nebbiolo1 Summary
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| Package: GRaNIE |
| Version: 0.99.3 |
| 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: 7 minutes 22.94 seconds |
| CheckCommand: BiocCheckGitClone('GRaNIE') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings GRaNIE_0.99.3.tar.gz && BiocCheck('GRaNIE_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 10 minutes 18.28 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 11537.73 KiB |
| BuildID:: GRaNIE_20220321234101 |
| 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: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 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_0.99.3.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...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
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
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2556/197f7c94eb0d68284743301fa87a02299dc16631/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 ‘0.99.3’
* 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/40s] OK
* checking installed package size ... NOTE
installed size is 10.1Mb
sub-directories of 1Mb or more:
R 2.5Mb
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 ... [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 ... [1s/1s] 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 ... [170s/175s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addConnections_peak_gene 25.064 1.328 26.553
plotPCA_all 15.733 1.296 17.189
generateStatsSummary 10.606 0.604 11.368
plotCommunitiesEnrichment 7.959 0.523 8.638
plotCommunitiesStats 6.149 0.436 6.743
addConnections_TF_peak 4.978 0.857 6.666
plotTFEnrichment 4.591 0.408 5.157
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [153s/213s]
[154s/213s] 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
‘/home/pkgbuild/packagebuilder/workers/jobs/2556/197f7c94eb0d68284743301fa87a02299dc16631/GRaNIE.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('GRaNIE_0.99.3.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/2556/197f7c94eb0d68284743301fa87a02299dc16631/GRaNIE_0.99.3.tar.gz" "/tmp/RtmprCarr4/file1a78894572dec1/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: 11.8146 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 642, column 14)
R/helperFunctions.R (line 620, column 39)
R/network.R (line 668, column 33)
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print() in R/plot.R (line 2620, column 7)
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* 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 1139, 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 433, column 23)
suppressMessages() in R/core.R (line 1085, 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 1762): 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; 2609 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 Output folder, either absolute or rel...
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:52 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, 5444
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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merida1 Summary
[top]
| Package: GRaNIE |
| Version: 0.99.3 |
| 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: 13 minutes 39.73 seconds |
| CheckCommand: BiocCheckGitClone('GRaNIE') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GRaNIE_0.99.3.tar.gz && BiocCheck('GRaNIE_0.99.3.tar.gz', `new-package`=TRUE) |
| CheckTime: 14 minutes 59.96 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh GRaNIE_0.99.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 35.08 seconds |
| PackageFileSize: 11537.67 KiB |
| BuildID:: GRaNIE_20220321234101 |
| 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: 0. Installing package status: 0. Build Package status: 0. Checking Package status: -9. 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_0.99.3.tar.gz’
merida1 CHECK output
[top]
===============================
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...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
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
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2556/197f7c94eb0d68284743301fa87a02299dc16631/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 ‘0.99.3’
* 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 ... [79s/95s] OK
* checking installed package size ... NOTE
installed size is 11.0Mb
sub-directories of 1Mb or more:
R 2.5Mb
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 ... [83s/99s] 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 ... [1s/1s] 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 14 mins
===============================
BiocCheck('GRaNIE_0.99.3.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/2556/197f7c94eb0d68284743301fa87a02299dc16631/GRaNIE_0.99.3.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpkMJqvr/file1239d3cfc5687/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: 11.8146 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...
[394s/480s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addConnections_peak_gene 64.426 2.502 82.477
plotPCA_all 44.479 0.870 52.935
generateStatsSummary 26.690 0.355 33.683
plotCommunitiesEnrichment 24.049 0.355 30.467
plotCommunitiesStats 18.653 0.410 23.279
plotTFEnrichment 13.676 0.278 16.897
addConnections_TF_peak 12.803 0.768 16.916
plotGeneralGraphStats 11.413 0.269 14.886
add_TF_gene_correlation 8.493 0.286 9.672
plotDiagnosticPlots_TFPeaks 6.995 0.250 7.890
filterGRNAndConnectGenes 6.299 0.240 7.453
plotGeneralEnrichment 5.991 0.285 8.195
calculateTFEnrichment 5.253 0.254 6.631
calculateCommunitiesEnrichment 5.135 0.230 6.706
getTopNodes 5.110 0.234 6.967
plot_stats_connectionSummary 4.984 0.289 7.429
loadExampleObject 5.015 0.238 6.831
build_eGRN_graph 4.961 0.287 6.271
changeOutputDirectory 4.900 0.339 6.013
calculateGeneralEnrichment 4.948 0.247 6.635
calculateCommunitiesStats 4.935 0.244 6.518
getGRNConnections 4.873 0.266 6.622
getParameters 4.881 0.241 6.694
getCounts 4.899 0.221 5.721
overlapPeaksAndTFBS 4.828 0.277 6.570
peaks-methods 4.861 0.235 6.472
genes-methods 4.863 0.229 5.669
filterData 4.836 0.216 5.643
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’* Checking for library/require of GRaNIE...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
Found in files:
R/core.R (line 335, column 22)
R/core.R (line 342, column 51)
R/core.R (line 343, column 52)
R/core.R (line 344, column 52)
R/core.R (line 355, column 13)
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R/network.R (line 668, column 33)
R/plot.R (line 3619, column 32)
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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
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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 1139, 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 433, column 23)
suppressMessages() in R/core.R (line 1085, 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 1762): 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; 2609 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 Output folder, either absolute or rel...
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:52 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, 5444
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_0.99.3.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
** 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)