merida1 Summary
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| Package: GRaNIE |
| Version: 0.99.4 |
| 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: 4 minutes 14.63 seconds |
| CheckCommand: BiocCheckGitClone('GRaNIE') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GRaNIE_0.99.4.tar.gz && BiocCheck('GRaNIE_0.99.4.tar.gz', `new-package`=TRUE) |
| CheckTime: 11 minutes 19.77 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh GRaNIE_0.99.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 1 minutes 5.29 seconds |
| PackageFileSize: 2885.42 KiB |
| BuildID:: GRaNIE_20220409033555 |
| 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: 0. 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘GRaNIE_0.99.4.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...
* 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/2556/8c502bd1c5fccbbcd136bade51c2e10189196c12/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 ‘0.99.4’
* 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 ... [60s/60s] OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 4.2Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘colorspace’
A package should be listed in only one of these fields.
* 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 ... [70s/70s] NOTE
.addStats: no visible binding for global variable ‘TF.name’
.addStats: no visible binding for global variable ‘peak.ID’
.addStats: no visible binding for global variable ‘gene.ENSEMBL’
.buildGraph: no visible binding for global variable ‘V1_name’
.buildGraph: no visible binding for global variable ‘V2_name’
.buildGraph: no visible binding for global variable ‘V1’
.buildGraph: no visible binding for global variable ‘nodeID’
.buildGraph: no visible binding for global variable ‘V2’
.buildGraph: no visible binding for global variable ‘GRN’
.calcGCContentPeaks: no visible binding for global variable ‘G|C’
.calcGCContentPeaks: no visible binding for global variable ‘GC_class’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘isFiltered’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘peakID’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘gene.ENSEMBL’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘ENSEMBL’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘peak.ID’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘tad.ID’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘r’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘p.raw’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘p_raw.robust’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘r_robust’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘bias_M_p.raw’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘bias_LS_p.raw’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘peakID’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘tadStart’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘tadEnd’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘tad.ID’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘gene.ENSEMBL’
.combineEnrichmentResults: no visible binding for global variable
‘pval’
.combineEnrichmentResults: no visible binding for global variable
‘Found’
.combineEnrichmentResults: no visible binding for global variable ‘ID’
.computeTF_peak.fdr: no visible binding for global variable ‘TF.name’
.computeTF_peak.fdr: no visible binding for global variable
‘isFiltered’
.computeTF_peak.fdr: no visible binding for global variable ‘GC_class’
.computeTF_peak.fdr: no visible binding for global variable
‘peak_width’
.computeTF_peak.fdr: no visible binding for global variable ‘n_rel’
.computeTF_peak.fdr: no visible binding for global variable
‘GC_class.all’
.computeTF_peak.fdr: no visible binding for global variable ‘n.bg’
.computeTF_peak.fdr: no visible binding for global variable ‘n_rel.fg’
.computeTF_peak.fdr: no visible binding for global variable
‘n.bg.needed’
.computeTF_peak.fdr: no visible binding for global variable ‘peakID’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.r_bin2’
.computeTF_peak.fdr: no visible binding for global variable ‘TF_peak.r’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.r_bin’
.computeTF_peak.fdr: no visible binding for global variable ‘tpvalue’
.computeTF_peak.fdr: no visible binding for global variable ‘fpvalue’
.computeTF_peak.fdr: no visible binding for global variable
‘fpvalue_norm’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.fdr’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.fdr_orig’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.fdr_direction’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.connectionType’
.computeTF_peak.fdr: no visible binding for global variable ‘peak.ID’
.correlateData: no visible binding for global variable ‘GRN’
.correlateData: no visible binding for global variable ‘perm’
.correlateMatrices: no visible binding for global variable ‘ENSEMBL’
.correlateMatrices: no visible binding for global variable ‘peakID’
.createEnichmentTable: no visible binding for global variable
‘Description’
.createEnichmentTable: no visible binding for global variable ‘Count’
.createTables_peakGeneQC: no visible binding for global variable
‘r_positive’
.createTables_peakGeneQC: no visible binding for global variable
‘peak_gene.p.raw.class’
.createTables_peakGeneQC: no visible binding for global variable
‘sum_pos’
.createTables_peakGeneQC: no visible binding for global variable
‘sum_neg’
.createTables_peakGeneQC: no visible binding for global variable
‘enrichment_pos’
.createTables_peakGeneQC: no visible binding for global variable
‘sum_n’
.createTables_peakGeneQC: no visible binding for global variable
‘n_real’
.createTables_peakGeneQC: no visible binding for global variable
‘n_permuted’
.createTables_peakGeneQC: no visible binding for global variable
‘ratio_real_raw’
.createTables_peakGeneQC: no visible binding for global variable
‘classAll’
.createTables_peakGeneQC: no visible binding for global variable
‘n_rneg_real’
.createTables_peakGeneQC: no visible binding for global variable
‘n_rpos_real’
.createTables_peakGeneQC: no visible binding for global variable
‘n_rneg_random’
.createTables_peakGeneQC: no visible binding for global variable
‘n_rpos_random’
.createTables_peakGeneQC: no visible binding for global variable
‘peak_gene.p.raw.class.bin’
.createTables_peakGeneQC: no visible binding for global variable
‘variable’
.facetLabel: no visible binding for global variable ‘Degree’
.filterGenesByMeanCV: no visible binding for global variable ‘gene.CV’
.filterGenesByMeanCV: no visible binding for global variable
‘gene.mean’
.filterPeaksByCV: no visible binding for global variable ‘peak.CV’
.filterPeaksByMeanCV: no visible binding for global variable ‘peak.CV’
.filterPeaksByMeanCV: no visible binding for global variable
‘peak.mean’
.filterSortAndShuffle_peakTF_overlapTable: no visible binding for
global variable ‘isFiltered’
.finalizeClassificationAndAppend: no visible binding for global
variable ‘TF’
.findMaxBackgroundSize: no visible binding for global variable
‘GC_class’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘GC_class’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘peak_width’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘n.bg.needed.perc’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘n_rel’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘n.bg.needed.relFreq’
.getBackgroundGenes: no visible binding for global variable
‘geneAnnotation’
.getDegreeStats: no visible binding for global variable
‘connectionType’
.getDegreeStats: no visible binding for global variable ‘V1_name’
.getDegreeStats: no visible binding for global variable ‘V1’
.getDegreeStats: no visible binding for global variable ‘name_plot’
.getDegreeStats: no visible binding for global variable ‘V2’
.getDegreeStats: no visible binding for global variable ‘V2_name’
.getDegreeStats: no visible binding for global variable ‘Degree’
.getDegreeStats: no visible binding for global variable ‘ID’
.getDegreeStats: no visible binding for global variable ‘ID_all’
.getEigenCentralVertices: no visible binding for global variable
‘connectionType’
.getEigenCentralVertices: no visible binding for global variable ‘V2’
.getEigenCentralVertices: no visible binding for global variable ‘V1’
.getEigenCentralVertices: no visible binding for global variable
‘V2_name’
.getEigenCentralVertices: no visible binding for global variable
‘gene.name’
.getEigenCentralVertices: no visible binding for global variable
‘gene.ENSEMBL’
.getEigenCentralVertices: no visible binding for global variable
‘Score’
.getEigenCentralVertices: no visible binding for global variable
‘V1_name’
.getEigenCentralVertices: no visible binding for global variable
‘TF.name’
.getEigenCentralVertices: no visible binding for global variable
‘TF.ENSEMBL’
.getEigenCentralVertices: no visible binding for global variable
‘name_plot’
.getFinalListOfTFs: no visible binding for global variable ‘ENSEMBL’
.getFinalListOfTFs: no visible binding for global variable ‘HOCOID’
.getKnownGeneAnnotationNew: no visible binding for global variable
‘gene.type’
.intersectTFBSPeaks: no visible binding for global variable
‘annotation’
.intersectTFBSPeaks: no visible binding for global variable ‘tfbs_chr’
.intersectTFBSPeaks: no visible binding for global variable
‘tfbs_start’
.intersectTFBSPeaks: no visible binding for global variable ‘tfbs_end’
.intersectTFBSPeaks: no visible binding for global variable
‘peak_start’
.intersectTFBSPeaks: no visible binding for global variable ‘peak_end’
.intersectTFBSPeaks: no visible binding for global variable
‘coordSummit’
.intersectTFBSPeaks: no visible binding for global variable
‘coordCentTfbs’
.intersectTFBSPeaks: no visible binding for global variable ‘peakID’
.optimizeSpaceGRN: no visible binding for global variable ‘TF.name’
.optimizeSpaceGRN: no visible binding for global variable
‘TF_peak.r_bin’
.optimizeSpaceGRN: no visible binding for global variable ‘peak.ID’
.optimizeSpaceGRN: no visible binding for global variable
‘TF_peak.fdr_direction’
.optimizeSpaceGRN: no visible binding for global variable
‘TF_peak.connectionType’
.performIHW: no visible binding for global variable ‘adj_pvalue’
.performIHW: no visible binding for global variable ‘group’
.performIHW: no visible binding for global variable ‘pValues’
.performIHW: no visible binding for global variable ‘covariate_group’
.performIHW: no visible binding for global variable ‘covariateRank’
.plotDensity: no visible binding for global variable ‘variable’
.plotDensity: no visible binding for global variable ‘value’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.ENSEMBL’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.type’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.mean’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.median’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.CV’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak.GC.perc’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak.ID’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.r’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.distance’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.p_raw’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.p_raw.robust’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘r_positive’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.p.raw.class’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘ratio’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘classAll’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.r.class’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘nnorm’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak.CV’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘classNew’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘ratio_pos_raw’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.distance_class_abs’
.plotEnrichmentGeneral: no visible binding for global variable ‘Term’
.plotEnrichmentGeneral: no visible binding for global variable ‘pval’
.plotEnrichmentGeneral: no visible binding for global variable
‘GeneRatio’
.plotEnrichmentGeneral: no visible binding for global variable ‘Found’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘TF_peak.connectionType’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘direction’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘nForeground’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘nBackground_orig’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘nBackground’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘ratio_fg_bg_orig’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘ratio_fg_bg’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘background_match_success’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘percBackgroundUsed’
.plot_PCA_wrapper: no visible binding for global variable ‘sampleID’
.plot_PCA_wrapper: no visible binding for global variable ‘variation’
.plot_PCA_wrapper: no visible binding for global variable ‘PCs’
.plot_PCA_wrapper: no visible binding for global variable
‘variation_sum’
.plot_PCA_wrapper: no visible binding for global variable ‘PC1’
.plot_PCA_wrapper: no visible binding for global variable ‘PC2’
.plot_TF_peak_fdr: no visible binding for global variable ‘TF.name’
.plot_TF_peak_fdr: no visible binding for global variable
‘TF_peak.fdr_direction’
.plot_TF_peak_fdr: no visible binding for global variable
‘TF_peak.r_bin’
.plot_TF_peak_fdr: no visible binding for global variable ‘variable’
.plot_TF_peak_fdr: no visible binding for global variable ‘value’
.plot_classCorrelations: no visible binding for global variable
‘baseMean’
.plot_classCorrelations: no visible binding for global variable
‘weighted_meanDifference’
.plot_classCorrelations: no visible binding for global variable
‘log2FoldChange’
.plot_classCorrelations: no visible binding for global variable
‘baseMeanNorm’
.plot_heatmapAR: no visible binding for global variable ‘HOCOID’
.plot_stats_connectionSummaryBoxplot: no visible binding for global
variable ‘networkType’
.plot_stats_connectionSummaryBoxplot: no visible binding for global
variable ‘Freq’
.plot_stats_connectionSummaryDensity: no visible binding for global
variable ‘TF_peak.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘allowMissingGenes’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘allowMissingTFs’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘TF_peak.connectionType’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘peak_gene.p_raw’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘perm’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘TF_peak.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘peak_gene.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘nTFs’
.populateGeneAnnotation: no visible binding for global variable
‘ENSEMBL’
.populatePeakAnnotation: no visible binding for global variable
‘peakID’
.populatePeakAnnotation: no visible binding for global variable
‘isFiltered’
.populatePeakAnnotation: no visible binding for global variable
‘annotation’
.populatePeakAnnotation: no visible binding for global variable
‘geneId’
.populatePeakAnnotation: no visible binding for global variable
‘distanceToTSS’
.populatePeakAnnotation: no visible binding for global variable
‘ENSEMBL’
.populatePeakAnnotation: no visible binding for global variable
‘SYMBOL’
.populatePeakAnnotation: no visible binding for global variable
‘GENENAME’
.populatePeakAnnotation: no visible binding for global variable
‘geneChr’
.populatePeakAnnotation: no visible binding for global variable
‘geneStart’
.populatePeakAnnotation: no visible binding for global variable
‘geneEnd’
.populatePeakAnnotation: no visible binding for global variable
‘geneLength’
.populatePeakAnnotation: no visible binding for global variable
‘geneStrand’
.printLoopsGraph: no visible binding for global variable ‘V1’
.printLoopsGraph: no visible binding for global variable ‘V2’
.printLoopsGraph: no visible binding for global variable ‘V1_name’
.printLoopsGraph: no visible binding for global variable
‘V1_name_combined’
.printMultipleEdges: no visible binding for global variable ‘V1’
.printMultipleEdges: no visible binding for global variable ‘V2’
.readHOCOMOCOTable: no visible binding for global variable ‘ENSEMBL’
.retrieveAnnotationData: no visible binding for global variable
‘chromosome_name’
.retrieveAnnotationData: no visible binding for global variable
‘start_position’
.retrieveAnnotationData: no visible binding for global variable
‘end_position’
.retrieveAnnotationData: no visible binding for global variable
‘ensembl_gene_id’
.retrieveAnnotationData: no visible binding for global variable
‘gene_biotype’
.retrieveAnnotationData: no visible binding for global variable
‘external_gene_name’
.retrieveAnnotationData: no visible binding for global variable
‘gene.strand’
.runEnrichment: no visible binding for global variable ‘GRN’
.runEnrichment: no visible binding for global variable ‘GO.ID’
.runEnrichment: no visible binding for global variable ‘Significant’
.runEnrichment: no visible binding for global variable ‘Found’
.selectCommunitesByRank: no visible binding for global variable
‘community’
AR_classification_wrapper: no visible binding for global variable
‘HOCOID’
AR_classification_wrapper: no visible binding for global variable
‘TF.name’
addData: no visible binding for global variable ‘ENSEMBL’
addData: no visible binding for global variable ‘peakID’
addData: no visible binding for global variable ‘sampleID’
addData: no visible binding for global variable ‘has_RNA’
addData: no visible binding for global variable ‘has_peaks’
addData: no visible binding for global variable ‘has_both’
addData_TFActivity: no visible binding for global variable ‘ENSEMBL’
addData_TFActivity: no visible binding for global variable ‘TF.name’
addSNPOverlap: no visible binding for global variable ‘peak’
addSNPOverlap: no visible binding for global variable ‘SNP_chr’
addTFBS: no visible binding for global variable ‘HOCOID’
addTFBS: no visible binding for global variable ‘ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
‘gene.ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
‘TF.name’
add_TF_gene_correlation: no visible binding for global variable
‘ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
‘TF.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘gene.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘TF.name’
build_eGRN_graph: no visible binding for global variable ‘peak.ID’
build_eGRN_graph: no visible binding for global variable ‘TF.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘TF_peak.r’
build_eGRN_graph: no visible binding for global variable ‘gene.name’
build_eGRN_graph: no visible binding for global variable ‘peak_gene.r’
build_eGRN_graph: no visible binding for global variable ‘V1’
build_eGRN_graph: no visible binding for global variable ‘V2’
build_eGRN_graph: no visible binding for global variable ‘V1_name’
build_eGRN_graph: no visible binding for global variable ‘V2_name’
build_eGRN_graph: no visible binding for global variable ‘r’
build_eGRN_graph: no visible binding for global variable
‘connectionType’
build_eGRN_graph: no visible binding for global variable ‘V2.peak_gene’
build_eGRN_graph: no visible binding for global variable
‘V1_name.TF_peak’
build_eGRN_graph: no visible binding for global variable
‘V2_name.peak_gene’
calculateCommunitiesEnrichment: no visible binding for global variable
‘community’
calculateCommunitiesEnrichment: no visible binding for global variable
‘name’
calculateTFEnrichment: no visible binding for global variable ‘TF.name’
calculateTFEnrichment: no visible binding for global variable
‘gene.ENSEMBL’
filterData: no visible binding for global variable ‘ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
‘HOCOID’
filterGRNAndConnectGenes: no visible binding for global variable
‘ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
‘TF.ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
‘peak_gene.distance’
filterGRNAndConnectGenes: no visible binding for global variable
‘peak.ID’
filterGRNAndConnectGenes: no visible binding for global variable
‘gene.ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
‘TF.name’
getBasic_metadata_visualization: no visible binding for global variable
‘ENSEMBL’
getBasic_metadata_visualization: no visible binding for global variable
‘ENSEMBL_ID’
getBasic_metadata_visualization: no visible binding for global variable
‘peakID’
getCounts: no visible binding for global variable ‘isFiltered’
getCounts: no visible binding for global variable ‘ENSEMBL’
getTopNodes: no visible binding for global variable ‘connectionType’
getTopNodes: no visible binding for global variable ‘Connections’
getTopNodes: no visible binding for global variable ‘V2’
getTopNodes: no visible binding for global variable ‘V2_name’
getTopNodes: no visible binding for global variable ‘V1’
getTopNodes: no visible binding for global variable ‘V1_name’
importTFData: no visible binding for global variable ‘ENSEMBL’
importTFData: no visible binding for global variable ‘TF.name’
nGenes: no visible binding for global variable ‘isFiltered’
nPeaks: no visible binding for global variable ‘isFiltered’
overlapPeaksAndTFBS: no visible binding for global variable
‘isFiltered’
overlapPeaksAndTFBS: no visible binding for global variable ‘peakID’
plotCommunitiesEnrichment: no visible binding for global variable
‘community’
plotCommunitiesEnrichment: no visible binding for global variable ‘ID’
plotCommunitiesEnrichment: no visible binding for global variable
‘pval’
plotCommunitiesEnrichment: no visible global function definition for
‘where’
plotCommunitiesEnrichment: no visible binding for global variable
‘nSig’
plotCommunitiesEnrichment: no visible binding for global variable
‘Term’
plotCommunitiesStats: no visible binding for global variable
‘community’
plotCommunitiesStats: no visible binding for global variable ‘isTF’
plotCommunitiesStats: no visible binding for global variable ‘Class’
plotCommunitiesStats: no visible binding for global variable ‘name’
plotCommunitiesStats: no visible binding for global variable
‘from_name’
plotCommunitiesStats: no visible binding for global variable ‘to_name’
plotCommunitiesStats: no visible binding for global variable
‘connectionType’
plotCommunitiesStats: no visible binding for global variable
‘from_names_TF_all’
plotCommunitiesStats: no visible binding for global variable
‘to_names_gene’
plotGeneralGraphStats: no visible binding for global variable ‘Count’
plotGeneralGraphStats: no visible binding for global variable ‘Class’
plotGeneralGraphStats: no visible binding for global variable ‘Freq’
plotGeneralGraphStats: no visible binding for global variable ‘Var1’
plotTFEnrichment: no visible binding for global variable ‘TF.name’
plotTFEnrichment: no visible binding for global variable ‘ID’
plotTFEnrichment: no visible binding for global variable ‘pval’
plotTFEnrichment: no visible global function definition for ‘where’
plotTFEnrichment: no visible binding for global variable ‘nSig’
plotTFEnrichment: no visible binding for global variable ‘Term’
visualizeGRN: no visible binding for global variable ‘V1_name’
visualizeGRN: no visible binding for global variable ‘TF.name’
visualizeGRN: no visible binding for global variable ‘V2’
visualizeGRN: no visible binding for global variable ‘TF_peak.r’
visualizeGRN: no visible binding for global variable ‘peak_gene.r’
visualizeGRN: no visible binding for global variable ‘TF_peak.fdr’
visualizeGRN: no visible binding for global variable ‘V1’
visualizeGRN: no visible binding for global variable ‘connectionType’
visualizeGRN: no visible binding for global variable ‘color_raw’
visualizeGRN: no visible binding for global variable ‘nCommunitiesMax’
show,GRN: no visible binding for global variable ‘community’
show,GRN: no visible global function definition for ‘desc’
show,GRN: no visible binding for global variable ‘n’
Undefined global functions or variables:
Class Connections Count Degree Description ENSEMBL ENSEMBL_ID Found
Freq GC_class GC_class.all GENENAME GO.ID GRN GeneRatio G|C HOCOID ID
ID_all PC1 PC2 PCs SNP_chr SYMBOL Score Significant TF TF.ENSEMBL
TF.name TF_peak.connectionType TF_peak.fdr TF_peak.fdr_direction
TF_peak.fdr_orig TF_peak.r TF_peak.r_bin TF_peak.r_bin2 Term V1
V1_name V1_name.TF_peak V1_name_combined V2 V2.peak_gene V2_name
V2_name.peak_gene Var1 adj_pvalue allowMissingGenes allowMissingTFs
annotation background_match_success baseMean baseMeanNorm
bias_LS_p.raw bias_M_p.raw chromosome_name classAll classNew
color_raw community connectionType coordCentTfbs coordSummit
covariateRank covariate_group desc direction distanceToTSS
end_position enrichment_pos ensembl_gene_id external_gene_name
fpvalue fpvalue_norm from_name from_names_TF_all gene.CV gene.ENSEMBL
gene.mean gene.median gene.name gene.strand gene.type geneAnnotation
geneChr geneEnd geneId geneLength geneStart geneStrand gene_biotype
group has_RNA has_both has_peaks isFiltered isTF log2FoldChange n
n.bg n.bg.needed n.bg.needed.perc n.bg.needed.relFreq nBackground
nBackground_orig nCommunitiesMax nForeground nSig nTFs n_permuted
n_real n_rel n_rel.fg n_rneg_random n_rneg_real n_rpos_random
n_rpos_real name name_plot networkType nnorm nodeID p.raw pValues
p_raw.robust peak peak.CV peak.GC.perc peak.ID peak.mean peakID
peak_end peak_gene.distance peak_gene.distance_class_abs
peak_gene.fdr peak_gene.p.raw.class peak_gene.p.raw.class.bin
peak_gene.p_raw peak_gene.p_raw.robust peak_gene.r peak_gene.r.class
peak_start peak_width percBackgroundUsed perm pval r r_positive
r_robust ratio ratio_fg_bg ratio_fg_bg_orig ratio_pos_raw
ratio_real_raw sampleID start_position sum_n sum_neg sum_pos tad.ID
tadEnd tadStart tfbs_chr tfbs_end tfbs_start to_name to_names_gene
tpvalue value variable variation variation_sum
weighted_meanDifference where
* checking Rd files ... [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [197s/205s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCommunitiesEnrichment 15.364 0.384 15.970
addConnections_TF_peak 13.250 1.514 17.687
plotCommunitiesStats 10.070 0.231 10.487
plotGeneralGraphStats 8.838 0.197 9.227
filterGRNAndConnectGenes 7.526 0.752 8.463
plotTFEnrichment 7.809 0.207 8.506
plot_stats_connectionSummary 6.762 0.182 7.121
add_TF_gene_correlation 5.501 0.222 5.901
visualizeGRN 5.260 0.178 5.615
plotDiagnosticPlots_TFPeaks 5.091 0.179 5.445
addConnections_peak_gene 4.479 0.228 5.005
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [64s/68s]
[65s/68s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2556/8c502bd1c5fccbbcd136bade51c2e10189196c12/GRaNIE.Rcheck/00check.log’
for details.
===============================
BiocCheck('GRaNIE_0.99.4.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/2556/8c502bd1c5fccbbcd136bade51c2e10189196c12/GRaNIE_0.99.4.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpHTuYsu/file17b154ab9d0f4/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...
* Checking package size...
* 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 335, column 22)
R/core.R (line 342, column 51)
R/core.R (line 343, column 52)
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R/core.R (line 3563, column 48)
R/core.R (line 3564, 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 664, column 33)
R/plot.R (line 3731, column 40)
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* NOTE: Avoid 1:...; use seq_len() or seq_along()
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plot.R (line 3670, column 139)
plot.R (line 3676, column 139)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/plot.R (line 1971, column 9)
print() in R/plot.R (line 1988, column 11)
print() in R/plot.R (line 1996, column 11)
print() in R/plot.R (line 2005, column 11)
print() in R/plot.R (line 2021, column 11)
print() in R/plot.R (line 2029, column 11)
print() in R/plot.R (line 2039, column 11)
print() in R/plot.R (line 2655, column 11)
print() in R/plot.R (line 2688, column 11)
print() in R/plot.R (line 2963, column 11)
print() in R/plot.R (line 2995, column 11)
* NOTE: Avoid using '=' for assignment and use '<-' instead
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R/plot.R (line 1140, column 17)
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R/plot.R (line 1263, column 22)
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R/plot.R (line 1271, column 21)
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R/plot.R (line 1300, column 20)
R/plot.R (line 1301, column 17)
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R/plot.R (line 1314, column 20)
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R/plot.R (line 1321, column 54)
R/plot.R (line 1322, column 54)
R/plot.R (line 1323, column 65)
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R/plot.R (line 1325, column 54)
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R/plot.R (line 1330, column 26)
R/plot.R (line 1337, column 17)
R/plot.R (line 1346, column 18)
R/plot.R (line 1358, column 64)
R/plot.R (line 1361, column 17)
R/plot.R (line 1374, column 23)
R/plot.R (line 1381, column 21)
R/plot.R (line 1387, column 25)
R/plot.R (line 1389, column 29)
R/plot.R (line 1392, column 24)
R/plot.R (line 1396, column 22)
R/plot.R (line 1398, column 20)
R/plot.R (line 1400, column 21)
R/plot.R (line 1408, column 24)
R/plot.R (line 1410, column 28)
R/plot.R (line 1413, column 17)
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R/plot.R (line 1453, column 21)
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R/plot.R (line 1466, column 23)
R/plot.R (line 1479, column 15)
R/plot.R (line 1487, column 21)
R/plot.R (line 1498, column 13)
R/plot.R (line 1505, column 19)
R/plot.R (line 1526, column 18)
R/plot.R (line 1527, column 25)
R/plot.R (line 1554, column 7)
R/plot.R (line 1566, column 16)
R/plot.R (line 1570, column 12)
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R/plot.R (line 1580, column 12)
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R/plot.R (line 1591, column 12)
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R/plot.R (line 1603, column 9)
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R/plot.R (line 1622, column 17)
R/plot.R (line 1635, column 24)
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R/plot.R (line 1640, column 33)
R/plot.R (line 1650, column 41)
R/plot.R (line 1652, column 51)
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R/plot.R (line 1671, column 29)
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R/plot.R (line 1753, column 23)
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R/plot.R (line 1761, column 17)
R/plot.R (line 1776, column 27)
R/plot.R (line 1777, column 31)
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R/plot.R (line 1781, column 35)
R/plot.R (line 1784, column 35)
R/plot.R (line 1787, column 30)
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R/plot.R (line 1800, column 39)
R/plot.R (line 1803, column 34)
R/plot.R (line 1809, column 42)
R/plot.R (line 1811, column 29)
R/plot.R (line 1819, column 25)
R/plot.R (line 1831, column 31)
R/plot.R (line 1835, column 27)
R/plot.R (line 1883, column 9)
R/plot.R (line 1884, column 7)
R/plot.R (line 1895, column 16)
R/plot.R (line 1897, column 11)
R/plot.R (line 1908, column 21)
R/plot.R (line 1909, column 16)
R/plot.R (line 1912, column 19)
R/plot.R (line 1917, column 17)
R/plot.R (line 1922, column 17)
R/plot.R (line 1927, column 21)
R/plot.R (line 1935, column 18)
R/plot.R (line 1937, column 23)
R/plot.R (line 1943, column 21)
R/plot.R (line 1947, column 23)
R/plot.R (line 1956, column 20)
R/plot.R (line 1958, column 22)
R/plot.R (line 1962, column 23)
R/plot.R (line 1973, column 17)
R/plot.R (line 1977, column 31)
R/plot.R (line 1978, column 12)
R/plot.R (line 1987, column 21)
R/plot.R (line 1990, column 19)
R/plot.R (line 1994, column 21)
R/plot.R (line 1995, column 21)
R/plot.R (line 1998, column 19)
R/plot.R (line 2002, column 23)
R/plot.R (line 2003, column 26)
R/plot.R (line 2004, column 26)
R/plot.R (line 2007, column 19)
R/plot.R (line 2012, column 14)
R/plot.R (line 2014, column 28)
R/plot.R (line 2019, column 26)
R/plot.R (line 2020, column 20)
R/plot.R (line 2023, column 19)
R/plot.R (line 2027, column 21)
R/plot.R (line 2028, column 19)
R/plot.R (line 2031, column 19)
R/plot.R (line 2036, column 23)
R/plot.R (line 2037, column 26)
R/plot.R (line 2038, column 24)
R/plot.R (line 2060, column 17)
R/plot.R (line 2092, column 9)
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R/plot.R (line 2265, column 9)
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R/plot.R (line 2367, column 64)
R/plot.R (line 2368, column 23)
R/plot.R (line 2370, column 54)
R/plot.R (line 2373, column 31)
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R/plot.R (line 2382, column 43)
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R/plot.R (line 2456, column 9)
R/plot.R (line 2457, column 7)
R/plot.R (line 2477, column 13)
R/plot.R (line 2481, column 16)
R/plot.R (line 2482, column 11)
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R/plot.R (line 2502, column 47)
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R/plot.R (line 3019, column 14)
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R/plot.R (line 3118, column 13)
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R/plot.R (line 3127, column 17)
R/plot.R (line 3129, column 15)
R/plot.R (line 3141, column 12)
R/plot.R (line 3153, column 13)
R/plot.R (line 3156, column 18)
R/plot.R (line 3161, column 16)
R/plot.R (line 3169, column 13)
R/plot.R (line 3171, column 11)
R/plot.R (line 3216, column 11)
R/plot.R (line 3217, column 9)
R/plot.R (line 3237, column 18)
R/plot.R (line 3239, column 30)
R/plot.R (line 3250, column 20)
R/plot.R (line 3253, column 21)
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R/plot.R (line 3261, column 51)
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R/plot.R (line 3283, column 11)
R/plot.R (line 3302, column 17)
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R/plot.R (line 3337, column 33)
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R/plot.R (line 3354, column 38)
R/plot.R (line 3355, column 38)
R/plot.R (line 3356, column 38)
R/plot.R (line 3357, column 29)
R/plot.R (line 3362, column 28)
R/plot.R (line 3363, column 43)
R/plot.R (line 3364, column 43)
R/plot.R (line 3365, column 44)
R/plot.R (line 3366, column 33)
R/plot.R (line 3371, column 24)
R/plot.R (line 3372, column 39)
R/plot.R (line 3373, column 39)
R/plot.R (line 3374, column 40)
R/plot.R (line 3375, column 29)
R/plot.R (line 3380, column 22)
R/plot.R (line 3381, column 29)
R/plot.R (line 3384, column 18)
R/plot.R (line 3399, column 22)
R/plot.R (line 3412, column 30)
R/plot.R (line 3419, column 30)
R/plot.R (line 3422, column 22)
R/plot.R (line 3436, column 20)
R/plot.R (line 3437, column 20)
R/plot.R (line 3439, column 28)
R/plot.R (line 3447, column 36)
R/plot.R (line 3453, column 36)
R/plot.R (line 3456, column 26)
R/plot.R (line 3475, column 24)
R/plot.R (line 3489, column 32)
R/plot.R (line 3495, column 32)
R/plot.R (line 3499, column 22)
R/plot.R (line 3510, column 18)
R/plot.R (line 3517, column 30)
R/plot.R (line 3520, column 34)
R/plot.R (line 3524, column 31)
R/plot.R (line 3530, column 31)
R/plot.R (line 3538, column 23)
R/plot.R (line 3539, column 39)
R/plot.R (line 3547, column 27)
R/plot.R (line 3548, column 45)
R/plot.R (line 3556, column 23)
R/plot.R (line 3557, column 41)
R/plot.R (line 3580, column 30)
R/plot.R (line 3586, column 41)
R/plot.R (line 3590, column 21)
R/plot.R (line 3593, column 26)
R/plot.R (line 3596, column 34)
R/plot.R (line 3598, column 30)
R/plot.R (line 3599, column 34)
R/plot.R (line 3602, column 34)
R/plot.R (line 3606, column 24)
R/plot.R (line 3607, column 26)
R/plot.R (line 3609, column 33)
R/plot.R (line 3611, column 33)
R/plot.R (line 3615, column 25)
R/plot.R (line 3616, column 41)
R/plot.R (line 3620, column 36)
R/plot.R (line 3623, column 30)
R/plot.R (line 3731, column 27)
R/plot.R (line 3736, column 27)
R/plot.R (line 3742, column 31)
R/plot.R (line 3748, column 31)
R/plot.R (line 3765, column 24)
R/plot.R (line 3766, column 27)
R/plot.R (line 3767, column 26)
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 21
times)
suppressWarnings() in R/core.R (line 1165, column 11)
suppressWarnings() in R/core.R (line 2378, column 5)
suppressWarnings() in R/core.R (line 2379, column 5)
suppressWarnings() in R/core.R (line 2399, column 17)
suppressWarnings() in R/core.R (line 2519, column 19)
suppressWarnings() in R/core.R (line 2540, column 20)
suppressWarnings() in R/core.R (line 2696, column 12)
suppressWarnings() in R/core.R (line 3002, column 18)
suppressWarnings() in R/core.R (line 3004, column 18)
suppressMessages() in R/core.R (line 461, column 23)
suppressMessages() in R/core.R (line 1111, column 13)
suppressMessages() in R/core.R (line 2363, column 20)
suppressMessages() in R/core.R (line 2364, column 20)
suppressMessages() in R/core.R (line 2634, column 12)
suppressMessages() in R/core.R (line 3419, column 18)
suppressWarnings() in R/network.R (line 378, column 24)
suppressMessages() in R/network.R (line 526, column 21)
suppressMessages() in R/network.R (line 535, column 14)
suppressWarnings() in R/plot.R (line 711, column 13)
suppressWarnings() in R/plot.R (line 754, column 13)
suppressWarnings() in R/plot.R (line 1826, column 23)
* 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 913): 612
lines
visualizeGRN() (R/plot.R, line 3209): 592 lines
filterGRNAndConnectGenes() (R/core.R, line 2787): 394 lines
.computeTF_peak.fdr() (R/core.R, line 1788): 391 lines
plotCommunitiesEnrichment() (R/plot.R, line 2449): 258 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, plotPCA_all.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; 2545 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:3746 # vertex.color Node color
R/plot.R:3747 # vertex.frame.color Node border color
R/plot.R:3748 # vertex.shape One of “none”, “circle”, “square”...
R/plot.R:3749 # vertex.size Size of the node (default is 15)
R/plot.R:3750 # vertex.size2 The second size of the node (e.g....
R/plot.R:3751 # vertex.label Character vector used to label th...
* NOTE: Consider multiples of 4 spaces for line indents, 5294
lines(38%) 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: 0
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
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir GRaNIE_0.99.4.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)
nebbiolo1 Summary
[top]
| Package: GRaNIE |
| Version: 0.99.4 |
| 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: 2 minutes 55.75 seconds |
| CheckCommand: BiocCheckGitClone('GRaNIE') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings GRaNIE_0.99.4.tar.gz && BiocCheck('GRaNIE_0.99.4.tar.gz', `new-package`=TRUE) |
| CheckTime: 5 minutes 39.16 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2990.04 KiB |
| BuildID:: GRaNIE_20220409033555 |
| 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: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘GRaNIE_0.99.4.tar.gz’
nebbiolo1 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 ‘/home/pkgbuild/packagebuilder/workers/jobs/2556/8c502bd1c5fccbbcd136bade51c2e10189196c12/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 ‘0.99.4’
* 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 ... [20s/20s] OK
* checking installed package size ... NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
doc 4.0Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘colorspace’
A package should be listed in only one of these fields.
* 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 ... [23s/23s] NOTE
.addStats: no visible binding for global variable ‘TF.name’
.addStats: no visible binding for global variable ‘peak.ID’
.addStats: no visible binding for global variable ‘gene.ENSEMBL’
.buildGraph: no visible binding for global variable ‘V1_name’
.buildGraph: no visible binding for global variable ‘V2_name’
.buildGraph: no visible binding for global variable ‘V1’
.buildGraph: no visible binding for global variable ‘nodeID’
.buildGraph: no visible binding for global variable ‘V2’
.buildGraph: no visible binding for global variable ‘GRN’
.calcGCContentPeaks: no visible binding for global variable ‘G|C’
.calcGCContentPeaks: no visible binding for global variable ‘GC_class’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘isFiltered’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘peakID’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘gene.ENSEMBL’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘ENSEMBL’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘peak.ID’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘tad.ID’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘r’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘p.raw’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘p_raw.robust’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘r_robust’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘bias_M_p.raw’
.calculatePeakGeneCorrelations: no visible binding for global variable
‘bias_LS_p.raw’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘peakID’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘tadStart’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘tadEnd’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘tad.ID’
.calculatePeakGeneOverlaps: no visible binding for global variable
‘gene.ENSEMBL’
.combineEnrichmentResults: no visible binding for global variable
‘pval’
.combineEnrichmentResults: no visible binding for global variable
‘Found’
.combineEnrichmentResults: no visible binding for global variable ‘ID’
.computeTF_peak.fdr: no visible binding for global variable ‘TF.name’
.computeTF_peak.fdr: no visible binding for global variable
‘isFiltered’
.computeTF_peak.fdr: no visible binding for global variable ‘GC_class’
.computeTF_peak.fdr: no visible binding for global variable
‘peak_width’
.computeTF_peak.fdr: no visible binding for global variable ‘n_rel’
.computeTF_peak.fdr: no visible binding for global variable
‘GC_class.all’
.computeTF_peak.fdr: no visible binding for global variable ‘n.bg’
.computeTF_peak.fdr: no visible binding for global variable ‘n_rel.fg’
.computeTF_peak.fdr: no visible binding for global variable
‘n.bg.needed’
.computeTF_peak.fdr: no visible binding for global variable ‘peakID’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.r_bin2’
.computeTF_peak.fdr: no visible binding for global variable ‘TF_peak.r’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.r_bin’
.computeTF_peak.fdr: no visible binding for global variable ‘tpvalue’
.computeTF_peak.fdr: no visible binding for global variable ‘fpvalue’
.computeTF_peak.fdr: no visible binding for global variable
‘fpvalue_norm’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.fdr’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.fdr_orig’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.fdr_direction’
.computeTF_peak.fdr: no visible binding for global variable
‘TF_peak.connectionType’
.computeTF_peak.fdr: no visible binding for global variable ‘peak.ID’
.correlateData: no visible binding for global variable ‘GRN’
.correlateData: no visible binding for global variable ‘perm’
.correlateMatrices: no visible binding for global variable ‘ENSEMBL’
.correlateMatrices: no visible binding for global variable ‘peakID’
.createEnichmentTable: no visible binding for global variable
‘Description’
.createEnichmentTable: no visible binding for global variable ‘Count’
.createTables_peakGeneQC: no visible binding for global variable
‘r_positive’
.createTables_peakGeneQC: no visible binding for global variable
‘peak_gene.p.raw.class’
.createTables_peakGeneQC: no visible binding for global variable
‘sum_pos’
.createTables_peakGeneQC: no visible binding for global variable
‘sum_neg’
.createTables_peakGeneQC: no visible binding for global variable
‘enrichment_pos’
.createTables_peakGeneQC: no visible binding for global variable
‘sum_n’
.createTables_peakGeneQC: no visible binding for global variable
‘n_real’
.createTables_peakGeneQC: no visible binding for global variable
‘n_permuted’
.createTables_peakGeneQC: no visible binding for global variable
‘ratio_real_raw’
.createTables_peakGeneQC: no visible binding for global variable
‘classAll’
.createTables_peakGeneQC: no visible binding for global variable
‘n_rneg_real’
.createTables_peakGeneQC: no visible binding for global variable
‘n_rpos_real’
.createTables_peakGeneQC: no visible binding for global variable
‘n_rneg_random’
.createTables_peakGeneQC: no visible binding for global variable
‘n_rpos_random’
.createTables_peakGeneQC: no visible binding for global variable
‘peak_gene.p.raw.class.bin’
.createTables_peakGeneQC: no visible binding for global variable
‘variable’
.facetLabel: no visible binding for global variable ‘Degree’
.filterGenesByMeanCV: no visible binding for global variable ‘gene.CV’
.filterGenesByMeanCV: no visible binding for global variable
‘gene.mean’
.filterPeaksByCV: no visible binding for global variable ‘peak.CV’
.filterPeaksByMeanCV: no visible binding for global variable ‘peak.CV’
.filterPeaksByMeanCV: no visible binding for global variable
‘peak.mean’
.filterSortAndShuffle_peakTF_overlapTable: no visible binding for
global variable ‘isFiltered’
.finalizeClassificationAndAppend: no visible binding for global
variable ‘TF’
.findMaxBackgroundSize: no visible binding for global variable
‘GC_class’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘GC_class’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘peak_width’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘n.bg.needed.perc’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘n_rel’
.generateTF_GC_diagnosticPlots: no visible binding for global variable
‘n.bg.needed.relFreq’
.getBackgroundGenes: no visible binding for global variable
‘geneAnnotation’
.getDegreeStats: no visible binding for global variable
‘connectionType’
.getDegreeStats: no visible binding for global variable ‘V1_name’
.getDegreeStats: no visible binding for global variable ‘V1’
.getDegreeStats: no visible binding for global variable ‘name_plot’
.getDegreeStats: no visible binding for global variable ‘V2’
.getDegreeStats: no visible binding for global variable ‘V2_name’
.getDegreeStats: no visible binding for global variable ‘Degree’
.getDegreeStats: no visible binding for global variable ‘ID’
.getDegreeStats: no visible binding for global variable ‘ID_all’
.getEigenCentralVertices: no visible binding for global variable
‘connectionType’
.getEigenCentralVertices: no visible binding for global variable ‘V2’
.getEigenCentralVertices: no visible binding for global variable ‘V1’
.getEigenCentralVertices: no visible binding for global variable
‘V2_name’
.getEigenCentralVertices: no visible binding for global variable
‘gene.name’
.getEigenCentralVertices: no visible binding for global variable
‘gene.ENSEMBL’
.getEigenCentralVertices: no visible binding for global variable
‘Score’
.getEigenCentralVertices: no visible binding for global variable
‘V1_name’
.getEigenCentralVertices: no visible binding for global variable
‘TF.name’
.getEigenCentralVertices: no visible binding for global variable
‘TF.ENSEMBL’
.getEigenCentralVertices: no visible binding for global variable
‘name_plot’
.getFinalListOfTFs: no visible binding for global variable ‘ENSEMBL’
.getFinalListOfTFs: no visible binding for global variable ‘HOCOID’
.getKnownGeneAnnotationNew: no visible binding for global variable
‘gene.type’
.intersectTFBSPeaks: no visible binding for global variable
‘annotation’
.intersectTFBSPeaks: no visible binding for global variable ‘tfbs_chr’
.intersectTFBSPeaks: no visible binding for global variable
‘tfbs_start’
.intersectTFBSPeaks: no visible binding for global variable ‘tfbs_end’
.intersectTFBSPeaks: no visible binding for global variable
‘peak_start’
.intersectTFBSPeaks: no visible binding for global variable ‘peak_end’
.intersectTFBSPeaks: no visible binding for global variable
‘coordSummit’
.intersectTFBSPeaks: no visible binding for global variable
‘coordCentTfbs’
.intersectTFBSPeaks: no visible binding for global variable ‘peakID’
.optimizeSpaceGRN: no visible binding for global variable ‘TF.name’
.optimizeSpaceGRN: no visible binding for global variable
‘TF_peak.r_bin’
.optimizeSpaceGRN: no visible binding for global variable ‘peak.ID’
.optimizeSpaceGRN: no visible binding for global variable
‘TF_peak.fdr_direction’
.optimizeSpaceGRN: no visible binding for global variable
‘TF_peak.connectionType’
.performIHW: no visible binding for global variable ‘adj_pvalue’
.performIHW: no visible binding for global variable ‘group’
.performIHW: no visible binding for global variable ‘pValues’
.performIHW: no visible binding for global variable ‘covariate_group’
.performIHW: no visible binding for global variable ‘covariateRank’
.plotDensity: no visible binding for global variable ‘variable’
.plotDensity: no visible binding for global variable ‘value’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.ENSEMBL’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.type’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.mean’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.median’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘gene.CV’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak.GC.perc’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak.ID’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.r’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.distance’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.p_raw’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.p_raw.robust’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘r_positive’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.p.raw.class’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘ratio’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘classAll’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.r.class’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘nnorm’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak.CV’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘classNew’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘ratio_pos_raw’
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable ‘peak_gene.distance_class_abs’
.plotEnrichmentGeneral: no visible binding for global variable ‘Term’
.plotEnrichmentGeneral: no visible binding for global variable ‘pval’
.plotEnrichmentGeneral: no visible binding for global variable
‘GeneRatio’
.plotEnrichmentGeneral: no visible binding for global variable ‘Found’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘TF_peak.connectionType’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘direction’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘nForeground’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘nBackground_orig’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘nBackground’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘ratio_fg_bg_orig’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘ratio_fg_bg’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘background_match_success’
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
‘percBackgroundUsed’
.plot_PCA_wrapper: no visible binding for global variable ‘sampleID’
.plot_PCA_wrapper: no visible binding for global variable ‘variation’
.plot_PCA_wrapper: no visible binding for global variable ‘PCs’
.plot_PCA_wrapper: no visible binding for global variable
‘variation_sum’
.plot_PCA_wrapper: no visible binding for global variable ‘PC1’
.plot_PCA_wrapper: no visible binding for global variable ‘PC2’
.plot_TF_peak_fdr: no visible binding for global variable ‘TF.name’
.plot_TF_peak_fdr: no visible binding for global variable
‘TF_peak.fdr_direction’
.plot_TF_peak_fdr: no visible binding for global variable
‘TF_peak.r_bin’
.plot_TF_peak_fdr: no visible binding for global variable ‘variable’
.plot_TF_peak_fdr: no visible binding for global variable ‘value’
.plot_classCorrelations: no visible binding for global variable
‘baseMean’
.plot_classCorrelations: no visible binding for global variable
‘weighted_meanDifference’
.plot_classCorrelations: no visible binding for global variable
‘log2FoldChange’
.plot_classCorrelations: no visible binding for global variable
‘baseMeanNorm’
.plot_heatmapAR: no visible binding for global variable ‘HOCOID’
.plot_stats_connectionSummaryBoxplot: no visible binding for global
variable ‘networkType’
.plot_stats_connectionSummaryBoxplot: no visible binding for global
variable ‘Freq’
.plot_stats_connectionSummaryDensity: no visible binding for global
variable ‘TF_peak.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘allowMissingGenes’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘allowMissingTFs’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘TF_peak.connectionType’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘peak_gene.p_raw’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘perm’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘TF_peak.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘peak_gene.fdr’
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable ‘nTFs’
.populateGeneAnnotation: no visible binding for global variable
‘ENSEMBL’
.populatePeakAnnotation: no visible binding for global variable
‘peakID’
.populatePeakAnnotation: no visible binding for global variable
‘isFiltered’
.populatePeakAnnotation: no visible binding for global variable
‘annotation’
.populatePeakAnnotation: no visible binding for global variable
‘geneId’
.populatePeakAnnotation: no visible binding for global variable
‘distanceToTSS’
.populatePeakAnnotation: no visible binding for global variable
‘ENSEMBL’
.populatePeakAnnotation: no visible binding for global variable
‘SYMBOL’
.populatePeakAnnotation: no visible binding for global variable
‘GENENAME’
.populatePeakAnnotation: no visible binding for global variable
‘geneChr’
.populatePeakAnnotation: no visible binding for global variable
‘geneStart’
.populatePeakAnnotation: no visible binding for global variable
‘geneEnd’
.populatePeakAnnotation: no visible binding for global variable
‘geneLength’
.populatePeakAnnotation: no visible binding for global variable
‘geneStrand’
.printLoopsGraph: no visible binding for global variable ‘V1’
.printLoopsGraph: no visible binding for global variable ‘V2’
.printLoopsGraph: no visible binding for global variable ‘V1_name’
.printLoopsGraph: no visible binding for global variable
‘V1_name_combined’
.printMultipleEdges: no visible binding for global variable ‘V1’
.printMultipleEdges: no visible binding for global variable ‘V2’
.readHOCOMOCOTable: no visible binding for global variable ‘ENSEMBL’
.retrieveAnnotationData: no visible binding for global variable
‘chromosome_name’
.retrieveAnnotationData: no visible binding for global variable
‘start_position’
.retrieveAnnotationData: no visible binding for global variable
‘end_position’
.retrieveAnnotationData: no visible binding for global variable
‘ensembl_gene_id’
.retrieveAnnotationData: no visible binding for global variable
‘gene_biotype’
.retrieveAnnotationData: no visible binding for global variable
‘external_gene_name’
.retrieveAnnotationData: no visible binding for global variable
‘gene.strand’
.runEnrichment: no visible binding for global variable ‘GRN’
.runEnrichment: no visible binding for global variable ‘GO.ID’
.runEnrichment: no visible binding for global variable ‘Significant’
.runEnrichment: no visible binding for global variable ‘Found’
.selectCommunitesByRank: no visible binding for global variable
‘community’
AR_classification_wrapper: no visible binding for global variable
‘HOCOID’
AR_classification_wrapper: no visible binding for global variable
‘TF.name’
addData: no visible binding for global variable ‘ENSEMBL’
addData: no visible binding for global variable ‘peakID’
addData: no visible binding for global variable ‘sampleID’
addData: no visible binding for global variable ‘has_RNA’
addData: no visible binding for global variable ‘has_peaks’
addData: no visible binding for global variable ‘has_both’
addData_TFActivity: no visible binding for global variable ‘ENSEMBL’
addData_TFActivity: no visible binding for global variable ‘TF.name’
addSNPOverlap: no visible binding for global variable ‘peak’
addSNPOverlap: no visible binding for global variable ‘SNP_chr’
addTFBS: no visible binding for global variable ‘HOCOID’
addTFBS: no visible binding for global variable ‘ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
‘gene.ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
‘TF.name’
add_TF_gene_correlation: no visible binding for global variable
‘ENSEMBL’
add_TF_gene_correlation: no visible binding for global variable
‘TF.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘gene.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘TF.name’
build_eGRN_graph: no visible binding for global variable ‘peak.ID’
build_eGRN_graph: no visible binding for global variable ‘TF.ENSEMBL’
build_eGRN_graph: no visible binding for global variable ‘TF_peak.r’
build_eGRN_graph: no visible binding for global variable ‘gene.name’
build_eGRN_graph: no visible binding for global variable ‘peak_gene.r’
build_eGRN_graph: no visible binding for global variable ‘V1’
build_eGRN_graph: no visible binding for global variable ‘V2’
build_eGRN_graph: no visible binding for global variable ‘V1_name’
build_eGRN_graph: no visible binding for global variable ‘V2_name’
build_eGRN_graph: no visible binding for global variable ‘r’
build_eGRN_graph: no visible binding for global variable
‘connectionType’
build_eGRN_graph: no visible binding for global variable ‘V2.peak_gene’
build_eGRN_graph: no visible binding for global variable
‘V1_name.TF_peak’
build_eGRN_graph: no visible binding for global variable
‘V2_name.peak_gene’
calculateCommunitiesEnrichment: no visible binding for global variable
‘community’
calculateCommunitiesEnrichment: no visible binding for global variable
‘name’
calculateTFEnrichment: no visible binding for global variable ‘TF.name’
calculateTFEnrichment: no visible binding for global variable
‘gene.ENSEMBL’
filterData: no visible binding for global variable ‘ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
‘HOCOID’
filterGRNAndConnectGenes: no visible binding for global variable
‘ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
‘TF.ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
‘peak_gene.distance’
filterGRNAndConnectGenes: no visible binding for global variable
‘peak.ID’
filterGRNAndConnectGenes: no visible binding for global variable
‘gene.ENSEMBL’
filterGRNAndConnectGenes: no visible binding for global variable
‘TF.name’
getBasic_metadata_visualization: no visible binding for global variable
‘ENSEMBL’
getBasic_metadata_visualization: no visible binding for global variable
‘ENSEMBL_ID’
getBasic_metadata_visualization: no visible binding for global variable
‘peakID’
getCounts: no visible binding for global variable ‘isFiltered’
getCounts: no visible binding for global variable ‘ENSEMBL’
getTopNodes: no visible binding for global variable ‘connectionType’
getTopNodes: no visible binding for global variable ‘Connections’
getTopNodes: no visible binding for global variable ‘V2’
getTopNodes: no visible binding for global variable ‘V2_name’
getTopNodes: no visible binding for global variable ‘V1’
getTopNodes: no visible binding for global variable ‘V1_name’
importTFData: no visible binding for global variable ‘ENSEMBL’
importTFData: no visible binding for global variable ‘TF.name’
nGenes: no visible binding for global variable ‘isFiltered’
nPeaks: no visible binding for global variable ‘isFiltered’
overlapPeaksAndTFBS: no visible binding for global variable
‘isFiltered’
overlapPeaksAndTFBS: no visible binding for global variable ‘peakID’
plotCommunitiesEnrichment: no visible binding for global variable
‘community’
plotCommunitiesEnrichment: no visible binding for global variable ‘ID’
plotCommunitiesEnrichment: no visible binding for global variable
‘pval’
plotCommunitiesEnrichment: no visible global function definition for
‘where’
plotCommunitiesEnrichment: no visible binding for global variable
‘nSig’
plotCommunitiesEnrichment: no visible binding for global variable
‘Term’
plotCommunitiesStats: no visible binding for global variable
‘community’
plotCommunitiesStats: no visible binding for global variable ‘isTF’
plotCommunitiesStats: no visible binding for global variable ‘Class’
plotCommunitiesStats: no visible binding for global variable ‘name’
plotCommunitiesStats: no visible binding for global variable
‘from_name’
plotCommunitiesStats: no visible binding for global variable ‘to_name’
plotCommunitiesStats: no visible binding for global variable
‘connectionType’
plotCommunitiesStats: no visible binding for global variable
‘from_names_TF_all’
plotCommunitiesStats: no visible binding for global variable
‘to_names_gene’
plotGeneralGraphStats: no visible binding for global variable ‘Count’
plotGeneralGraphStats: no visible binding for global variable ‘Class’
plotGeneralGraphStats: no visible binding for global variable ‘Freq’
plotGeneralGraphStats: no visible binding for global variable ‘Var1’
plotTFEnrichment: no visible binding for global variable ‘TF.name’
plotTFEnrichment: no visible binding for global variable ‘ID’
plotTFEnrichment: no visible binding for global variable ‘pval’
plotTFEnrichment: no visible global function definition for ‘where’
plotTFEnrichment: no visible binding for global variable ‘nSig’
plotTFEnrichment: no visible binding for global variable ‘Term’
visualizeGRN: no visible binding for global variable ‘V1_name’
visualizeGRN: no visible binding for global variable ‘TF.name’
visualizeGRN: no visible binding for global variable ‘V2’
visualizeGRN: no visible binding for global variable ‘TF_peak.r’
visualizeGRN: no visible binding for global variable ‘peak_gene.r’
visualizeGRN: no visible binding for global variable ‘TF_peak.fdr’
visualizeGRN: no visible binding for global variable ‘V1’
visualizeGRN: no visible binding for global variable ‘connectionType’
visualizeGRN: no visible binding for global variable ‘color_raw’
visualizeGRN: no visible binding for global variable ‘nCommunitiesMax’
show,GRN: no visible binding for global variable ‘community’
show,GRN: no visible global function definition for ‘desc’
show,GRN: no visible binding for global variable ‘n’
Undefined global functions or variables:
Class Connections Count Degree Description ENSEMBL ENSEMBL_ID Found
Freq GC_class GC_class.all GENENAME GO.ID GRN GeneRatio G|C HOCOID ID
ID_all PC1 PC2 PCs SNP_chr SYMBOL Score Significant TF TF.ENSEMBL
TF.name TF_peak.connectionType TF_peak.fdr TF_peak.fdr_direction
TF_peak.fdr_orig TF_peak.r TF_peak.r_bin TF_peak.r_bin2 Term V1
V1_name V1_name.TF_peak V1_name_combined V2 V2.peak_gene V2_name
V2_name.peak_gene Var1 adj_pvalue allowMissingGenes allowMissingTFs
annotation background_match_success baseMean baseMeanNorm
bias_LS_p.raw bias_M_p.raw chromosome_name classAll classNew
color_raw community connectionType coordCentTfbs coordSummit
covariateRank covariate_group desc direction distanceToTSS
end_position enrichment_pos ensembl_gene_id external_gene_name
fpvalue fpvalue_norm from_name from_names_TF_all gene.CV gene.ENSEMBL
gene.mean gene.median gene.name gene.strand gene.type geneAnnotation
geneChr geneEnd geneId geneLength geneStart geneStrand gene_biotype
group has_RNA has_both has_peaks isFiltered isTF log2FoldChange n
n.bg n.bg.needed n.bg.needed.perc n.bg.needed.relFreq nBackground
nBackground_orig nCommunitiesMax nForeground nSig nTFs n_permuted
n_real n_rel n_rel.fg n_rneg_random n_rneg_real n_rpos_random
n_rpos_real name name_plot networkType nnorm nodeID p.raw pValues
p_raw.robust peak peak.CV peak.GC.perc peak.ID peak.mean peakID
peak_end peak_gene.distance peak_gene.distance_class_abs
peak_gene.fdr peak_gene.p.raw.class peak_gene.p.raw.class.bin
peak_gene.p_raw peak_gene.p_raw.robust peak_gene.r peak_gene.r.class
peak_start peak_width percBackgroundUsed perm pval r r_positive
r_robust ratio ratio_fg_bg ratio_fg_bg_orig ratio_pos_raw
ratio_real_raw sampleID start_position sum_n sum_neg sum_pos tad.ID
tadEnd tadStart tfbs_chr tfbs_end tfbs_start to_name to_names_gene
tpvalue value variable variation variation_sum
weighted_meanDifference where
* checking Rd files ... [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [68s/123s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
addConnections_TF_peak 5.326 0.953 56.925
plotCommunitiesEnrichment 4.773 0.151 5.084
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [26s/78s]
[26s/78s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2556/8c502bd1c5fccbbcd136bade51c2e10189196c12/GRaNIE.Rcheck/00check.log’
for details.
===============================
BiocCheck('GRaNIE_0.99.4.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/2556/8c502bd1c5fccbbcd136bade51c2e10189196c12/GRaNIE_0.99.4.tar.gz" "/tmp/RtmpAWBjAO/file3dbd354acd89b1/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...
* Checking package size...
* 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/core.R (line 342, column 51)
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R/core.R (line 3563, column 48)
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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 664, column 33)
R/plot.R (line 3731, column 40)
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* NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
plot.R (line 3670, column 139)
plot.R (line 3676, column 139)
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/plot.R (line 1971, column 9)
print() in R/plot.R (line 1988, column 11)
print() in R/plot.R (line 1996, column 11)
print() in R/plot.R (line 2005, column 11)
print() in R/plot.R (line 2021, column 11)
print() in R/plot.R (line 2029, column 11)
print() in R/plot.R (line 2039, column 11)
print() in R/plot.R (line 2655, column 11)
print() in R/plot.R (line 2688, column 11)
print() in R/plot.R (line 2963, column 11)
print() in R/plot.R (line 2995, column 11)
* NOTE: Avoid using '=' for assignment and use '<-' instead
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R/DataClasses.R (line 149, column 28)
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R/DataClasses.R (line 181, column 24)
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R/DataClasses.R (line 191, column 20)
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R/plot.R (line 3580, column 30)
R/plot.R (line 3586, column 41)
R/plot.R (line 3590, column 21)
R/plot.R (line 3593, column 26)
R/plot.R (line 3596, column 34)
R/plot.R (line 3598, column 30)
R/plot.R (line 3599, column 34)
R/plot.R (line 3602, column 34)
R/plot.R (line 3606, column 24)
R/plot.R (line 3607, column 26)
R/plot.R (line 3609, column 33)
R/plot.R (line 3611, column 33)
R/plot.R (line 3615, column 25)
R/plot.R (line 3616, column 41)
R/plot.R (line 3620, column 36)
R/plot.R (line 3623, column 30)
R/plot.R (line 3731, column 27)
R/plot.R (line 3736, column 27)
R/plot.R (line 3742, column 31)
R/plot.R (line 3748, column 31)
R/plot.R (line 3765, column 24)
R/plot.R (line 3766, column 27)
R/plot.R (line 3767, column 26)
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 21
times)
suppressWarnings() in R/core.R (line 1165, column 11)
suppressWarnings() in R/core.R (line 2378, column 5)
suppressWarnings() in R/core.R (line 2379, column 5)
suppressWarnings() in R/core.R (line 2399, column 17)
suppressWarnings() in R/core.R (line 2519, column 19)
suppressWarnings() in R/core.R (line 2540, column 20)
suppressWarnings() in R/core.R (line 2696, column 12)
suppressWarnings() in R/core.R (line 3002, column 18)
suppressWarnings() in R/core.R (line 3004, column 18)
suppressMessages() in R/core.R (line 461, column 23)
suppressMessages() in R/core.R (line 1111, column 13)
suppressMessages() in R/core.R (line 2363, column 20)
suppressMessages() in R/core.R (line 2364, column 20)
suppressMessages() in R/core.R (line 2634, column 12)
suppressMessages() in R/core.R (line 3419, column 18)
suppressWarnings() in R/network.R (line 378, column 24)
suppressMessages() in R/network.R (line 526, column 21)
suppressMessages() in R/network.R (line 535, column 14)
suppressWarnings() in R/plot.R (line 711, column 13)
suppressWarnings() in R/plot.R (line 754, column 13)
suppressWarnings() in R/plot.R (line 1826, column 23)
* 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 913): 612
lines
visualizeGRN() (R/plot.R, line 3209): 592 lines
filterGRNAndConnectGenes() (R/core.R, line 2787): 394 lines
.computeTF_peak.fdr() (R/core.R, line 1788): 391 lines
plotCommunitiesEnrichment() (R/plot.R, line 2449): 258 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, plotPCA_all.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; 2545 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:3746 # vertex.color Node color
R/plot.R:3747 # vertex.frame.color Node border color
R/plot.R:3748 # vertex.shape One of “none”, “circle”, “square”...
R/plot.R:3749 # vertex.size Size of the node (default is 15)
R/plot.R:3750 # vertex.size2 The second size of the node (e.g....
R/plot.R:3751 # vertex.label Character vector used to label th...
* NOTE: Consider multiples of 4 spaces for line indents, 5294
lines(38%) 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: 0
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
nebbiolo1 BUILD BIN output
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