Christian Arnold
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/GRaNIE |
| git_branch: RELEASE_3_15 |
| git_last_commit: 2ff0659 |
| git_last_commit_date: 2022-09-27 06:50:11 -0400 (Tue, 27 Sep 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:21:36 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the GRaNIE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRaNIE.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 839/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GRaNIE 1.0.7 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: GRaNIE |
| Version: 1.0.7 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GRaNIE_1.0.7.tar.gz |
| StartedAt: 2022-10-19 00:47:34 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 00:53:05 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 331.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GRaNIE.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GRaNIE_1.0.7.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/GRaNIE.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GRaNIE/DESCRIPTION' ... OK
* this is package 'GRaNIE' version '1.0.7'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GRaNIE' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
See 'F:/biocbuild/bbs-3.15-bioc/meat/GRaNIE.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addStats: no visible binding for global variable 'TF.name'
.addStats: no visible binding for global variable 'peak.ID'
.addStats: no visible binding for global variable 'gene.ENSEMBL'
.buildGraph: no visible binding for global variable 'V1_name'
.buildGraph: no visible binding for global variable 'V2_name'
.buildGraph: no visible binding for global variable 'V1'
.buildGraph: no visible binding for global variable 'nodeID'
.buildGraph: no visible binding for global variable 'V2'
.buildGraph: no visible binding for global variable 'GRN'
.calcGCContentPeaks: no visible binding for global variable 'G|C'
.calcGCContentPeaks: no visible binding for global variable 'GC_class'
.calculatePeakGeneCorrelations: no visible binding for global variable
'isFiltered'
.calculatePeakGeneCorrelations: no visible binding for global variable
'peakID'
.calculatePeakGeneCorrelations: no visible binding for global variable
'gene.ENSEMBL'
.calculatePeakGeneCorrelations: no visible binding for global variable
'ENSEMBL'
.calculatePeakGeneCorrelations: no visible binding for global variable
'peak.ID'
.calculatePeakGeneCorrelations: no visible binding for global variable
'tad.ID'
.calculatePeakGeneCorrelations: no visible binding for global variable
'r'
.calculatePeakGeneCorrelations: no visible binding for global variable
'p.raw'
.calculatePeakGeneCorrelations: no visible binding for global variable
'p_raw.robust'
.calculatePeakGeneCorrelations: no visible binding for global variable
'r_robust'
.calculatePeakGeneCorrelations: no visible binding for global variable
'bias_M_p.raw'
.calculatePeakGeneCorrelations: no visible binding for global variable
'bias_LS_p.raw'
.calculatePeakGeneOverlaps: no visible binding for global variable
'peakID'
.calculatePeakGeneOverlaps: no visible binding for global variable
'tadStart'
.calculatePeakGeneOverlaps: no visible binding for global variable
'tadEnd'
.calculatePeakGeneOverlaps: no visible binding for global variable
'tad.ID'
.calculatePeakGeneOverlaps: no visible binding for global variable
'gene.ENSEMBL'
.combineEnrichmentResults: no visible binding for global variable
'pval'
.combineEnrichmentResults: no visible binding for global variable
'Found'
.combineEnrichmentResults: no visible binding for global variable 'ID'
.computeTF_peak.fdr: no visible binding for global variable 'TF.name'
.computeTF_peak.fdr: no visible binding for global variable
'isFiltered'
.computeTF_peak.fdr: no visible binding for global variable 'GC_class'
.computeTF_peak.fdr: no visible binding for global variable
'peak_width'
.computeTF_peak.fdr: no visible binding for global variable 'n_rel'
.computeTF_peak.fdr: no visible binding for global variable
'GC_class.all'
.computeTF_peak.fdr: no visible binding for global variable 'n.bg'
.computeTF_peak.fdr: no visible binding for global variable 'n_rel.fg'
.computeTF_peak.fdr: no visible binding for global variable
'n.bg.needed'
.computeTF_peak.fdr: no visible binding for global variable 'peakID'
.computeTF_peak.fdr: no visible binding for global variable
'TF_peak.r_bin2'
.computeTF_peak.fdr: no visible binding for global variable 'TF_peak.r'
.computeTF_peak.fdr: no visible binding for global variable
'TF_peak.r_bin'
.computeTF_peak.fdr: no visible binding for global variable 'tpvalue'
.computeTF_peak.fdr: no visible binding for global variable 'fpvalue'
.computeTF_peak.fdr: no visible binding for global variable
'fpvalue_norm'
.computeTF_peak.fdr: no visible binding for global variable
'TF_peak.fdr'
.computeTF_peak.fdr: no visible binding for global variable
'TF_peak.fdr_orig'
.computeTF_peak.fdr: no visible binding for global variable
'TF_peak.fdr_direction'
.computeTF_peak.fdr: no visible binding for global variable
'TF_peak.connectionType'
.computeTF_peak.fdr: no visible binding for global variable 'peak.ID'
.correlateData: no visible binding for global variable 'GRN'
.correlateData: no visible binding for global variable 'perm'
.correlateMatrices: no visible binding for global variable 'ENSEMBL'
.correlateMatrices: no visible binding for global variable 'peakID'
.createEnichmentTable: no visible binding for global variable
'Description'
.createEnichmentTable: no visible binding for global variable 'Count'
.createTables_peakGeneQC: no visible binding for global variable
'r_positive'
.createTables_peakGeneQC: no visible binding for global variable
'peak_gene.p.raw.class'
.createTables_peakGeneQC: no visible binding for global variable
'sum_pos'
.createTables_peakGeneQC: no visible binding for global variable
'sum_neg'
.createTables_peakGeneQC: no visible binding for global variable
'enrichment_pos'
.createTables_peakGeneQC: no visible binding for global variable
'sum_n'
.createTables_peakGeneQC: no visible binding for global variable
'n_real'
.createTables_peakGeneQC: no visible binding for global variable
'n_permuted'
.createTables_peakGeneQC: no visible binding for global variable
'ratio_real_raw'
.createTables_peakGeneQC: no visible binding for global variable
'classAll'
.createTables_peakGeneQC: no visible binding for global variable
'n_rneg_real'
.createTables_peakGeneQC: no visible binding for global variable
'n_rpos_real'
.createTables_peakGeneQC: no visible binding for global variable
'n_rneg_random'
.createTables_peakGeneQC: no visible binding for global variable
'n_rpos_random'
.createTables_peakGeneQC: no visible binding for global variable
'peak_gene.p.raw.class.bin'
.createTables_peakGeneQC: no visible binding for global variable
'variable'
.facetLabel: no visible binding for global variable 'Degree'
.filterGenesByMeanCV: no visible binding for global variable 'gene.CV'
.filterGenesByMeanCV: no visible binding for global variable
'gene.mean'
.filterPeaksByCV: no visible binding for global variable 'peak.CV'
.filterPeaksByMeanCV: no visible binding for global variable 'peak.CV'
.filterPeaksByMeanCV: no visible binding for global variable
'peak.mean'
.filterSortAndShuffle_peakTF_overlapTable: no visible binding for
global variable 'isFiltered'
.finalizeClassificationAndAppend: no visible binding for global
variable 'TF'
.findMaxBackgroundSize: no visible binding for global variable
'GC_class'
.generateTF_GC_diagnosticPlots: no visible binding for global variable
'GC_class'
.generateTF_GC_diagnosticPlots: no visible binding for global variable
'peak_width'
.generateTF_GC_diagnosticPlots: no visible binding for global variable
'n.bg.needed.perc'
.generateTF_GC_diagnosticPlots: no visible binding for global variable
'n_rel'
.generateTF_GC_diagnosticPlots: no visible binding for global variable
'n.bg.needed.relFreq'
.getBackgroundGenes: no visible binding for global variable
'geneAnnotation'
.getDegreeStats: no visible binding for global variable
'connectionType'
.getDegreeStats: no visible binding for global variable 'V1_name'
.getDegreeStats: no visible binding for global variable 'V1'
.getDegreeStats: no visible binding for global variable 'name_plot'
.getDegreeStats: no visible binding for global variable 'V2'
.getDegreeStats: no visible binding for global variable 'V2_name'
.getDegreeStats: no visible binding for global variable 'Degree'
.getDegreeStats: no visible binding for global variable 'ID'
.getDegreeStats: no visible binding for global variable 'ID_all'
.getEigenCentralVertices: no visible binding for global variable
'connectionType'
.getEigenCentralVertices: no visible binding for global variable 'V2'
.getEigenCentralVertices: no visible binding for global variable 'V1'
.getEigenCentralVertices: no visible binding for global variable
'V2_name'
.getEigenCentralVertices: no visible binding for global variable
'gene.name'
.getEigenCentralVertices: no visible binding for global variable
'gene.ENSEMBL'
.getEigenCentralVertices: no visible binding for global variable
'Score'
.getEigenCentralVertices: no visible binding for global variable
'V1_name'
.getEigenCentralVertices: no visible binding for global variable
'TF.name'
.getEigenCentralVertices: no visible binding for global variable
'TF.ENSEMBL'
.getEigenCentralVertices: no visible binding for global variable
'name_plot'
.getFinalListOfTFs: no visible binding for global variable 'ENSEMBL'
.getFinalListOfTFs: no visible binding for global variable 'HOCOID'
.getKnownGeneAnnotationNew: no visible binding for global variable
'gene.type'
.intersectTFBSPeaks: no visible binding for global variable
'annotation'
.intersectTFBSPeaks: no visible binding for global variable 'tfbs_chr'
.intersectTFBSPeaks: no visible binding for global variable
'tfbs_start'
.intersectTFBSPeaks: no visible binding for global variable 'tfbs_end'
.intersectTFBSPeaks: no visible binding for global variable
'peak_start'
.intersectTFBSPeaks: no visible binding for global variable 'peak_end'
.intersectTFBSPeaks: no visible binding for global variable
'coordSummit'
.intersectTFBSPeaks: no visible binding for global variable
'coordCentTfbs'
.intersectTFBSPeaks: no visible binding for global variable 'peakID'
.optimizeSpaceGRN: no visible binding for global variable 'TF.name'
.optimizeSpaceGRN: no visible binding for global variable
'TF_peak.r_bin'
.optimizeSpaceGRN: no visible binding for global variable 'peak.ID'
.optimizeSpaceGRN: no visible binding for global variable
'TF_peak.fdr_direction'
.optimizeSpaceGRN: no visible binding for global variable
'TF_peak.connectionType'
.performIHW: no visible binding for global variable 'adj_pvalue'
.performIHW: no visible binding for global variable 'group'
.performIHW: no visible binding for global variable 'pValues'
.performIHW: no visible binding for global variable 'covariate_group'
.performIHW: no visible binding for global variable 'covariateRank'
.plotDensity: no visible binding for global variable 'variable'
.plotDensity: no visible binding for global variable 'value'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'gene.ENSEMBL'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'gene.type'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'gene.mean'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'gene.median'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'gene.CV'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak.GC.perc'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak.ID'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak_gene.r'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak_gene.distance'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak_gene.p_raw'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak_gene.p_raw.robust'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'r_positive'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak_gene.p.raw.class'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'ratio'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'classAll'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak_gene.r.class'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'nnorm'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak.CV'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'classNew'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'ratio_pos_raw'
.plotDiagnosticPlots_peakGene_all: no visible binding for global
variable 'peak_gene.distance_class_abs'
.plotEnrichmentGeneral: no visible binding for global variable 'Term'
.plotEnrichmentGeneral: no visible binding for global variable 'pval'
.plotEnrichmentGeneral: no visible binding for global variable
'GeneRatio'
.plotEnrichmentGeneral: no visible binding for global variable 'Found'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'TF_peak.connectionType'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'direction'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'nForeground'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'nBackground_orig'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'nBackground'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'ratio_fg_bg_orig'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'ratio_fg_bg'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'background_match_success'
.plotTF_peak_GC_diagnosticPlots: no visible binding for global variable
'percBackgroundUsed'
.plot_PCA_wrapper: no visible binding for global variable 'sampleID'
.plot_PCA_wrapper: no visible binding for global variable 'variation'
.plot_PCA_wrapper: no visible binding for global variable 'PCs'
.plot_PCA_wrapper: no visible binding for global variable
'variation_sum'
.plot_PCA_wrapper: no visible binding for global variable 'PC1'
.plot_PCA_wrapper: no visible binding for global variable 'PC2'
.plot_TF_peak_fdr: no visible binding for global variable 'TF.name'
.plot_TF_peak_fdr: no visible binding for global variable
'TF_peak.fdr_direction'
.plot_TF_peak_fdr: no visible binding for global variable
'TF_peak.r_bin'
.plot_TF_peak_fdr: no visible binding for global variable 'variable'
.plot_TF_peak_fdr: no visible binding for global variable 'value'
.plot_classCorrelations: no visible binding for global variable
'baseMean'
.plot_classCorrelations: no visible binding for global variable
'weighted_meanDifference'
.plot_classCorrelations: no visible binding for global variable
'log2FoldChange'
.plot_classCorrelations: no visible binding for global variable
'baseMeanNorm'
.plot_heatmapAR: no visible binding for global variable 'HOCOID'
.plot_stats_connectionSummaryBoxplot: no visible binding for global
variable 'networkType'
.plot_stats_connectionSummaryBoxplot: no visible binding for global
variable 'Freq'
.plot_stats_connectionSummaryDensity: no visible binding for global
variable 'TF_peak.fdr'
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable 'allowMissingGenes'
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable 'allowMissingTFs'
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable 'TF_peak.connectionType'
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable 'peak_gene.p_raw'
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable 'perm'
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable 'TF_peak.fdr'
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable 'peak_gene.fdr'
.plot_stats_connectionSummaryHeatmap: no visible binding for global
variable 'nTFs'
.populateGeneAnnotation: no visible binding for global variable
'ENSEMBL'
.populatePeakAnnotation: no visible binding for global variable
'peakID'
.populatePeakAnnotation: no visible binding for global variable
'isFiltered'
.populatePeakAnnotation: no visible binding for global variable
'annotation'
.populatePeakAnnotation: no visible binding for global variable
'geneId'
.populatePeakAnnotation: no visible binding for global variable
'distanceToTSS'
.populatePeakAnnotation: no visible binding for global variable
'ENSEMBL'
.populatePeakAnnotation: no visible binding for global variable
'SYMBOL'
.populatePeakAnnotation: no visible binding for global variable
'GENENAME'
.populatePeakAnnotation: no visible binding for global variable
'geneChr'
.populatePeakAnnotation: no visible binding for global variable
'geneStart'
.populatePeakAnnotation: no visible binding for global variable
'geneEnd'
.populatePeakAnnotation: no visible binding for global variable
'geneLength'
.populatePeakAnnotation: no visible binding for global variable
'geneStrand'
.printLoopsGraph: no visible binding for global variable 'V1'
.printLoopsGraph: no visible binding for global variable 'V2'
.printLoopsGraph: no visible binding for global variable 'V1_name'
.printLoopsGraph: no visible binding for global variable
'V1_name_combined'
.printMultipleEdges: no visible binding for global variable 'V1'
.printMultipleEdges: no visible binding for global variable 'V2'
.readHOCOMOCOTable: no visible binding for global variable 'ENSEMBL'
.retrieveAnnotationData: no visible binding for global variable
'chromosome_name'
.retrieveAnnotationData: no visible binding for global variable
'start_position'
.retrieveAnnotationData: no visible binding for global variable
'end_position'
.retrieveAnnotationData: no visible binding for global variable
'ensembl_gene_id'
.retrieveAnnotationData: no visible binding for global variable
'gene_biotype'
.retrieveAnnotationData: no visible binding for global variable
'external_gene_name'
.retrieveAnnotationData: no visible binding for global variable
'gene.strand'
.runEnrichment: no visible binding for global variable 'GRN'
.runEnrichment: no visible binding for global variable 'GO.ID'
.runEnrichment: no visible binding for global variable 'Significant'
.runEnrichment: no visible binding for global variable 'Found'
.selectCommunitesByRank: no visible binding for global variable
'community'
AR_classification_wrapper: no visible binding for global variable
'HOCOID'
AR_classification_wrapper: no visible binding for global variable
'TF.name'
addData: no visible binding for global variable 'ENSEMBL'
addData: no visible binding for global variable 'peakID'
addData: no visible binding for global variable 'sampleID'
addData: no visible binding for global variable 'has_RNA'
addData: no visible binding for global variable 'has_peaks'
addData: no visible binding for global variable 'has_both'
addData_TFActivity: no visible binding for global variable 'ENSEMBL'
addData_TFActivity: no visible binding for global variable 'TF.name'
addSNPOverlap: no visible binding for global variable 'peak'
addSNPOverlap: no visible binding for global variable 'SNP_chr'
addTFBS: no visible binding for global variable 'HOCOID'
addTFBS: no visible binding for global variable 'ENSEMBL'
add_TF_gene_correlation: no visible binding for global variable
'gene.ENSEMBL'
add_TF_gene_correlation: no visible binding for global variable
'TF.name'
add_TF_gene_correlation: no visible binding for global variable
'ENSEMBL'
add_TF_gene_correlation: no visible binding for global variable
'TF.ENSEMBL'
build_eGRN_graph: no visible binding for global variable 'gene.ENSEMBL'
build_eGRN_graph: no visible binding for global variable 'TF.name'
build_eGRN_graph: no visible binding for global variable 'peak.ID'
build_eGRN_graph: no visible binding for global variable 'TF.ENSEMBL'
build_eGRN_graph: no visible binding for global variable 'TF_peak.r'
build_eGRN_graph: no visible binding for global variable 'gene.name'
build_eGRN_graph: no visible binding for global variable 'peak_gene.r'
build_eGRN_graph: no visible binding for global variable 'V1'
build_eGRN_graph: no visible binding for global variable 'V2'
build_eGRN_graph: no visible binding for global variable 'V1_name'
build_eGRN_graph: no visible binding for global variable 'V2_name'
build_eGRN_graph: no visible binding for global variable 'r'
build_eGRN_graph: no visible binding for global variable
'connectionType'
build_eGRN_graph: no visible binding for global variable 'V2.peak_gene'
build_eGRN_graph: no visible binding for global variable
'V1_name.TF_peak'
build_eGRN_graph: no visible binding for global variable
'V2_name.peak_gene'
calculateCommunitiesEnrichment: no visible binding for global variable
'community'
calculateCommunitiesEnrichment: no visible binding for global variable
'name'
calculateTFEnrichment: no visible binding for global variable 'TF.name'
calculateTFEnrichment: no visible binding for global variable
'gene.ENSEMBL'
filterData: no visible binding for global variable 'ENSEMBL'
filterGRNAndConnectGenes: no visible binding for global variable
'HOCOID'
filterGRNAndConnectGenes: no visible binding for global variable
'ENSEMBL'
filterGRNAndConnectGenes: no visible binding for global variable
'TF.ENSEMBL'
filterGRNAndConnectGenes: no visible binding for global variable
'peak_gene.distance'
filterGRNAndConnectGenes: no visible binding for global variable
'peak.ID'
filterGRNAndConnectGenes: no visible binding for global variable
'gene.ENSEMBL'
filterGRNAndConnectGenes: no visible binding for global variable
'TF.name'
getBasic_metadata_visualization: no visible binding for global variable
'ENSEMBL'
getBasic_metadata_visualization: no visible binding for global variable
'ENSEMBL_ID'
getBasic_metadata_visualization: no visible binding for global variable
'peakID'
getCounts: no visible binding for global variable 'isFiltered'
getCounts: no visible binding for global variable 'ENSEMBL'
getTopNodes: no visible binding for global variable 'connectionType'
getTopNodes: no visible binding for global variable 'Connections'
getTopNodes: no visible binding for global variable 'V2'
getTopNodes: no visible binding for global variable 'V2_name'
getTopNodes: no visible binding for global variable 'V1'
getTopNodes: no visible binding for global variable 'V1_name'
importTFData: no visible binding for global variable 'ENSEMBL'
importTFData: no visible binding for global variable 'TF.name'
nGenes: no visible binding for global variable 'isFiltered'
nPeaks: no visible binding for global variable 'isFiltered'
overlapPeaksAndTFBS: no visible binding for global variable
'isFiltered'
overlapPeaksAndTFBS: no visible binding for global variable 'peakID'
plotCommunitiesEnrichment: no visible binding for global variable
'community'
plotCommunitiesEnrichment: no visible binding for global variable 'ID'
plotCommunitiesEnrichment: no visible binding for global variable
'pval'
plotCommunitiesEnrichment: no visible global function definition for
'where'
plotCommunitiesEnrichment: no visible binding for global variable
'nSig'
plotCommunitiesEnrichment: no visible binding for global variable
'Term'
plotCommunitiesStats: no visible binding for global variable
'community'
plotCommunitiesStats: no visible binding for global variable 'isTF'
plotCommunitiesStats: no visible binding for global variable 'Class'
plotCommunitiesStats: no visible binding for global variable 'name'
plotCommunitiesStats: no visible binding for global variable
'from_name'
plotCommunitiesStats: no visible binding for global variable 'to_name'
plotCommunitiesStats: no visible binding for global variable
'connectionType'
plotCommunitiesStats: no visible binding for global variable
'from_names_TF_all'
plotCommunitiesStats: no visible binding for global variable
'to_names_gene'
plotGeneralGraphStats: no visible binding for global variable 'Count'
plotGeneralGraphStats: no visible binding for global variable 'Class'
plotGeneralGraphStats: no visible binding for global variable 'Freq'
plotGeneralGraphStats: no visible binding for global variable 'Var1'
plotTFEnrichment: no visible binding for global variable 'TF.name'
plotTFEnrichment: no visible binding for global variable 'ID'
plotTFEnrichment: no visible binding for global variable 'pval'
plotTFEnrichment: no visible global function definition for 'where'
plotTFEnrichment: no visible binding for global variable 'nSig'
plotTFEnrichment: no visible binding for global variable 'Term'
visualizeGRN: no visible binding for global variable 'V1_name'
visualizeGRN: no visible binding for global variable 'TF.name'
visualizeGRN: no visible binding for global variable 'V2'
visualizeGRN: no visible binding for global variable 'TF_peak.r'
visualizeGRN: no visible binding for global variable 'peak_gene.r'
visualizeGRN: no visible binding for global variable 'TF_peak.fdr'
visualizeGRN: no visible binding for global variable 'V1'
visualizeGRN: no visible binding for global variable 'connectionType'
visualizeGRN: no visible binding for global variable 'color_raw'
visualizeGRN: no visible binding for global variable 'nCommunitiesMax'
show,GRN: no visible binding for global variable 'community'
show,GRN: no visible global function definition for 'desc'
show,GRN: no visible binding for global variable 'n'
Undefined global functions or variables:
Class Connections Count Degree Description ENSEMBL ENSEMBL_ID Found
Freq GC_class GC_class.all GENENAME GO.ID GRN GeneRatio G|C HOCOID ID
ID_all PC1 PC2 PCs SNP_chr SYMBOL Score Significant TF TF.ENSEMBL
TF.name TF_peak.connectionType TF_peak.fdr TF_peak.fdr_direction
TF_peak.fdr_orig TF_peak.r TF_peak.r_bin TF_peak.r_bin2 Term V1
V1_name V1_name.TF_peak V1_name_combined V2 V2.peak_gene V2_name
V2_name.peak_gene Var1 adj_pvalue allowMissingGenes allowMissingTFs
annotation background_match_success baseMean baseMeanNorm
bias_LS_p.raw bias_M_p.raw chromosome_name classAll classNew
color_raw community connectionType coordCentTfbs coordSummit
covariateRank covariate_group desc direction distanceToTSS
end_position enrichment_pos ensembl_gene_id external_gene_name
fpvalue fpvalue_norm from_name from_names_TF_all gene.CV gene.ENSEMBL
gene.mean gene.median gene.name gene.strand gene.type geneAnnotation
geneChr geneEnd geneId geneLength geneStart geneStrand gene_biotype
group has_RNA has_both has_peaks isFiltered isTF log2FoldChange n
n.bg n.bg.needed n.bg.needed.perc n.bg.needed.relFreq nBackground
nBackground_orig nCommunitiesMax nForeground nSig nTFs n_permuted
n_real n_rel n_rel.fg n_rneg_random n_rneg_real n_rpos_random
n_rpos_real name name_plot networkType nnorm nodeID p.raw pValues
p_raw.robust peak peak.CV peak.GC.perc peak.ID peak.mean peakID
peak_end peak_gene.distance peak_gene.distance_class_abs
peak_gene.fdr peak_gene.p.raw.class peak_gene.p.raw.class.bin
peak_gene.p_raw peak_gene.p_raw.robust peak_gene.r peak_gene.r.class
peak_start peak_width percBackgroundUsed perm pval r r_positive
r_robust ratio ratio_fg_bg ratio_fg_bg_orig ratio_pos_raw
ratio_real_raw sampleID start_position sum_n sum_neg sum_pos tad.ID
tadEnd tadStart tfbs_chr tfbs_end tfbs_start to_name to_names_gene
tpvalue value variable variation variation_sum
weighted_meanDifference where
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotCommunitiesEnrichment':
plotCommunitiesEnrichment
Code: function(GRN, outputFolder = NULL, basenameOutput = NULL,
display = "byRank", communities = NULL, topn_pvalue =
30, p = 0.05, nSignificant = 2, nID = 10,
maxWidth_nchar_plot = 50, display_pAdj = FALSE,
plotAsPDF = TRUE, pdf_width = 12, pdf_height = 12,
pages = NULL, forceRerun = FALSE)
Docs: function(GRN, outputFolder = NULL, basenameOutput = NULL,
display = "byRank", communities = NULL, topn_pvalue =
30, p = 0.05, nSignificant = 2, nID = 10,
maxWidth_nchar_plot = 100, display_pAdj = FALSE,
plotAsPDF = TRUE, pdf_width = 12, pdf_height = 12,
pages = NULL, forceRerun = FALSE)
Mismatches in argument default values:
Name: 'maxWidth_nchar_plot' Code: 50 Docs: 100
Codoc mismatches from documentation object 'plotGeneralEnrichment':
plotGeneralEnrichment
Code: function(GRN, outputFolder = NULL, basenameOutput = NULL,
ontology = NULL, topn_pvalue = 30, p = 0.05,
display_pAdj = FALSE, maxWidth_nchar_plot = 50,
plotAsPDF = TRUE, pdf_width = 12, pdf_height = 12,
pages = NULL, forceRerun = FALSE)
Docs: function(GRN, outputFolder = NULL, basenameOutput = NULL,
ontology = NULL, topn_pvalue = 30, p = 0.05,
display_pAdj = FALSE, plotAsPDF = TRUE, pdf_width =
12, pdf_height = 12, pages = NULL, forceRerun = FALSE)
Argument names in code not in docs:
maxWidth_nchar_plot
Mismatches in argument names (first 3):
Position: 8 Code: maxWidth_nchar_plot Docs: plotAsPDF
Position: 9 Code: plotAsPDF Docs: pdf_width
Position: 10 Code: pdf_width Docs: pdf_height
Codoc mismatches from documentation object 'plotTFEnrichment':
plotTFEnrichment
Code: function(GRN, rankType = "degree", n = NULL, TF.names = NULL,
topn_pvalue = 30, p = 0.05, nSignificant = 2, nID =
10, display_pAdj = FALSE, maxWidth_nchar_plot = 50,
outputFolder = NULL, basenameOutput = NULL, plotAsPDF
= TRUE, pdf_width = 12, pdf_height = 12, pages = NULL,
forceRerun = FALSE)
Docs: function(GRN, rankType = "degree", n = NULL, TF.names = NULL,
topn_pvalue = 30, p = 0.05, nSignificant = 2, nID =
10, display_pAdj = FALSE, maxWidth_nchar_plot = 100,
outputFolder = NULL, basenameOutput = NULL, plotAsPDF
= TRUE, pdf_width = 12, pdf_height = 12, pages = NULL,
forceRerun = FALSE)
Mismatches in argument default values:
Name: 'maxWidth_nchar_plot' Code: 50 Docs: 100
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCommunitiesEnrichment 12.20 0.78 13.69
plotCommunitiesStats 11.86 0.56 12.70
plotGeneralGraphStats 10.69 0.61 11.59
plotTFEnrichment 8.54 0.50 9.36
plot_stats_connectionSummary 8.18 0.56 9.03
plotGeneralEnrichment 5.49 0.36 6.14
plotDiagnosticPlots_TFPeaks 5.29 0.56 6.17
filterGRNAndConnectGenes 4.27 1.37 5.83
visualizeGRN 5.04 0.47 5.85
addConnections_TF_peak 4.25 0.57 7.96
* 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: 2 WARNINGs, 1 NOTE
See
'F:/biocbuild/bbs-3.15-bioc/meat/GRaNIE.Rcheck/00check.log'
for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'GRaNIE' ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE' ** 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. Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE' ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE' ** testing if installed package keeps a record of temporary installation path * DONE (GRaNIE)
GRaNIE.Rcheck/GRaNIE-Ex.timings
| name | user | system | elapsed | |
| AR_classification_wrapper | 0 | 0 | 0 | |
| addConnections_TF_peak | 4.25 | 0.57 | 7.96 | |
| addConnections_peak_gene | 2.12 | 0.23 | 2.50 | |
| addData | 0 | 0 | 0 | |
| addTFBS | 0 | 0 | 0 | |
| add_TF_gene_correlation | 3.16 | 0.29 | 3.61 | |
| build_eGRN_graph | 2.34 | 0.28 | 2.86 | |
| calculateCommunitiesEnrichment | 2.23 | 0.24 | 2.63 | |
| calculateCommunitiesStats | 2.18 | 0.31 | 2.64 | |
| calculateGeneralEnrichment | 2.14 | 0.28 | 2.56 | |
| calculateTFEnrichment | 2.32 | 0.16 | 2.63 | |
| changeOutputDirectory | 2.16 | 0.25 | 2.56 | |
| deleteIntermediateData | 0 | 0 | 0 | |
| filterData | 2.25 | 0.22 | 2.63 | |
| filterGRNAndConnectGenes | 4.27 | 1.37 | 5.83 | |
| generateStatsSummary | 2.42 | 0.24 | 2.80 | |
| genes-methods | 2.23 | 0.28 | 2.66 | |
| getCounts | 2.22 | 0.30 | 2.65 | |
| getGRNConnections | 2.45 | 0.31 | 2.92 | |
| getParameters | 2.30 | 0.23 | 2.68 | |
| getTopNodes | 2.64 | 0.27 | 3.05 | |
| initializeGRN | 0.02 | 0.00 | 0.01 | |
| loadExampleObject | 3.11 | 0.17 | 3.43 | |
| overlapPeaksAndTFBS | 2.17 | 0.36 | 2.68 | |
| peaks-methods | 2.53 | 0.33 | 3.00 | |
| performAllNetworkAnalyses | 0 | 0 | 0 | |
| plotCommunitiesEnrichment | 12.20 | 0.78 | 13.69 | |
| plotCommunitiesStats | 11.86 | 0.56 | 12.70 | |
| plotDiagnosticPlots_TFPeaks | 5.29 | 0.56 | 6.17 | |
| plotDiagnosticPlots_peakGene | 0 | 0 | 0 | |
| plotGeneralEnrichment | 5.49 | 0.36 | 6.14 | |
| plotGeneralGraphStats | 10.69 | 0.61 | 11.59 | |
| plotPCA_all | 0 | 0 | 0 | |
| plotTFEnrichment | 8.54 | 0.50 | 9.36 | |
| plot_stats_connectionSummary | 8.18 | 0.56 | 9.03 | |
| visualizeGRN | 5.04 | 0.47 | 5.85 | |