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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GRaNIE_1.0.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GRaNIE.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.0.7’
* 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 ‘GRaNIE’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addStats: no visible binding for global variable ‘TF.name’
.addStats: no visible binding for global variable ‘peak.ID’
.addStats: no visible binding for global variable ‘gene.ENSEMBL’
.buildGraph: no visible binding for global variable ‘V1_name’
.buildGraph: no visible binding for global variable ‘V2_name’
.buildGraph: no visible binding for global variable ‘V1’
.buildGraph: no visible binding for global variable ‘nodeID’
.buildGraph: no visible binding for global variable ‘V2’
.buildGraph: no visible binding for global variable ‘GRN’
.calcGCContentPeaks: no visible binding for global variable ‘G|C’
.calcGCContentPeaks: no visible binding for global variable ‘GC_class’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘isFiltered’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘peakID’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘gene.ENSEMBL’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘ENSEMBL’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘peak.ID’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘tad.ID’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘r’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘p.raw’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘p_raw.robust’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘r_robust’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘bias_M_p.raw’
.calculatePeakGeneCorrelations: no visible binding for global variable
  ‘bias_LS_p.raw’
.calculatePeakGeneOverlaps: no visible binding for global variable
  ‘peakID’
.calculatePeakGeneOverlaps: no visible binding for global variable
  ‘tadStart’
.calculatePeakGeneOverlaps: no visible binding for global variable
  ‘tadEnd’
.calculatePeakGeneOverlaps: no visible binding for global variable
  ‘tad.ID’
.calculatePeakGeneOverlaps: no visible binding for global variable
  ‘gene.ENSEMBL’
.combineEnrichmentResults: no visible binding for global variable
  ‘pval’
.combineEnrichmentResults: no visible binding for global variable
  ‘Found’
.combineEnrichmentResults: no visible binding for global variable ‘ID’
.computeTF_peak.fdr: no visible binding for global variable ‘TF.name’
.computeTF_peak.fdr: no visible binding for global variable
  ‘isFiltered’
.computeTF_peak.fdr: no visible binding for global variable ‘GC_class’
.computeTF_peak.fdr: no visible binding for global variable
  ‘peak_width’
.computeTF_peak.fdr: no visible binding for global variable ‘n_rel’
.computeTF_peak.fdr: no visible binding for global variable
  ‘GC_class.all’
.computeTF_peak.fdr: no visible binding for global variable ‘n.bg’
.computeTF_peak.fdr: no visible binding for global variable ‘n_rel.fg’
.computeTF_peak.fdr: no visible binding for global variable
  ‘n.bg.needed’
.computeTF_peak.fdr: no visible binding for global variable ‘peakID’
.computeTF_peak.fdr: no visible binding for global variable
  ‘TF_peak.r_bin2’
.computeTF_peak.fdr: no visible binding for global variable ‘TF_peak.r’
.computeTF_peak.fdr: no visible binding for global variable
  ‘TF_peak.r_bin’
.computeTF_peak.fdr: no visible binding for global variable ‘tpvalue’
.computeTF_peak.fdr: no visible binding for global variable ‘fpvalue’
.computeTF_peak.fdr: no visible binding for global variable
  ‘fpvalue_norm’
.computeTF_peak.fdr: no visible binding for global variable
  ‘TF_peak.fdr’
.computeTF_peak.fdr: no visible binding for global variable
  ‘TF_peak.fdr_orig’
.computeTF_peak.fdr: no visible binding for global variable
  ‘TF_peak.fdr_direction’
.computeTF_peak.fdr: no visible binding for global variable
  ‘TF_peak.connectionType’
.computeTF_peak.fdr: no visible binding for global variable ‘peak.ID’
.correlateData: no visible binding for global variable ‘GRN’
.correlateData: no visible binding for global variable ‘perm’
.correlateMatrices: no visible binding for global variable ‘ENSEMBL’
.correlateMatrices: no visible binding for global variable ‘peakID’
.createEnichmentTable: no visible binding for global variable
  ‘Description’
.createEnichmentTable: no visible binding for global variable ‘Count’
.createTables_peakGeneQC: no visible binding for global variable
  ‘r_positive’
.createTables_peakGeneQC: no visible binding for global variable
  ‘peak_gene.p.raw.class’
.createTables_peakGeneQC: no visible binding for global variable
  ‘sum_pos’
.createTables_peakGeneQC: no visible binding for global variable
  ‘sum_neg’
.createTables_peakGeneQC: no visible binding for global variable
  ‘enrichment_pos’
.createTables_peakGeneQC: no visible binding for global variable
  ‘sum_n’
.createTables_peakGeneQC: no visible binding for global variable
  ‘n_real’
.createTables_peakGeneQC: no visible binding for global variable
  ‘n_permuted’
.createTables_peakGeneQC: no visible binding for global variable
  ‘ratio_real_raw’
.createTables_peakGeneQC: no visible binding for global variable
  ‘classAll’
.createTables_peakGeneQC: no visible binding for global variable
  ‘n_rneg_real’
.createTables_peakGeneQC: no visible binding for global variable
  ‘n_rpos_real’
.createTables_peakGeneQC: no visible binding for global variable
  ‘n_rneg_random’
.createTables_peakGeneQC: no visible binding for global variable
  ‘n_rpos_random’
.createTables_peakGeneQC: no visible binding for global variable
  ‘peak_gene.p.raw.class.bin’
.createTables_peakGeneQC: no visible binding for global variable
  ‘variable’
.facetLabel: no visible binding for global variable ‘Degree’
.filterGenesByMeanCV: no visible binding for global variable ‘gene.CV’
.filterGenesByMeanCV: no visible binding for global variable
  ‘gene.mean’
.filterPeaksByCV: no visible binding for global variable ‘peak.CV’
.filterPeaksByMeanCV: no visible binding for global variable ‘peak.CV’
.filterPeaksByMeanCV: no visible binding for global variable
  ‘peak.mean’
.filterSortAndShuffle_peakTF_overlapTable: no visible binding for
  global variable ‘isFiltered’
.finalizeClassificationAndAppend: no visible binding for global
  variable ‘TF’
.findMaxBackgroundSize: no visible binding for global variable
  ‘GC_class’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
  ‘GC_class’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
  ‘peak_width’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
  ‘n.bg.needed.perc’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
  ‘n_rel’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
  ‘n.bg.needed.relFreq’
.getBackgroundGenes: no visible binding for global variable
  ‘geneAnnotation’
.getDegreeStats: no visible binding for global variable
  ‘connectionType’
.getDegreeStats: no visible binding for global variable ‘V1_name’
.getDegreeStats: no visible binding for global variable ‘V1’
.getDegreeStats: no visible binding for global variable ‘name_plot’
.getDegreeStats: no visible binding for global variable ‘V2’
.getDegreeStats: no visible binding for global variable ‘V2_name’
.getDegreeStats: no visible binding for global variable ‘Degree’
.getDegreeStats: no visible binding for global variable ‘ID’
.getDegreeStats: no visible binding for global variable ‘ID_all’
.getEigenCentralVertices: no visible binding for global variable
  ‘connectionType’
.getEigenCentralVertices: no visible binding for global variable ‘V2’
.getEigenCentralVertices: no visible binding for global variable ‘V1’
.getEigenCentralVertices: no visible binding for global variable
  ‘V2_name’
.getEigenCentralVertices: no visible binding for global variable
  ‘gene.name’
.getEigenCentralVertices: no visible binding for global variable
  ‘gene.ENSEMBL’
.getEigenCentralVertices: no visible binding for global variable
  ‘Score’
.getEigenCentralVertices: no visible binding for global variable
  ‘V1_name’
.getEigenCentralVertices: no visible binding for global variable
  ‘TF.name’
.getEigenCentralVertices: no visible binding for global variable
  ‘TF.ENSEMBL’
.getEigenCentralVertices: no visible binding for global variable
  ‘name_plot’
.getFinalListOfTFs: no visible binding for global variable ‘ENSEMBL’
.getFinalListOfTFs: no visible binding for global variable ‘HOCOID’
.getKnownGeneAnnotationNew: no visible binding for global variable
  ‘gene.type’
.intersectTFBSPeaks: no visible binding for global variable
  ‘annotation’
.intersectTFBSPeaks: no visible binding for global variable ‘tfbs_chr’
.intersectTFBSPeaks: no visible binding for global variable
  ‘tfbs_start’
.intersectTFBSPeaks: no visible binding for global variable ‘tfbs_end’
.intersectTFBSPeaks: no visible binding for global variable
  ‘peak_start’
.intersectTFBSPeaks: no visible binding for global variable ‘peak_end’
.intersectTFBSPeaks: no visible binding for global variable
  ‘coordSummit’
.intersectTFBSPeaks: no visible binding for global variable
  ‘coordCentTfbs’
.intersectTFBSPeaks: no visible binding for global variable ‘peakID’
.optimizeSpaceGRN: no visible binding for global variable ‘TF.name’
.optimizeSpaceGRN: no visible binding for global variable
  ‘TF_peak.r_bin’
.optimizeSpaceGRN: no visible binding for global variable ‘peak.ID’
.optimizeSpaceGRN: no visible binding for global variable
  ‘TF_peak.fdr_direction’
.optimizeSpaceGRN: no visible binding for global variable
  ‘TF_peak.connectionType’
.performIHW: no visible binding for global variable ‘adj_pvalue’
.performIHW: no visible binding for global variable ‘group’
.performIHW: no visible binding for global variable ‘pValues’
.performIHW: no visible binding for global variable ‘covariate_group’
.performIHW: no visible binding for global variable ‘covariateRank’
.plotDensity: no visible binding for global variable ‘variable’
.plotDensity: no visible binding for global variable ‘value’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘gene.ENSEMBL’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘gene.type’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘gene.mean’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘gene.median’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘gene.CV’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak.GC.perc’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak.ID’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak_gene.r’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak_gene.distance’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak_gene.p_raw’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak_gene.p_raw.robust’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘r_positive’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak_gene.p.raw.class’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘ratio’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘classAll’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak_gene.r.class’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘nnorm’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak.CV’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘classNew’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘ratio_pos_raw’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
  variable ‘peak_gene.distance_class_abs’
.plotEnrichmentGeneral: no visible binding for global variable ‘Term’
.plotEnrichmentGeneral: no visible binding for global variable ‘pval’
.plotEnrichmentGeneral: no visible binding for global variable
  ‘GeneRatio’
.plotEnrichmentGeneral: no visible binding for global variable ‘Found’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘TF_peak.connectionType’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘direction’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘nForeground’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘nBackground_orig’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘nBackground’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘ratio_fg_bg_orig’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘ratio_fg_bg’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘background_match_success’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
  ‘percBackgroundUsed’
.plot_PCA_wrapper: no visible binding for global variable ‘sampleID’
.plot_PCA_wrapper: no visible binding for global variable ‘variation’
.plot_PCA_wrapper: no visible binding for global variable ‘PCs’
.plot_PCA_wrapper: no visible binding for global variable
  ‘variation_sum’
.plot_PCA_wrapper: no visible binding for global variable ‘PC1’
.plot_PCA_wrapper: no visible binding for global variable ‘PC2’
.plot_TF_peak_fdr: no visible binding for global variable ‘TF.name’
.plot_TF_peak_fdr: no visible binding for global variable
  ‘TF_peak.fdr_direction’
.plot_TF_peak_fdr: no visible binding for global variable
  ‘TF_peak.r_bin’
.plot_TF_peak_fdr: no visible binding for global variable ‘variable’
.plot_TF_peak_fdr: no visible binding for global variable ‘value’
.plot_classCorrelations: no visible binding for global variable
  ‘baseMean’
.plot_classCorrelations: no visible binding for global variable
  ‘weighted_meanDifference’
.plot_classCorrelations: no visible binding for global variable
  ‘log2FoldChange’
.plot_classCorrelations: no visible binding for global variable
  ‘baseMeanNorm’
.plot_heatmapAR: no visible binding for global variable ‘HOCOID’
.plot_stats_connectionSummaryBoxplot: no visible binding for global
  variable ‘networkType’
.plot_stats_connectionSummaryBoxplot: no visible binding for global
  variable ‘Freq’
.plot_stats_connectionSummaryDensity: no visible binding for global
  variable ‘TF_peak.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
  variable ‘allowMissingGenes’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
  variable ‘allowMissingTFs’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
  variable ‘TF_peak.connectionType’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
  variable ‘peak_gene.p_raw’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
  variable ‘perm’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
  variable ‘TF_peak.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
  variable ‘peak_gene.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
  variable ‘nTFs’
.populateGeneAnnotation: no visible binding for global variable
  ‘ENSEMBL’
.populatePeakAnnotation: no visible binding for global variable
  ‘peakID’
.populatePeakAnnotation: no visible binding for global variable
  ‘isFiltered’
.populatePeakAnnotation: no visible binding for global variable
  ‘annotation’
.populatePeakAnnotation: no visible binding for global variable
  ‘geneId’
.populatePeakAnnotation: no visible binding for global variable
  ‘distanceToTSS’
.populatePeakAnnotation: no visible binding for global variable
  ‘ENSEMBL’
.populatePeakAnnotation: no visible binding for global variable
  ‘SYMBOL’
.populatePeakAnnotation: no visible binding for global variable
  ‘GENENAME’
.populatePeakAnnotation: no visible binding for global variable
  ‘geneChr’
.populatePeakAnnotation: no visible binding for global variable
  ‘geneStart’
.populatePeakAnnotation: no visible binding for global variable
  ‘geneEnd’
.populatePeakAnnotation: no visible binding for global variable
  ‘geneLength’
.populatePeakAnnotation: no visible binding for global variable
  ‘geneStrand’
.printLoopsGraph: no visible binding for global variable ‘V1’
.printLoopsGraph: no visible binding for global variable ‘V2’
.printLoopsGraph: no visible binding for global variable ‘V1_name’
.printLoopsGraph: no visible binding for global variable
  ‘V1_name_combined’
.printMultipleEdges: no visible binding for global variable ‘V1’
.printMultipleEdges: no visible binding for global variable ‘V2’
.readHOCOMOCOTable: no visible binding for global variable ‘ENSEMBL’
.retrieveAnnotationData: no visible binding for global variable
  ‘chromosome_name’
.retrieveAnnotationData: no visible binding for global variable
  ‘start_position’
.retrieveAnnotationData: no visible binding for global variable
  ‘end_position’
.retrieveAnnotationData: no visible binding for global variable
  ‘ensembl_gene_id’
.retrieveAnnotationData: no visible binding for global variable
  ‘gene_biotype’
.retrieveAnnotationData: no visible binding for global variable
  ‘external_gene_name’
.retrieveAnnotationData: no visible binding for global variable
  ‘gene.strand’
.runEnrichment: no visible binding for global variable ‘GRN’
.runEnrichment: no visible binding for global variable ‘GO.ID’
.runEnrichment: no visible binding for global variable ‘Significant’
.runEnrichment: no visible binding for global variable ‘Found’
.selectCommunitesByRank: no visible binding for global variable
  ‘community’
AR_classification_wrapper: no visible binding for global variable
  ‘HOCOID’
AR_classification_wrapper: no visible binding for global variable
  ‘TF.name’
addData: no visible binding for global variable ‘ENSEMBL’
addData: no visible binding for global variable ‘peakID’
addData: no visible binding for global variable ‘sampleID’
addData: no visible binding for global variable ‘has_RNA’
addData: no visible binding for global variable ‘has_peaks’
addData: no visible binding for global variable ‘has_both’
addData_TFActivity: no visible binding for global variable ‘ENSEMBL’
addData_TFActivity: no visible binding for global variable ‘TF.name’
addSNPOverlap: no visible binding for global variable ‘peak’
addSNPOverlap: no visible binding for global variable ‘SNP_chr’
addTFBS: no visible binding for global variable ‘HOCOID’
addTFBS: no visible binding for global variable ‘ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
  ‘gene.ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
  ‘TF.name’
add_TF_gene_correlation: no visible binding for global variable
  ‘ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
  ‘TF.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘gene.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘TF.name’
build_eGRN_graph: no visible binding for global variable ‘peak.ID’
build_eGRN_graph: no visible binding for global variable ‘TF.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘TF_peak.r’
build_eGRN_graph: no visible binding for global variable ‘gene.name’
build_eGRN_graph: no visible binding for global variable ‘peak_gene.r’
build_eGRN_graph: no visible binding for global variable ‘V1’
build_eGRN_graph: no visible binding for global variable ‘V2’
build_eGRN_graph: no visible binding for global variable ‘V1_name’
build_eGRN_graph: no visible binding for global variable ‘V2_name’
build_eGRN_graph: no visible binding for global variable ‘r’
build_eGRN_graph: no visible binding for global variable
  ‘connectionType’
build_eGRN_graph: no visible binding for global variable ‘V2.peak_gene’
build_eGRN_graph: no visible binding for global variable
  ‘V1_name.TF_peak’
build_eGRN_graph: no visible binding for global variable
  ‘V2_name.peak_gene’
calculateCommunitiesEnrichment: no visible binding for global variable
  ‘community’
calculateCommunitiesEnrichment: no visible binding for global variable
  ‘name’
calculateTFEnrichment: no visible binding for global variable ‘TF.name’
calculateTFEnrichment: no visible binding for global variable
  ‘gene.ENSEMBL’
filterData: no visible binding for global variable ‘ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
  ‘HOCOID’
filterGRNAndConnectGenes: no visible binding for global variable
  ‘ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
  ‘TF.ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
  ‘peak_gene.distance’
filterGRNAndConnectGenes: no visible binding for global variable
  ‘peak.ID’
filterGRNAndConnectGenes: no visible binding for global variable
  ‘gene.ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
  ‘TF.name’
getBasic_metadata_visualization: no visible binding for global variable
  ‘ENSEMBL’
getBasic_metadata_visualization: no visible binding for global variable
  ‘ENSEMBL_ID’
getBasic_metadata_visualization: no visible binding for global variable
  ‘peakID’
getCounts: no visible binding for global variable ‘isFiltered’
getCounts: no visible binding for global variable ‘ENSEMBL’
getTopNodes: no visible binding for global variable ‘connectionType’
getTopNodes: no visible binding for global variable ‘Connections’
getTopNodes: no visible binding for global variable ‘V2’
getTopNodes: no visible binding for global variable ‘V2_name’
getTopNodes: no visible binding for global variable ‘V1’
getTopNodes: no visible binding for global variable ‘V1_name’
importTFData: no visible binding for global variable ‘ENSEMBL’
importTFData: no visible binding for global variable ‘TF.name’
nGenes: no visible binding for global variable ‘isFiltered’
nPeaks: no visible binding for global variable ‘isFiltered’
overlapPeaksAndTFBS: no visible binding for global variable
  ‘isFiltered’
overlapPeaksAndTFBS: no visible binding for global variable ‘peakID’
plotCommunitiesEnrichment: no visible binding for global variable
  ‘community’
plotCommunitiesEnrichment: no visible binding for global variable ‘ID’
plotCommunitiesEnrichment: no visible binding for global variable
  ‘pval’
plotCommunitiesEnrichment: no visible global function definition for
  ‘where’
plotCommunitiesEnrichment: no visible binding for global variable
  ‘nSig’
plotCommunitiesEnrichment: no visible binding for global variable
  ‘Term’
plotCommunitiesStats: no visible binding for global variable
  ‘community’
plotCommunitiesStats: no visible binding for global variable ‘isTF’
plotCommunitiesStats: no visible binding for global variable ‘Class’
plotCommunitiesStats: no visible binding for global variable ‘name’
plotCommunitiesStats: no visible binding for global variable
  ‘from_name’
plotCommunitiesStats: no visible binding for global variable ‘to_name’
plotCommunitiesStats: no visible binding for global variable
  ‘connectionType’
plotCommunitiesStats: no visible binding for global variable
  ‘from_names_TF_all’
plotCommunitiesStats: no visible binding for global variable
  ‘to_names_gene’
plotGeneralGraphStats: no visible binding for global variable ‘Count’
plotGeneralGraphStats: no visible binding for global variable ‘Class’
plotGeneralGraphStats: no visible binding for global variable ‘Freq’
plotGeneralGraphStats: no visible binding for global variable ‘Var1’
plotTFEnrichment: no visible binding for global variable ‘TF.name’
plotTFEnrichment: no visible binding for global variable ‘ID’
plotTFEnrichment: no visible binding for global variable ‘pval’
plotTFEnrichment: no visible global function definition for ‘where’
plotTFEnrichment: no visible binding for global variable ‘nSig’
plotTFEnrichment: no visible binding for global variable ‘Term’
visualizeGRN: no visible binding for global variable ‘V1_name’
visualizeGRN: no visible binding for global variable ‘TF.name’
visualizeGRN: no visible binding for global variable ‘V2’
visualizeGRN: no visible binding for global variable ‘TF_peak.r’
visualizeGRN: no visible binding for global variable ‘peak_gene.r’
visualizeGRN: no visible binding for global variable ‘TF_peak.fdr’
visualizeGRN: no visible binding for global variable ‘V1’
visualizeGRN: no visible binding for global variable ‘connectionType’
visualizeGRN: no visible binding for global variable ‘color_raw’
visualizeGRN: no visible binding for global variable ‘nCommunitiesMax’
show,GRN: no visible binding for global variable ‘community’
show,GRN: no visible global function definition for ‘desc’
show,GRN: no visible binding for global variable ‘n’
Undefined global functions or variables:
  Class Connections Count Degree Description ENSEMBL ENSEMBL_ID Found
  Freq GC_class GC_class.all GENENAME GO.ID GRN GeneRatio G|C HOCOID ID
  ID_all PC1 PC2 PCs SNP_chr SYMBOL Score Significant TF TF.ENSEMBL
  TF.name TF_peak.connectionType TF_peak.fdr TF_peak.fdr_direction
  TF_peak.fdr_orig TF_peak.r TF_peak.r_bin TF_peak.r_bin2 Term V1
  V1_name V1_name.TF_peak V1_name_combined V2 V2.peak_gene V2_name
  V2_name.peak_gene Var1 adj_pvalue allowMissingGenes allowMissingTFs
  annotation background_match_success baseMean baseMeanNorm
  bias_LS_p.raw bias_M_p.raw chromosome_name classAll classNew
  color_raw community connectionType coordCentTfbs coordSummit
  covariateRank covariate_group desc direction distanceToTSS
  end_position enrichment_pos ensembl_gene_id external_gene_name
  fpvalue fpvalue_norm from_name from_names_TF_all gene.CV gene.ENSEMBL
  gene.mean gene.median gene.name gene.strand gene.type geneAnnotation
  geneChr geneEnd geneId geneLength geneStart geneStrand gene_biotype
  group has_RNA has_both has_peaks isFiltered isTF log2FoldChange n
  n.bg n.bg.needed n.bg.needed.perc n.bg.needed.relFreq nBackground
  nBackground_orig nCommunitiesMax nForeground nSig nTFs n_permuted
  n_real n_rel n_rel.fg n_rneg_random n_rneg_real n_rpos_random
  n_rpos_real name name_plot networkType nnorm nodeID p.raw pValues
  p_raw.robust peak peak.CV peak.GC.perc peak.ID peak.mean peakID
  peak_end peak_gene.distance peak_gene.distance_class_abs
  peak_gene.fdr peak_gene.p.raw.class peak_gene.p.raw.class.bin
  peak_gene.p_raw peak_gene.p_raw.robust peak_gene.r peak_gene.r.class
  peak_start peak_width percBackgroundUsed perm pval r r_positive
  r_robust ratio ratio_fg_bg ratio_fg_bg_orig ratio_pos_raw
  ratio_real_raw sampleID start_position sum_n sum_neg sum_pos tad.ID
  tadEnd tadStart tfbs_chr tfbs_end tfbs_start to_name to_names_gene
  tpvalue value variable variation variation_sum
  weighted_meanDifference where
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotCommunitiesEnrichment':
plotCommunitiesEnrichment
  Code: function(GRN, outputFolder = NULL, basenameOutput = NULL,
                 display = "byRank", communities = NULL, topn_pvalue =
                 30, p = 0.05, nSignificant = 2, nID = 10,
                 maxWidth_nchar_plot = 50, display_pAdj = FALSE,
                 plotAsPDF = TRUE, pdf_width = 12, pdf_height = 12,
                 pages = NULL, forceRerun = FALSE)
  Docs: function(GRN, outputFolder = NULL, basenameOutput = NULL,
                 display = "byRank", communities = NULL, topn_pvalue =
                 30, p = 0.05, nSignificant = 2, nID = 10,
                 maxWidth_nchar_plot = 100, display_pAdj = FALSE,
                 plotAsPDF = TRUE, pdf_width = 12, pdf_height = 12,
                 pages = NULL, forceRerun = FALSE)
  Mismatches in argument default values:
    Name: 'maxWidth_nchar_plot' Code: 50 Docs: 100

Codoc mismatches from documentation object 'plotGeneralEnrichment':
plotGeneralEnrichment
  Code: function(GRN, outputFolder = NULL, basenameOutput = NULL,
                 ontology = NULL, topn_pvalue = 30, p = 0.05,
                 display_pAdj = FALSE, maxWidth_nchar_plot = 50,
                 plotAsPDF = TRUE, pdf_width = 12, pdf_height = 12,
                 pages = NULL, forceRerun = FALSE)
  Docs: function(GRN, outputFolder = NULL, basenameOutput = NULL,
                 ontology = NULL, topn_pvalue = 30, p = 0.05,
                 display_pAdj = FALSE, plotAsPDF = TRUE, pdf_width =
                 12, pdf_height = 12, pages = NULL, forceRerun = FALSE)
  Argument names in code not in docs:
    maxWidth_nchar_plot
  Mismatches in argument names (first 3):
    Position: 8 Code: maxWidth_nchar_plot Docs: plotAsPDF
    Position: 9 Code: plotAsPDF Docs: pdf_width
    Position: 10 Code: pdf_width Docs: pdf_height

Codoc mismatches from documentation object 'plotTFEnrichment':
plotTFEnrichment
  Code: function(GRN, rankType = "degree", n = NULL, TF.names = NULL,
                 topn_pvalue = 30, p = 0.05, nSignificant = 2, nID =
                 10, display_pAdj = FALSE, maxWidth_nchar_plot = 50,
                 outputFolder = NULL, basenameOutput = NULL, plotAsPDF
                 = TRUE, pdf_width = 12, pdf_height = 12, pages = NULL,
                 forceRerun = FALSE)
  Docs: function(GRN, rankType = "degree", n = NULL, TF.names = NULL,
                 topn_pvalue = 30, p = 0.05, nSignificant = 2, nID =
                 10, display_pAdj = FALSE, maxWidth_nchar_plot = 100,
                 outputFolder = NULL, basenameOutput = NULL, plotAsPDF
                 = TRUE, pdf_width = 12, pdf_height = 12, pages = NULL,
                 forceRerun = FALSE)
  Mismatches in argument default values:
    Name: 'maxWidth_nchar_plot' Code: 50 Docs: 100

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
plotCommunitiesEnrichment    20.191  1.563  25.541
plotCommunitiesStats         16.719  1.476  19.056
plotGeneralGraphStats        11.446  1.028  12.846
plotTFEnrichment              8.033  0.732   9.107
plot_stats_connectionSummary  7.436  0.704   8.484
visualizeGRN                  6.912  0.835   8.086
plotGeneralEnrichment         5.477  0.756   6.659
plotDiagnosticPlots_TFPeaks   5.234  0.552   6.185
loadExampleObject             4.613  0.495   5.753
getCounts                     4.407  0.372   5.927
addConnections_TF_peak        4.147  0.611   5.939
getGRNConnections             3.844  0.412   5.173
getTopNodes                   3.806  0.360   5.702
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘GRaNIE’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (GRaNIE)