############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.0.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/GRaNIE.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (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 25.603 0.612 26.691 plotCommunitiesStats 25.240 0.514 32.072 plotGeneralGraphStats 23.687 0.558 37.586 plotTFEnrichment 16.691 0.427 20.474 plot_stats_connectionSummary 16.291 0.460 17.691 addConnections_TF_peak 12.296 0.628 13.393 visualizeGRN 12.065 0.415 12.812 plotDiagnosticPlots_TFPeaks 11.384 0.466 19.622 plotGeneralEnrichment 11.363 0.468 19.808 filterGRNAndConnectGenes 8.578 0.879 12.937 add_TF_gene_correlation 6.773 0.236 7.233 getTopNodes 4.942 0.178 5.282 genes-methods 4.870 0.226 8.327 generateStatsSummary 4.881 0.208 8.413 getCounts 4.825 0.225 8.235 getGRNConnections 4.808 0.227 7.772 getParameters 4.757 0.245 6.650 calculateTFEnrichment 4.761 0.204 5.128 overlapPeaksAndTFBS 4.759 0.192 5.142 loadExampleObject 4.755 0.192 5.146 calculateCommunitiesEnrichment 4.744 0.198 5.103 peaks-methods 4.692 0.204 5.108 build_eGRN_graph 4.618 0.249 5.031 calculateGeneralEnrichment 4.659 0.194 5.014 * 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 ‘/Users/biocbuild/bbs-3.15-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.