding for global variable
‘Variant_Classification’
plotmafSummary: no visible global function definition for ‘boxplot’
plotmafSummary: no visible binding for global variable ‘boxStat’
plotmafSummary: no visible global function definition for ‘plot.new’
plotmafSummary: no visible global function definition for ‘legend’
prepAscat : <anonymous>: no visible binding for global variable ‘loci’
prepAscat : <anonymous>: no visible binding for global variable
‘tot_depth’
prepAscat : <anonymous>: no visible global function definition for ‘.’
prepAscat : <anonymous>: no visible binding for global variable ‘A’
prepAscat : <anonymous>: no visible binding for global variable ‘G’
prepAscat : <anonymous>: no visible binding for global variable ‘C’
prepAscat : <anonymous>: no visible binding for global variable ‘baf’
prepAscat : <anonymous>: no visible global function definition for
‘runif’
prepAscat_t : <anonymous>: no visible binding for global variable
‘loci’
prepAscat_t : <anonymous>: no visible binding for global variable
‘tot_depth’
prepAscat_t : <anonymous>: no visible global function definition for
‘.’
prepAscat_t : <anonymous>: no visible binding for global variable ‘A’
prepAscat_t : <anonymous>: no visible binding for global variable ‘G’
prepAscat_t : <anonymous>: no visible binding for global variable ‘C’
prepAscat_t : <anonymous>: no visible binding for global variable ‘baf’
prepAscat_t : <anonymous>: no visible global function definition for
‘runif’
prepAscat_t: no visible global function definition for ‘median’
prepareMutSig: no visible binding for global variable
‘Variant_Classification’
prepareMutSig: no visible binding for global variable ‘OG_Hugo_Symbol’
prepareMutSig: no visible binding for global variable ‘Hugo_Symbol’
prepareMutSig: no visible global function definition for ‘.’
prepareMutSig: no visible binding for global variable ‘MutSig_Synonym’
prepareMutSig: no visible binding for global variable ‘N’
prepareMutSig: no visible global function definition for ‘write.table’
print_mat: no visible binding for global variable
‘Tumor_Sample_Barcode’
print_mat: no visible global function definition for ‘par’
print_mat: no visible global function definition for ‘image’
print_mat: no visible global function definition for ‘rect’
print_mat : <anonymous>: no visible binding for global variable
‘temp_af’
print_mat : <anonymous> : <anonymous> : <anonymous>: no visible global
function definition for ‘points’
print_mat: no visible global function definition for ‘abline’
print_mat: no visible global function definition for ‘mtext’
rainfallPlot: no visible binding for global variable
‘Tumor_Sample_Barcode’
rainfallPlot: no visible global function definition for ‘.’
rainfallPlot: no visible binding for global variable ‘Chromosome’
rainfallPlot: no visible binding for global variable ‘Hugo_Symbol’
rainfallPlot: no visible binding for global variable ‘Start_Position’
rainfallPlot: no visible binding for global variable ‘End_Position’
rainfallPlot: no visible binding for global variable ‘Reference_Allele’
rainfallPlot: no visible binding for global variable
‘Tumor_Seq_Allele2’
rainfallPlot: no visible binding for global variable ‘Variant_Type’
rainfallPlot: no visible global function definition for
‘complete.cases’
rainfallPlot: no visible global function definition for ‘par’
rainfallPlot: no visible global function definition for ‘segments’
rainfallPlot: no visible global function definition for ‘points’
rainfallPlot: no visible global function definition for ‘axis’
rainfallPlot: no visible global function definition for ‘mtext’
rainfallPlot: no visible global function definition for ‘arrows’
rainfallPlot: no visible global function definition for ‘title’
rainfallPlot: no visible global function definition for ‘legend’
rainfallPlot: no visible global function definition for ‘dev.copy’
read.maf: no visible binding for global variable ‘Mutation_Status’
read.maf: no visible binding for global variable ‘Hugo_Symbol’
read.maf: no visible binding for global variable
‘Variant_Classification’
read.maf: no visible global function definition for ‘.’
read.maf: no visible binding for global variable ‘Tumor_Sample_Barcode’
read.maf: no visible binding for global variable ‘Unique_Name’
read.maf: no visible binding for global variable ‘Wide_Peak_Limits’
read.maf: no visible binding for global variable ‘id’
readGistic: no visible binding for global variable ‘Unique_Name’
readGistic: no visible binding for global variable ‘Wide_Peak_Limits’
readGistic: no visible binding for global variable ‘cytoband’
readGistic: no visible binding for global variable ‘value’
readGistic: no visible global function definition for ‘.’
readGistic: no visible binding for global variable ‘variable’
readGistic : <anonymous>: no visible binding for global variable
‘variable’
readGistic : <anonymous>: no visible binding for global variable
‘cytoband’
readGistic : <anonymous>: no visible binding for global variable
‘TumorSampleBarcode’
readGistic: no visible binding for global variable ‘CN’
readGistic: no visible binding for global variable ‘TumorSampleBarcode’
readGistic: no visible binding for global variable ‘Variant_Type’
readGistic: no visible binding for global variable ‘Cytoband’
readGistic: no visible binding for global variable ‘peakID’
readGistic: no visible binding for global variable
‘Tumor_Sample_Barcode’
readGistic: no visible binding for global variable ‘qvalues’
readSegs: no visible binding for global variable ‘Chromosome’
readSegs: no visible binding for global variable ‘Start_Position’
readSegs: no visible binding for global variable ‘End_Position’
refineClusters: no visible binding for global variable ‘t_vaf’
repelPoints: no visible binding for global variable ‘pos’
repelPoints: no visible binding for global variable ‘distance’
repelPoints: no visible global function definition for ‘.’
run_surv: no visible binding for global variable ‘Group’
run_surv: no visible global function definition for ‘pchisq’
run_surv: no visible global function definition for ‘par’
run_surv: no visible global function definition for ‘abline’
run_surv: no visible global function definition for ‘points’
run_surv: no visible binding for global variable ‘Time’
run_surv: no visible binding for global variable ‘survProb’
run_surv: no visible global function definition for ‘lines’
run_surv: no visible global function definition for ‘axis’
run_surv: no visible global function definition for ‘mtext’
run_surv: no visible global function definition for ‘legend’
run_surv: no visible global function definition for ‘title’
sampleSwaps: no visible binding for global variable ‘id’
sampleSwaps: no visible binding for global variable ‘chr’
sampleSwaps: no visible binding for global variable ‘start’
sampleSwaps : <anonymous>: no visible global function definition for
‘.’
sampleSwaps : <anonymous>: no visible binding for global variable ‘id’
sampleSwaps : <anonymous>: no visible binding for global variable ‘ref’
sampleSwaps : <anonymous>: no visible binding for global variable ‘alt’
sampleSwaps : <anonymous> : <anonymous>: no visible binding for global
variable ‘vaf’
sampleSwaps : <anonymous>: no visible binding for global variable
‘loci’
sampleSwaps : <anonymous>: no visible binding for global variable
‘ref_rc’
sampleSwaps : <anonymous>: no visible binding for global variable
‘alt_rc’
sampleSwaps : <anonymous>: no visible binding for global variable ‘vaf’
sampleSwaps: no visible binding for global variable ‘vaf’
sampleSwaps: no visible binding for global variable ‘total’
sampleSwaps: no visible binding for global variable ‘ref_rc’
sampleSwaps: no visible binding for global variable ‘alt_rc’
sampleSwaps: no visible global function definition for ‘complete.cases’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘fisher.test’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
binding for global variable ‘ref_rc’
sampleSwaps : <anonymous> : <anonymous> : <anonymous>: no visible
binding for global variable ‘alt_rc’
sampleSwaps : <anonymous> : <anonymous>: no visible global function
definition for ‘cor.test’
sampleSwaps : <anonymous>: no visible binding for global variable
‘XY_possibly_paired’
sampleSwaps : <anonymous>: no visible binding for global variable
‘fract_concordant_snps’
sampleSwaps : <anonymous>: no visible binding for global variable
‘cor_coef’
sampleSwaps : <anonymous>: no visible binding for global variable
‘X_bam’
sampleSwaps : <anonymous>: no visible binding for global variable
‘Y_bam’
sampleSwaps: no visible binding for global variable
‘XY_possibly_paired’
segmentLogR: no visible binding for global variable ‘contig’
segmentLogR: no visible binding for global variable ‘logR’
segmentLogR: no visible binding for global variable ‘pos’
segmentLogR: no visible global function definition for ‘write.table’
segmentLogR: no visible global function definition for ‘png’
setdiffMAF: no visible binding for global variable ‘Chromosome’
setdiffMAF: no visible binding for global variable ‘Start_Position’
setdiffMAF: no visible binding for global variable ‘End_Position’
setdiffMAF: no visible global function definition for ‘.’
setdiffMAF: no visible binding for global variable ‘Reference_Allele’
setdiffMAF: no visible binding for global variable ‘Tumor_Seq_Allele2’
setdiffMAF: no visible binding for global variable ‘variant_ID’
setdiffMAF: no visible binding for global variable ‘maf_slot’
shiftPoints: no visible binding for global variable ‘pos’
signatureEnrichment: no visible global function definition for ‘kmeans’
signatureEnrichment: no visible binding for global variable ‘Cluster’
signatureEnrichment: no visible binding for global variable ‘Signature’
signatureEnrichment : <anonymous>: no visible binding for global
variable ‘Signature’
signatureEnrichment : <anonymous>: no visible binding for global
variable ‘Tumor_Sample_Barcode’
signatureEnrichment : <anonymous>: no visible binding for global
variable ‘sd’
signatureEnrichment : <anonymous>: no visible binding for global
variable ‘N’
signatureEnrichment : add_legend: no visible global function definition
for ‘par’
signatureEnrichment : add_legend: no visible global function definition
for ‘legend’
signatureEnrichment: no visible global function definition for ‘par’
signatureEnrichment: no visible global function definition for
‘barplot’
signatureEnrichment: no visible global function definition for
‘segments’
signatureEnrichment: no visible global function definition for ‘axis’
signatureEnrichment: no visible global function definition for ‘mtext’
signatureEnrichment: no visible global function definition for ‘title’
signatureEnrichment: no visible global function definition for
‘boxplot’
signatureEnrichment: no visible global function definition for ‘.’
signatureEnrichment: no visible global function definition for ‘median’
signatureEnrichment: no visible binding for global variable ‘N’
signatureEnrichment: no visible global function definition for
‘write.table’
somaticInteractions: no visible binding for global variable
‘Hugo_Symbol’
somaticInteractions: no visible binding for global variable
‘Tumor_Sample_Barcode’
somaticInteractions : <anonymous> : <anonymous>: no visible global
function definition for ‘fisher.test’
somaticInteractions: no visible binding for global variable ‘pAdj’
somaticInteractions: no visible global function definition for
‘p.adjust’
somaticInteractions: no visible binding for global variable ‘pValue’
somaticInteractions: no visible global function definition for ‘.’
somaticInteractions: no visible binding for global variable ‘gene1’
somaticInteractions: no visible binding for global variable ‘gene2’
somaticInteractions: no visible binding for global variable
‘event_ratio’
somaticInteractions: no visible binding for global variable ‘01’
somaticInteractions: no visible binding for global variable ‘10’
somaticInteractions: no visible binding for global variable ‘11’
somaticInteractions: no visible binding for global variable ‘pair’
somaticInteractions: no visible binding for global variable
‘AlteredSamples’
somaticInteractions: no visible global function definition for ‘par’
somaticInteractions: no visible global function definition for ‘image’
somaticInteractions: no visible global function definition for ‘abline’
somaticInteractions: no visible global function definition for ‘mtext’
somaticInteractions: no visible binding for global variable ‘Event’
somaticInteractions: no visible global function definition for ‘text’
somaticInteractions: no visible global function definition for ‘points’
somaticInteractions: no visible global function definition for ‘axis’
sortByMutation: no visible binding for global variable ‘MutatedSamples’
sortByMutation: no visible binding for global variable ‘Hugo_Symbol’
subsetMaf: no visible binding for global variable
‘Tumor_Sample_Barcode’
subsetMaf: no visible binding for global variable ‘Variant_Type’
subsetMaf: no visible binding for global variable ‘Hugo_Symbol’
subsetMaf: no visible binding for global variable ‘Chromosome’
subsetMaf: no visible binding for global variable ‘Start_Position’
subsetMaf: no visible binding for global variable ‘End_Position’
summarizeGistic: no visible binding for global variable ‘Hugo_Symbol’
summarizeGistic: no visible binding for global variable
‘Tumor_Sample_Barcode’
summarizeGistic: no visible global function definition for ‘.’
summarizeGistic: no visible binding for global variable
‘Variant_Classification’
summarizeGistic: no visible binding for global variable ‘total’
summarizeGistic: no visible binding for global variable ‘median’
summarizeGistic: no visible binding for global variable ‘Cytoband’
summarizeMaf: no visible binding for global variable ‘Variant_Type’
summarizeMaf: no visible binding for global variable ‘Hugo_Symbol’
summarizeMaf: no visible binding for global variable
‘Tumor_Sample_Barcode’
summarizeMaf: no visible global function definition for ‘.’
summarizeMaf: no visible binding for global variable
‘Variant_Classification’
summarizeMaf: no visible binding for global variable ‘total’
summarizeMaf: no visible binding for global variable ‘CNV_total’
summarizeMaf: no visible binding for global variable ‘median’
summarizeMaf: no visible binding for global variable ‘CNV’
summarizeMaf: no visible binding for global variable ‘MutatedSamples’
summarizeMaf: no visible binding for global variable ‘Mean’
summarizeMaf: no visible binding for global variable ‘Median’
survGroup: no visible binding for global variable ‘Hugo_Symbol’
survGroup: no visible global function definition for ‘combn’
survGroup: no visible binding for global variable ‘Time’
survGroup: no visible binding for global variable
‘Tumor_Sample_Barcode’
survGroup: no visible binding for global variable ‘P_value’
tcgaCompare: no visible global function definition for ‘.’
tcgaCompare: no visible binding for global variable
‘Tumor_Sample_Barcode’
tcgaCompare: no visible binding for global variable ‘total’
tcgaCompare: no visible binding for global variable ‘site’
tcgaCompare: no visible binding for global variable ‘cohort’
tcgaCompare : <anonymous>: no visible global function definition for
‘.’
tcgaCompare : <anonymous>: no visible binding for global variable
‘Tumor_Sample_Barcode’
tcgaCompare : <anonymous>: no visible binding for global variable
‘total’
tcgaCompare : <anonymous>: no visible binding for global variable
‘cohort’
tcgaCompare: no visible global function definition for
‘pairwise.t.test’
tcgaCompare: no visible binding for global variable ‘plot_total’
tcgaCompare: no visible binding for global variable ‘total_perMB’
tcgaCompare: no visible global function definition for ‘median’
tcgaCompare: no visible binding for global variable ‘V2’
tcgaCompare : <anonymous>: no visible binding for global variable
‘plot_total’
tcgaCompare : <anonymous>: no visible binding for global variable
‘TCGA’
tcgaCompare: no visible global function definition for ‘rect’
tcgaCompare: no visible global function definition for ‘par’
tcgaCompare: no visible global function definition for ‘abline’
tcgaCompare : <anonymous>: no visible binding for global variable ‘V3’
tcgaCompare : <anonymous>: no visible global function definition for
‘points’
tcgaCompare: no visible global function definition for ‘axis’
tcgaCompare: no visible binding for global variable
‘Median_Mutations_log10’
tcgaCompare: no visible binding for global variable ‘Median_Mutations’
tcgaCompare: no visible global function definition for ‘mtext’
tcgaCompare : <anonymous>: no visible global function definition for
‘segments’
tcgaCompare : <anonymous>: no visible binding for global variable
‘Median_Mutations_log10’
tcgaCompare : <anonymous>: no visible binding for global variable
‘Median_Mutations’
tcgaCompare: no visible binding for global variable ‘TCGA’
tcgaCompare: no visible binding for global variable ‘Pval’
tcgaDriverBP: no visible binding for global variable ‘Hugo_Symbol’
tcgaDriverBP: no visible global function definition for ‘.’
tcgaDriverBP: no visible binding for global variable ‘AlteredSamples’
tcgaDriverBP: no visible global function definition for ‘par’
tcgaDriverBP: no visible global function definition for ‘image’
tcgaDriverBP: no visible global function definition for ‘abline’
tcgaDriverBP: no visible global function definition for ‘points’
tcgaDriverBP: no visible global function definition for ‘mtext’
tcgaDriverBP: no visible global function definition for ‘text’
tcgaDriverBP: no visible global function definition for ‘title’
tcgaDriverBP : <anonymous>: no visible binding for global variable
‘Gene’
tcgaDriverBP: no visible binding for global variable ‘Cancer_type’
tcgaDriverBP: no visible binding for global variable ‘Pathway’
tcgaDriverBP: no visible binding for global variable ‘ID’
tcgaDriverBP: no visible binding for global variable ‘pctAltered’
tcgaDriverBP: no visible binding for global variable ‘tcga_driver’
titv: no visible binding for global variable ‘Reference_Allele’
titv: no visible binding for global variable ‘Tumor_Seq_Allele2’
titv: no visible binding for global variable ‘con’
titv: no visible global function definition for ‘.’
titv: no visible binding for global variable ‘Tumor_Sample_Barcode’
titv: no visible binding for global variable ‘N’
titv: no visible binding for global variable ‘con.class’
titv: no visible binding for global variable ‘fract’
titv: no visible binding for global variable ‘nVars’
titv: no visible binding for global variable ‘TiTv’
titv: no visible global function definition for ‘write.table’
tmb: no visible global function definition for ‘.’
tmb: no visible binding for global variable ‘Tumor_Sample_Barcode’
tmb: no visible binding for global variable ‘total’
tmb: no visible binding for global variable ‘total_perMB’
tmb: no visible binding for global variable ‘total_perMB_log’
tmb: no visible global function definition for ‘median’
tmb: no visible global function definition for ‘par’
tmb: no visible global function definition for ‘abline’
tmb: no visible global function definition for ‘points’
tmb: no visible global function definition for ‘title’
tmb: no visible global function definition for ‘axis’
tmb: no visible global function definition for ‘mtext’
transformSegments: no visible binding for global variable
‘Start_Position’
transformSegments: no visible binding for global variable
‘End_Position’
transformSegments: no visible binding for global variable ‘Chromosome’
trinucleotideMatrix: no visible binding for global variable ‘pkgname’
trinucleotideMatrix: no visible binding for global variable
‘Chromosome’
trinucleotideMatrix: no visible binding for global variable
‘Start_Position’
trinucleotideMatrix: no visible binding for global variable
‘End_Position’
trinucleotideMatrix: no visible binding for global variable ‘N’
trinucleotideMatrix: no visible binding for global variable ‘Start’
trinucleotideMatrix: no visible binding for global variable ‘End’
trinucleotideMatrix: no visible binding for global variable ‘upstream’
trinucleotideMatrix: no visible binding for global variable
‘downstream’
trinucleotideMatrix: no visible global function definition for ‘.’
trinucleotideMatrix: no visible binding for global variable ‘A’
trinucleotideMatrix: no visible binding for global variable ‘C’
trinucleotideMatrix: no visible binding for global variable ‘G’
trinucleotideMatrix: no visible binding for global variable
‘trinucleotide’
trinucleotideMatrix: no visible binding for global variable ‘updown’
trinucleotideMatrix: no visible binding for global variable ‘TCA’
trinucleotideMatrix: no visible binding for global variable ‘TCT’
trinucleotideMatrix: no visible binding for global variable ‘AGA’
trinucleotideMatrix: no visible binding for global variable ‘TGA’
trinucleotideMatrix: no visible binding for global variable ‘tcw’
trinucleotideMatrix: no visible binding for global variable ‘wga’
trinucleotideMatrix: no visible binding for global variable
‘Substitution’
trinucleotideMatrix: no visible binding for global variable
‘SubstitutionType’
trinucleotideMatrix: no visible binding for global variable
‘Tumor_Sample_Barcode’
trinucleotideMatrix: no visible binding for global variable ‘n_A’
trinucleotideMatrix: no visible binding for global variable ‘A>C’
trinucleotideMatrix: no visible binding for global variable ‘A>G’
trinucleotideMatrix: no visible binding for global variable ‘A>T’
trinucleotideMatrix: no visible binding for global variable ‘n_T’
trinucleotideMatrix: no visible binding for global variable ‘T>A’
trinucleotideMatrix: no visible binding for global variable ‘T>C’
trinucleotideMatrix: no visible binding for global variable ‘T>G’
trinucleotideMatrix: no visible binding for global variable ‘n_G’
trinucleotideMatrix: no visible binding for global variable ‘G>A’
trinucleotideMatrix: no visible binding for global variable ‘G>C’
trinucleotideMatrix: no visible binding for global variable ‘G>T’
trinucleotideMatrix: no visible binding for global variable ‘n_C’
trinucleotideMatrix: no visible binding for global variable ‘C>A’
trinucleotideMatrix: no visible binding for global variable ‘C>G’
trinucleotideMatrix: no visible binding for global variable ‘C>T’
trinucleotideMatrix: no visible binding for global variable
‘n_mutations’
trinucleotideMatrix: no visible binding for global variable
‘SubstitutionMotif’
trinucleotideMatrix: no visible binding for global variable ‘tCw_to_A’
trinucleotideMatrix: no visible binding for global variable ‘T[C>A]A’
trinucleotideMatrix: no visible binding for global variable ‘T[C>A]T’
trinucleotideMatrix: no visible binding for global variable ‘tCw_to_G’
trinucleotideMatrix: no visible binding for global variable ‘T[C>G]A’
trinucleotideMatrix: no visible binding for global variable ‘T[C>G]T’
trinucleotideMatrix: no visible binding for global variable ‘tCw_to_T’
trinucleotideMatrix: no visible binding for global variable ‘T[C>T]A’
trinucleotideMatrix: no visible binding for global variable ‘T[C>T]T’
trinucleotideMatrix: no visible binding for global variable ‘tCw’
trinucleotideMatrix: no visible binding for global variable ‘wGa_to_C’
trinucleotideMatrix: no visible binding for global variable ‘A[G>C]A’
trinucleotideMatrix: no visible binding for global variable ‘T[G>C]A’
trinucleotideMatrix: no visible binding for global variable ‘wGa_to_T’
trinucleotideMatrix: no visible binding for global variable ‘A[G>T]A’
trinucleotideMatrix: no visible binding for global variable ‘T[G>T]A’
trinucleotideMatrix: no visible binding for global variable ‘wGa_to_A’
trinucleotideMatrix: no visible binding for global variable ‘A[G>A]A’
trinucleotideMatrix: no visible binding for global variable ‘T[G>A]A’
trinucleotideMatrix: no visible binding for global variable ‘wGa’
trinucleotideMatrix: no visible binding for global variable
‘tCw_to_G+tCw_to_T’
trinucleotideMatrix: no visible binding for global variable
‘APOBEC_Enrichment’
trinucleotideMatrix: no visible binding for global variable
‘n_C>G_and_C>T’
trinucleotideMatrix: no visible binding for global variable
‘non_APOBEC_mutations’
trinucleotideMatrix: no visible binding for global variable
‘fraction_APOBEC_mutations’
trinucleotideMatrix : <anonymous>: no visible global function
definition for ‘fisher.test’
trinucleotideMatrix: no visible binding for global variable
‘fisher_pvalue’
trinucleotideMatrix: no visible binding for global variable ‘fdr’
trinucleotideMatrix: no visible global function definition for
‘p.adjust’
trinucleotideMatrix: no visible binding for global variable
‘APOBEC_Enriched’
trinucleotideMatrix: no visible binding for global variable
‘SubstitutionTypeMotif’
trinucleotideMatrix: no visible global function definition for
‘write.table’
vafCompare: no visible binding for global variable ‘Hugo_Symbol’
vafCompare: no visible binding for global variable ‘t_vaf’
vafCompare: no visible binding for global variable ‘t_alt_count’
vafCompare: no visible binding for global variable ‘t_ref_count’
vafCompare: no visible global function definition for ‘.’
vafCompare: no visible binding for global variable ‘Cohort’
vafCompare: no visible global function definition for ‘layout’
vafCompare: no visible global function definition for ‘par’
vafCompare: no visible global function definition for ‘boxplot’
vafCompare: no visible global function definition for ‘stripchart’
vafCompare: no visible global function definition for ‘axis’
vafCompare: no visible global function definition for ‘title’
vafCompare: no visible global function definition for ‘abline’
vafCompare: no visible global function definition for ‘t.test’
vafCompare: no visible global function definition for ‘text’
validateMaf: no visible binding for global variable ‘variantId’
validateMaf: no visible binding for global variable ‘Chromosome’
validateMaf: no visible binding for global variable ‘Start_Position’
validateMaf: no visible binding for global variable
‘Tumor_Sample_Barcode’
validateMaf: no visible binding for global variable ‘Reference_Allele’
validateMaf: no visible binding for global variable ‘Tumor_Seq_Allele2’
validateMaf: no visible binding for global variable ‘Hugo_Symbol’
validateMaf: no visible binding for global variable
‘Variant_Classification’
validateMaf: no visible binding for global variable ‘Variant_Type’
validateMaf: no visible binding for global variable ‘End_Position’
write.GisticSummary: no visible global function definition for
‘write.table’
write.mafSummary: no visible global function definition for
‘write.table’
Undefined global functions or variables:
. 01 10 11 A A>C A>G A>T AAChange AAChange_ AGA APOBEC_Enriched
APOBEC_Enrichment A[G>A]A A[G>C]A A[G>T]A Alt AlteredSamples Amp
Analysis C C>A C>G C>T CN CNV CNV_total Cancer_type Chromosome
Cluster Cohort Cytoband Del Description DomainLabel End End_Position
End_Position_updated Entrez Entrez_Gene_Id Event ExonicFunc.refGene
Feature_1 Feature_2 Fraction_mutated_samples Freq Func.refGene G G>A
G>C G>T G_Score Gene Gene.refGene Genotype Group Group1 Group2 HGNC
Hugo_Symbol ID Ins Label MATH Mean Median Median_Mutations
Median_Mutations_log10 MutSig_Synonym MutatedSamples MutatedSamples.x
MutatedSamples.y Mutated_samples Mutation_Status N N.x N.y
OG_Hugo_Symbol OR OR_high OR_low P_value Pathway Pval Ref
Reference_Allele Sample SampleSize Segment_End Segment_Mean
Segment_Start Signature Size Start Start_Position
Start_Position_updated Substitution SubstitutionMotif
SubstitutionType SubstitutionTypeMotif T>A T>C T>G TCA TCGA TCT TGA
T[C>A]A T[C>A]T T[C>G]A T[C>G]T T[C>T]A T[C>T]T T[G>A]A T[G>C]A
T[G>T]A TiTv Time TumorSampleBarcode Tumor_Sample_Barcode
Tumor_Seq_Allele2 Unique_Name V1 V2 V3 VAF Var1 Var2
Variant_Classification Variant_Classification_temp Variant_Type
Wide_Peak_Limits XY_possibly_paired X_bam Y_bam aa.length abline
adjPval alt alt_rc amp arrows assembly_version axis baf barplot bg
box boxStat boxplot browseURL category cf chr chromosome
chromosome_end chromosome_start ci.low ci.up cohort colorRampPalette
combn complete.cases con con.class consequence_type contig conv
cophenetic cor.test cor_coef count count2 cytoband dbinom density
dev.copy distance doc doc_n doc_norm doc_t domainCol domain_lenght
download.file downstream dp endDist ens_id event_ratio fdr
fisher.test fisher_pvalue fract fractMutated fract_concordant_snps
fract_muts_in_clusters fraction fraction_APOBEC_mutations
fraction_affected fs g1_muts g1_title g1_tot g2_muts g2_title g2_tot
gene1 gene2 gene_affected glm heat.colors hgnc_symbol i.End_Position
i.Start_Position icgc_sample_id id idx image kmeans lab labThis label
layout legend lines loc loci logR log_fdr log_q lower maf_slot
max_alt median mtext mutated_from_allele mutated_to_allele mutload
muts_in_clusters n nGenes nMut nMuts nVars n_A n_C n_C>G_and_C>T n_G
n_T n_affected_genes n_mutated_Feature n_mutated_Feature1
n_mutated_Feature2 n_mutated_group1 n_mutated_group2 n_mutations
na.omit nonApobec non_APOBEC_mutations or or_new p.adjust pAdj pValue
p_value pair pairwise.t.test pairwise.table par pchisq pctAltered
pct_alt peakID pfam pie pkgname plot.new plot_total png pnorm points
poisson poisson.test poissonFdr pos pos2 posRounded protein.ID pval
qf qnorm qvalues read.csv rect ref ref_alt_diff ref_rc
reference_genome_allele refseq.ID row_id row_idx runif sd segments
sequencing_strategy setTxtProgressBar significant site start
startDist statFontSize stripchart survProb symbols t.test tCw
tCw_to_A tCw_to_G tCw_to_G+tCw_to_T tCw_to_T tFdr t_alt_count t_depth
t_ref_count t_vaf tcga_driver tcw temp_af text th title tot tot_depth
total total_perMB total_perMB_log trinucleotide txtProgressBar unit
updown upper upstream vaf value variable variantId variant_ID
verification_platform verification_status wGa wGa_to_A wGa_to_C
wGa_to_T wga wilcox.test write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.copy", "heat.colors",
"png")
importFrom("graphics", "abline", "arrows", "axis", "barplot", "box",
"boxplot", "image", "layout", "legend", "lines", "mtext",
"par", "pie", "plot.new", "points", "rect", "segments",
"stripchart", "symbols", "text", "title")
importFrom("stats", "C", "complete.cases", "cophenetic", "cor.test",
"dbinom", "density", "fisher.test", "glm", "kmeans",
"median", "na.omit", "p.adjust", "pairwise.t.test",
"pairwise.table", "pchisq", "pnorm", "poisson",
"poisson.test", "qf", "qnorm", "runif", "sd", "start",
"t.test", "wilcox.test")
importFrom("utils", "browseURL", "combn", "download.file", "read.csv",
"setTxtProgressBar", "txtProgressBar", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/maftools/libs/maftools.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
maf2mae 17.843 0.476 18.306
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘cancer_hotspots.Rmd’ using ‘UTF-8’... OK
‘cnv_analysis.Rmd’ using ‘UTF-8’... OK
‘maftools.Rmd’ using ‘UTF-8’... OK
‘oncoplots.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/maftools.Rcheck/00check.log’
for details.
maftools.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL maftools
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘maftools’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -c ntcounts.c -o ntcounts.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -c snpcounts.c -o snpcounts.o
snpcounts.c: In function ‘snpcounts’:
snpcounts.c:56:26: warning: passing argument 1 of ‘countlines’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
56 | int nloci = countlines(bedfile);
| ^~~~~~~
snpcounts.c:13:22: note: expected ‘char *’ but argument is of type ‘const char *’
13 | int countlines(char *filename){
| ~~~~~~^~~~~~~~
snpcounts.c:89:47: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=]
89 | fprintf(tsv_fp, "#idxstats_mapped_reads\t%llu\n", tot_mapped);
| ~~~^ ~~~~~~~~~~
| | |
| | uint64_t {aka long unsigned int}
| long long unsigned int
| %lu
gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/zlibbioc/include' -I/usr/local/include -fPIC -g -O2 -c somaticfreq.c -o somaticfreq.o
gcc -shared -L/usr/local/lib -o maftools.so ntcounts.o snpcounts.o somaticfreq.o /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/Rhtslib/usrlib/libhts.a -lcurl
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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 | 0.245 | 0.013 | 0.247 | |
| OncogenicPathways | 0.943 | 0.023 | 0.951 | |
| PlotOncogenicPathways | 0.379 | 0.023 | 0.387 | |
| annovarToMaf | 0.219 | 0.004 | 0.214 | |
| clinicalEnrichment | 0.001 | 0.000 | 0.001 | |
| coBarplot | 0.351 | 0.012 | 0.362 | |
| coOncoplot | 0.410 | 0.016 | 0.425 | |
| drugInteractions | 0.563 | 0.064 | 0.612 | |
| estimateSignatures | 0 | 0 | 0 | |
| extractSignatures | 0.000 | 0.001 | 0.000 | |
| filterMaf | 0.968 | 0.014 | 0.940 | |
| forestPlot | 0.307 | 0.004 | 0.309 | |
| genesToBarcodes | 0.418 | 0.004 | 0.407 | |
| genotypeMatrix | 0.379 | 0.016 | 0.379 | |
| getClinicalData | 0.402 | 0.048 | 0.436 | |
| getCytobandSummary | 0.758 | 0.034 | 0.777 | |
| getFields | 0.599 | 0.033 | 0.616 | |
| getGeneSummary | 0.359 | 0.006 | 0.350 | |
| getSampleSummary | 0.363 | 0.001 | 0.349 | |
| gisticBubblePlot | 0.725 | 0.012 | 0.718 | |
| gisticChromPlot | 0.846 | 0.004 | 0.825 | |
| gisticOncoPlot | 0.750 | 0.004 | 0.734 | |
| icgcSimpleMutationToMAF | 0.078 | 0.004 | 0.084 | |
| inferHeterogeneity | 0 | 0 | 0 | |
| lollipopPlot | 0.901 | 0.021 | 0.905 | |
| lollipopPlot2 | 1.291 | 0.016 | 1.293 | |
| maf2mae | 17.843 | 0.476 | 18.306 | |
| mafCompare | 0.281 | 0.012 | 0.290 | |
| mafSummary | 1.424 | 0.044 | 1.440 | |
| mafSurvGroup | 0.419 | 0.012 | 0.417 | |
| mafSurvival | 0.398 | 0.016 | 0.399 | |
| mafbarplot | 0.366 | 0.001 | 0.353 | |
| math.score | 0.392 | 0.000 | 0.377 | |
| mutCountMatrix | 0.507 | 0.300 | 0.788 | |
| oncodrive | 1.515 | 0.022 | 1.491 | |
| oncoplot | 1.279 | 0.031 | 1.295 | |
| oncostrip | 0.388 | 0.009 | 0.381 | |
| pfamDomains | 1.157 | 0.016 | 1.086 | |
| plotApobecDiff | 0 | 0 | 0 | |
| plotCBSsegments | 0.042 | 0.000 | 0.042 | |
| plotClusters | 0 | 0 | 0 | |
| plotOncodrive | 1.614 | 0.006 | 1.569 | |
| plotProtein | 0.934 | 0.004 | 0.927 | |
| plotTiTv | 0.492 | 0.009 | 0.480 | |
| plotVaf | 0.402 | 0.000 | 0.387 | |
| plotmafSummary | 0.440 | 0.008 | 0.431 | |
| prepareMutSig | 0.461 | 0.008 | 0.452 | |
| read.maf | 0.356 | 0.004 | 0.346 | |
| readGistic | 0.715 | 0.039 | 0.733 | |
| setMaf | 0.524 | 0.020 | 0.529 | |
| somaticInteractions | 0.606 | 0.020 | 0.610 | |
| subsetMaf | 0.757 | 0.024 | 0.757 | |
| survGroup | 0.768 | 0.036 | 0.785 | |
| tcgaAvailable | 0.286 | 0.017 | 1.084 | |
| tcgaCompare | 0.790 | 0.267 | 1.040 | |
| tcgaDriverBP | 0.915 | 0.016 | 0.918 | |
| tcgaLoad | 0.617 | 0.032 | 2.679 | |
| titv | 0.510 | 0.044 | 0.536 | |
| tmb | 0.414 | 0.027 | 0.426 | |
| trinucleotideMatrix | 0 | 0 | 0 | |
| write.GisticSummary | 0.813 | 0.038 | 0.830 | |
| write.mafSummary | 0.400 | 0.052 | 0.438 | |