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) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:03 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (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 | ||||
|
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. |
| Package 839/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GRaNIE 1.0.7 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| 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 |
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### Running command:
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### /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
###
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* 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.
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)
GRaNIE.Rcheck/GRaNIE-Ex.timings
| name | user | system | elapsed | |
| AR_classification_wrapper | 0 | 0 | 0 | |
| addConnections_TF_peak | 12.296 | 0.628 | 13.393 | |
| addConnections_peak_gene | 4.422 | 0.201 | 4.785 | |
| addData | 0.000 | 0.000 | 0.001 | |
| addTFBS | 0 | 0 | 0 | |
| add_TF_gene_correlation | 6.773 | 0.236 | 7.233 | |
| build_eGRN_graph | 4.618 | 0.249 | 5.031 | |
| calculateCommunitiesEnrichment | 4.744 | 0.198 | 5.103 | |
| calculateCommunitiesStats | 4.519 | 0.193 | 4.870 | |
| calculateGeneralEnrichment | 4.659 | 0.194 | 5.014 | |
| calculateTFEnrichment | 4.761 | 0.204 | 5.128 | |
| changeOutputDirectory | 4.608 | 0.184 | 4.952 | |
| deleteIntermediateData | 0 | 0 | 0 | |
| filterData | 4.600 | 0.188 | 4.947 | |
| filterGRNAndConnectGenes | 8.578 | 0.879 | 12.937 | |
| generateStatsSummary | 4.881 | 0.208 | 8.413 | |
| genes-methods | 4.870 | 0.226 | 8.327 | |
| getCounts | 4.825 | 0.225 | 8.235 | |
| getGRNConnections | 4.808 | 0.227 | 7.772 | |
| getParameters | 4.757 | 0.245 | 6.650 | |
| getTopNodes | 4.942 | 0.178 | 5.282 | |
| initializeGRN | 0.022 | 0.001 | 0.025 | |
| loadExampleObject | 4.755 | 0.192 | 5.146 | |
| overlapPeaksAndTFBS | 4.759 | 0.192 | 5.142 | |
| peaks-methods | 4.692 | 0.204 | 5.108 | |
| performAllNetworkAnalyses | 0.000 | 0.001 | 0.001 | |
| plotCommunitiesEnrichment | 25.603 | 0.612 | 26.691 | |
| plotCommunitiesStats | 25.240 | 0.514 | 32.072 | |
| plotDiagnosticPlots_TFPeaks | 11.384 | 0.466 | 19.622 | |
| plotDiagnosticPlots_peakGene | 0 | 0 | 0 | |
| plotGeneralEnrichment | 11.363 | 0.468 | 19.808 | |
| plotGeneralGraphStats | 23.687 | 0.558 | 37.586 | |
| plotPCA_all | 0.000 | 0.000 | 0.001 | |
| plotTFEnrichment | 16.691 | 0.427 | 20.474 | |
| plot_stats_connectionSummary | 16.291 | 0.460 | 17.691 | |
| visualizeGRN | 12.065 | 0.415 | 12.812 | |