############################################################################## ############################################################################## ### ### Running command: ### ### /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 ### ############################################################################## ############################################################################## * 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.