merida1 Summary
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| Package: GRaNIE |
| Version: 0.99.1 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GRaNIE |
| BuildTime: 6 minutes 4.44 seconds |
| CheckCommand: BiocCheckGitClone('GRaNIE') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GRaNIE_0.99.1.tar.gz && BiocCheck('GRaNIE_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 12 minutes 13.71 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh GRaNIE_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 43.22 seconds |
| PackageFileSize: 41968.46 KiB |
| BuildID:: GRaNIE_20220321183527 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GRaNIE. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* preparing ‘GRaNIE’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
Omitted ‘LazyData’ from DESCRIPTION
* building ‘GRaNIE_0.99.1.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('GRaNIE')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git
tracked:R/.Rhistory
R/.Rhistory
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2556/GRaNIE_20220321183527/GRaNIE.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* 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 ‘0.99.1’
* 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 ... [40s/41s] OK
* checking installed package size ... NOTE
installed size is 11.8Mb
sub-directories of 1Mb or more:
R 2.9Mb
doc 8.3Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [40s/40s] 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’
.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’
.plotTF_peak_TFActivity_QC: no visible binding for global variable
‘permIndex’
.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’
.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 ‘fileCur’
visualizeGRN: no visible binding for global variable ‘TF’
visualizeGRN: no visible binding for global variable ‘peak’
visualizeGRN: no visible binding for global variable ‘TF_peak.fdr’
visualizeGRN: no visible binding for global variable ‘TF_peak.r’
visualizeGRN: no visible binding for global variable ‘ENSEMBL’
visualizeGRN: no visible binding for global variable ‘peak_gene.r’
visualizeGRN: no visible binding for global variable
‘peak_gene.distance’
visualizeGRN: no visible binding for global variable ‘color_raw’
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 classAll classNew color_raw community
connectionType coordCentTfbs coordSummit covariateRank
covariate_group desc direction distanceToTSS enrichment_pos fileCur
fpvalue fpvalue_norm from_name from_names_TF_all gene.CV gene.ENSEMBL
gene.mean gene.median gene.name gene.type geneChr geneEnd geneId
geneLength geneStart geneStrand 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 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 permIndex pval r r_positive r_robust ratio
ratio_fg_bg ratio_fg_bg_orig ratio_pos_raw ratio_real_raw sampleID
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 ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [244s/346s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addConnections_peak_gene 30.030 1.585 34.928
plotPCA_all 23.064 0.930 27.664
generateStatsSummary 13.196 0.726 17.297
plotCommunitiesEnrichment 12.560 0.725 17.066
plotCommunitiesStats 10.081 0.760 14.519
plotTFEnrichment 8.111 0.739 13.596
addConnections_TF_peak 6.792 1.302 14.572
plotGeneralGraphStats 7.108 0.701 11.363
add_TF_gene_correlation 5.488 0.711 9.562
plotDiagnosticPlots_TFPeaks 4.938 0.666 9.296
plotGeneralEnrichment 4.549 0.684 8.882
filterGRNAndConnectGenes 4.347 0.638 8.340
plot_stats_connectionSummary 4.048 0.693 10.833
getTopNodes 3.968 0.659 7.984
overlapPeaksAndTFBS 3.908 0.679 7.765
peaks-methods 3.870 0.667 7.933
loadExampleObject 3.858 0.677 7.635
calculateTFEnrichment 3.783 0.676 7.668
calculateCommunitiesEnrichment 3.746 0.638 7.819
getParameters 3.678 0.658 7.568
build_eGRN_graph 3.667 0.667 7.757
calculateGeneralEnrichment 3.696 0.637 7.577
getGRNConnections 3.680 0.653 7.712
genes-methods 3.675 0.655 7.561
changeOutputDirectory 3.669 0.652 7.508
getCounts 3.674 0.632 7.749
calculateCommunitiesStats 3.664 0.635 7.671
filterData 3.651 0.628 7.631
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [146s/153s]
[146s/154s] OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘png’
'library' or 'require' call not declared from: ‘png’
* 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: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2556/GRaNIE_20220321183527/GRaNIE.Rcheck/00check.log’
for details.
===============================
BiocCheck('GRaNIE_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2556/GRaNIE_20220321183527/GRaNIE_0.99.1.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpLjWjKD/file107914c4737c0/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 42.9757 MB
Size Requirement: 5.0000 MB
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Microarray, Network
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of GRaNIE...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
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R/diffTF_sharedFunctions.R (line 52, column 14)
R/diffTF_sharedFunctions.R (line 642, column 14)
R/helperFunctions.R (line 620, column 39)
R/network.R (line 668, column 33)
R/plot.R (line 3619, column 32)
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print() in R/plot.R (line 1972, column 5)
print() in R/plot.R (line 1989, column 7)
print() in R/plot.R (line 1990, column 7)
print() in R/plot.R (line 1991, column 7)
print() in R/plot.R (line 2010, column 7)
print() in R/plot.R (line 2011, column 7)
print() in R/plot.R (line 2012, column 7)
print() in R/plot.R (line 2591, column 7)
print() in R/plot.R (line 2620, column 7)
print() in R/plot.R (line 2884, column 7)
print() in R/plot.R (line 2913, column 7)
* NOTE: Avoid using '=' for assignment and use '<-' instead
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* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/helperFunctions.R (line 254, column 17)
R/helperFunctions.R (line 611, column 10)
R/helperFunctions.R (line 611, column 48)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 19
times)
suppressWarnings() in R/core.R (line 1138, column 11)
suppressWarnings() in R/core.R (line 2352, column 5)
suppressWarnings() in R/core.R (line 2353, column 5)
suppressWarnings() in R/core.R (line 2514, column 20)
suppressWarnings() in R/core.R (line 2670, column 12)
suppressWarnings() in R/core.R (line 2976, column 18)
suppressWarnings() in R/core.R (line 2978, column 18)
suppressMessages() in R/core.R (line 432, column 23)
suppressMessages() in R/core.R (line 1084, column 13)
suppressMessages() in R/core.R (line 2337, column 20)
suppressMessages() in R/core.R (line 2338, column 20)
suppressMessages() in R/core.R (line 2608, column 12)
suppressMessages() in R/core.R (line 3393, column 18)
suppressWarnings() in R/network.R (line 378, column 24)
suppressMessages() in R/network.R (line 530, column 21)
suppressMessages() in R/network.R (line 539, column 14)
suppressWarnings() in R/plot.R (line 653, column 13)
suppressWarnings() in R/plot.R (line 692, column 13)
suppressWarnings() in R/plot.R (line 1837, column 17)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 68 functions > 50 lines.
The longest 5 functions are:
.plotDiagnosticPlots_peakGene_all() (R/plot.R, line 856): 583
lines
visualizeGRN() (R/plot.R, line 3192): 471 lines
filterGRNAndConnectGenes() (R/core.R, line 2761): 394 lines
.computeTF_peak.fdr() (R/core.R, line 1761): 391 lines
plotTFEnrichment() (R/plot.R, line 2702): 302 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
addData.Rd, addTFBS.Rd, AR_classification_wrapper.Rd,
deleteIntermediateData.Rd, performAllNetworkAnalyses.Rd,
plotDiagnosticPlots_peakGene.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 2604 lines (18%) are > 80
characters long.
First 6 lines:
R/core.R:6 #' @param objectMetadata List. Default \code{list()}. Option...
R/core.R:7 #' @param outputFolder Absolute file path. No default. Defau...
R/core.R:8 #' @param genomeAssembly Character. No default. The genome a...
R/core.R:12 #' GRN = initializeGRN(objectMetadata = meta.l, outputFolde...
R/core.R:20 checkmate::assert(checkmate::checkNull(objectMetadata), c...
R/core.R:51 par.l$packageVersion = ifelse(is.null(packageName), NA, p...
* NOTE: Consider 4 spaces instead of tabs; 23 lines (0%) contain
tabs.
First 6 lines:
R/plot.R:3639 # vertex.color Node color
R/plot.R:3640 # vertex.frame.color Node border color
R/plot.R:3641 # vertex.shape One of “none”, “circle”, “square”, “c...
R/plot.R:3642 # vertex.size Size of the node (default is 15)
R/plot.R:3643 # vertex.size2 The second size of the node (e.g. for...
R/plot.R:3644 # vertex.label Character vector used to label the nodes
* NOTE: Consider multiples of 4 spaces for line indents, 5441
lines(39%) are not.
First 6 lines:
R/core.R:17 outputFolder,
R/core.R:18 genomeAssembly) {
R/core.R:19
R/core.R:20 checkmate::assert(checkmate::checkNull(objectMetadata), c...
R/core.R:21 checkmate::assertSubset(genomeAssembly, c("hg19","hg38", ...
R/core.R:22
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir GRaNIE_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘GRaNIE’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
*** copying figures
** 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)
nebbiolo1 Summary
[top]
| Package: GRaNIE |
| Version: 0.99.1 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GRaNIE |
| BuildTime: 4 minutes 52.41 seconds |
| CheckCommand: BiocCheckGitClone('GRaNIE') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings GRaNIE_0.99.1.tar.gz && BiocCheck('GRaNIE_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 15 minutes 0.00 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 41967.54 KiB |
| BuildID:: GRaNIE_20220321183527 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: GRaNIE. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: -9. |
nebbiolo1 BUILD SRC output
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R CMD BUILD
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* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* preparing ‘GRaNIE’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
Omitted ‘LazyData’ from DESCRIPTION
* building ‘GRaNIE_0.99.1.tar.gz’
nebbiolo1 CHECK output
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BiocCheckGitClone('GRaNIE')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git
tracked:R/.Rhistory
R/.Rhistory
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2556/GRaNIE_20220321183527/GRaNIE.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* 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 ‘0.99.1’
* 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 ... [25s/26s] OK
* checking installed package size ... NOTE
installed size is 10.9Mb
sub-directories of 1Mb or more:
R 2.9Mb
doc 7.3Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [26s/26s] 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’
.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’
.plotTF_peak_TFActivity_QC: no visible binding for global variable
‘permIndex’
.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’
.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 ‘fileCur’
visualizeGRN: no visible binding for global variable ‘TF’
visualizeGRN: no visible binding for global variable ‘peak’
visualizeGRN: no visible binding for global variable ‘TF_peak.fdr’
visualizeGRN: no visible binding for global variable ‘TF_peak.r’
visualizeGRN: no visible binding for global variable ‘ENSEMBL’
visualizeGRN: no visible binding for global variable ‘peak_gene.r’
visualizeGRN: no visible binding for global variable
‘peak_gene.distance’
visualizeGRN: no visible binding for global variable ‘color_raw’
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 classAll classNew color_raw community
connectionType coordCentTfbs coordSummit covariateRank
covariate_group desc direction distanceToTSS enrichment_pos fileCur
fpvalue fpvalue_norm from_name from_names_TF_all gene.CV gene.ENSEMBL
gene.mean gene.median gene.name gene.type geneChr geneEnd geneId
geneLength geneStart geneStrand 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 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 permIndex pval r r_positive r_robust ratio
ratio_fg_bg ratio_fg_bg_orig ratio_pos_raw ratio_real_raw sampleID
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 ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('GRaNIE_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2556/GRaNIE_20220321183527/GRaNIE_0.99.1.tar.gz" "/tmp/Rtmpra2Zsl/file39043f457872c9/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 to 4.2.0.
* Checking package size...
* ERROR: Package Source tarball exceeds Bioconductor size
requirement.
Package Size: 42.9748 MB
Size Requirement: 5.0000 MB
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Microarray, Network
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of GRaNIE...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/core.R (line 334, column 22)
R/core.R (line 341, column 51)
R/core.R (line 342, column 52)
R/core.R (line 343, column 52)
R/core.R (line 354, column 13)
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R/core.R (line 358, column 11)
R/core.R (line 690, column 13)
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R/core.R (line 693, column 11)
R/core.R (line 694, column 11)
R/core.R (line 3536, column 37)
R/core.R (line 3537, column 48)
R/core.R (line 3538, column 48)
R/diffTF_sharedFunctions.R (line 52, column 14)
R/diffTF_sharedFunctions.R (line 642, column 14)
R/helperFunctions.R (line 620, column 39)
R/network.R (line 668, column 33)
R/plot.R (line 3619, column 32)
R/plot.R (line 3620, column 25)
R/plot.R (line 3621, column 32)
R/plot.R (line 3624, column 25)
R/plot.R (line 3625, column 25)
R/plot.R (line 3626, column 25)
R/plot.R (line 3629, column 25)
R/plot.R (line 3631, column 25)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/plot.R (line 1972, column 5)
print() in R/plot.R (line 1989, column 7)
print() in R/plot.R (line 1990, column 7)
print() in R/plot.R (line 1991, column 7)
print() in R/plot.R (line 2010, column 7)
print() in R/plot.R (line 2011, column 7)
print() in R/plot.R (line 2012, column 7)
print() in R/plot.R (line 2591, column 7)
print() in R/plot.R (line 2620, column 7)
print() in R/plot.R (line 2884, column 7)
print() in R/plot.R (line 2913, column 7)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/core.R (line 27, column 16)
R/core.R (line 31, column 18)
R/core.R (line 35, column 20)
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R/core.R (line 336, column 13)
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R/core.R (line 353, column 7)
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R/core.R (line 355, column 11)
R/core.R (line 356, column 11)
R/core.R (line 357, column 9)
R/core.R (line 358, column 9)
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R/core.R (line 377, column 21)
R/core.R (line 389, column 17)
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R/core.R (line 410, column 20)
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R/core.R (line 418, column 33)
R/core.R (line 421, column 13)
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R/core.R (line 432, column 21)
R/core.R (line 449, column 39)
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R/core.R (line 452, column 81)
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R/core.R (line 455, column 35)
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R/zzz.R (line 4, column 13)
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/helperFunctions.R (line 254, column 17)
R/helperFunctions.R (line 611, column 10)
R/helperFunctions.R (line 611, column 48)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 19
times)
suppressWarnings() in R/core.R (line 1138, column 11)
suppressWarnings() in R/core.R (line 2352, column 5)
suppressWarnings() in R/core.R (line 2353, column 5)
suppressWarnings() in R/core.R (line 2514, column 20)
suppressWarnings() in R/core.R (line 2670, column 12)
suppressWarnings() in R/core.R (line 2976, column 18)
suppressWarnings() in R/core.R (line 2978, column 18)
suppressMessages() in R/core.R (line 432, column 23)
suppressMessages() in R/core.R (line 1084, column 13)
suppressMessages() in R/core.R (line 2337, column 20)
suppressMessages() in R/core.R (line 2338, column 20)
suppressMessages() in R/core.R (line 2608, column 12)
suppressMessages() in R/core.R (line 3393, column 18)
suppressWarnings() in R/network.R (line 378, column 24)
suppressMessages() in R/network.R (line 530, column 21)
suppressMessages() in R/network.R (line 539, column 14)
suppressWarnings() in R/plot.R (line 653, column 13)
suppressWarnings() in R/plot.R (line 692, column 13)
suppressWarnings() in R/plot.R (line 1837, column 17)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 68 functions > 50 lines.
The longest 5 functions are:
.plotDiagnosticPlots_peakGene_all() (R/plot.R, line 856): 583
lines
visualizeGRN() (R/plot.R, line 3192): 471 lines
filterGRNAndConnectGenes() (R/core.R, line 2761): 394 lines
.computeTF_peak.fdr() (R/core.R, line 1761): 391 lines
plotTFEnrichment() (R/plot.R, line 2702): 302 lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
addData.Rd, addTFBS.Rd, AR_classification_wrapper.Rd,
deleteIntermediateData.Rd, performAllNetworkAnalyses.Rd,
plotDiagnosticPlots_peakGene.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 2604 lines (18%) are > 80
characters long.
First 6 lines:
R/core.R:6 #' @param objectMetadata List. Default \code{list()}. Option...
R/core.R:7 #' @param outputFolder Absolute file path. No default. Defau...
R/core.R:8 #' @param genomeAssembly Character. No default. The genome a...
R/core.R:12 #' GRN = initializeGRN(objectMetadata = meta.l, outputFolde...
R/core.R:20 checkmate::assert(checkmate::checkNull(objectMetadata), c...
R/core.R:51 par.l$packageVersion = ifelse(is.null(packageName), NA, p...
* NOTE: Consider 4 spaces instead of tabs; 23 lines (0%) contain
tabs.
First 6 lines:
R/plot.R:3639 # vertex.color Node color
R/plot.R:3640 # vertex.frame.color Node border color
R/plot.R:3641 # vertex.shape One of “none”, “circle”, “square”, “c...
R/plot.R:3642 # vertex.size Size of the node (default is 15)
R/plot.R:3643 # vertex.size2 The second size of the node (e.g. for...
R/plot.R:3644 # vertex.label Character vector used to label the nodes
* NOTE: Consider multiples of 4 spaces for line indents, 5441
lines(39%) are not.
First 6 lines:
R/core.R:17 outputFolder,
R/core.R:18 genomeAssembly) {
R/core.R:19
R/core.R:20 checkmate::assert(checkmate::checkNull(objectMetadata), c...
R/core.R:21 checkmate::assertSubset(genomeAssembly, c("hg19","hg38", ...
R/core.R:22
See http://bioconductor.org/developers/how-to/coding-style/
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 12
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
nebbiolo1 BUILD BIN output
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