Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:03 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GRaNIE on merida1


To the developers/maintainers of the GRaNIE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRaNIE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 839/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.0.7  (landing page)
Christian Arnold
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: RELEASE_3_15
git_last_commit: 2ff0659
git_last_commit_date: 2022-09-27 06:50:11 -0400 (Tue, 27 Sep 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GRaNIE
Version: 1.0.7
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
StartedAt: 2022-10-19 03:09:51 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 03:20:16 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 625.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GRaNIE.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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.



Installation output

GRaNIE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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)

Tests output


Example timings

GRaNIE.Rcheck/GRaNIE-Ex.timings

nameusersystemelapsed
AR_classification_wrapper000
addConnections_TF_peak12.296 0.62813.393
addConnections_peak_gene4.4220.2014.785
addData0.0000.0000.001
addTFBS000
add_TF_gene_correlation6.7730.2367.233
build_eGRN_graph4.6180.2495.031
calculateCommunitiesEnrichment4.7440.1985.103
calculateCommunitiesStats4.5190.1934.870
calculateGeneralEnrichment4.6590.1945.014
calculateTFEnrichment4.7610.2045.128
changeOutputDirectory4.6080.1844.952
deleteIntermediateData000
filterData4.6000.1884.947
filterGRNAndConnectGenes 8.578 0.87912.937
generateStatsSummary4.8810.2088.413
genes-methods4.8700.2268.327
getCounts4.8250.2258.235
getGRNConnections4.8080.2277.772
getParameters4.7570.2456.650
getTopNodes4.9420.1785.282
initializeGRN0.0220.0010.025
loadExampleObject4.7550.1925.146
overlapPeaksAndTFBS4.7590.1925.142
peaks-methods4.6920.2045.108
performAllNetworkAnalyses0.0000.0010.001
plotCommunitiesEnrichment25.603 0.61226.691
plotCommunitiesStats25.240 0.51432.072
plotDiagnosticPlots_TFPeaks11.384 0.46619.622
plotDiagnosticPlots_peakGene000
plotGeneralEnrichment11.363 0.46819.808
plotGeneralGraphStats23.687 0.55837.586
plotPCA_all0.0000.0000.001
plotTFEnrichment16.691 0.42720.474
plot_stats_connectionSummary16.291 0.46017.691
visualizeGRN12.065 0.41512.812