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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.2.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/GRaNIE.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.2.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GRaNIE’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getFinalListOfTFs: no visible binding for global variable
  ‘external_gene_name’
.getFinalListOfTFs: no visible binding for global variable
  ‘ensembl_gene_id’
.getFinalListOfTFs: no visible binding for global variable ‘SYMBOL’
.makeObjectCompatible: no visible binding for global variable ‘TF.name’
.performIHW: no visible binding for global variable ‘adj_pvalue’
.printGene: no visible binding for global variable ‘gene.ENSEMBL’
.printTF: no visible binding for global variable ‘TF.ID’
getGRNSummary: no visible binding for global variable ‘pval’
Undefined global functions or variables:
  SYMBOL TF.ID TF.name adj_pvalue ensembl_gene_id external_gene_name
  gene.ENSEMBL pval
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated name 'nGenes':
  ‘genes-methods.Rd’ ‘nGenes.Rd’
Rd files with duplicated name 'nPeaks':
  ‘nPeaks.Rd’ ‘peaks-methods.Rd’
Rd files with duplicated alias 'genes':
  ‘genes-methods.Rd’ ‘nGenes.Rd’
Rd files with duplicated alias 'nGenes':
  ‘genes-methods.Rd’ ‘nGenes.Rd’
Rd files with duplicated alias 'nPeaks':
  ‘nPeaks.Rd’ ‘peaks-methods.Rd’
Rd files with duplicated alias 'peaks':
  ‘nPeaks.Rd’ ‘peaks-methods.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'installSuggestedPackages' but not in code:
  ‘installSuggestedPackages’

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'plotCorrelations':
  ‘peak_gene_max_adjP’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
generateStatsSummary           9.251  0.321   9.791
addConnections_TF_peak         8.461  0.926  13.854
plotCommunitiesStats           6.627  0.356   9.081
calculateCommunitiesEnrichment 6.018  0.456   8.068
plotCommunitiesEnrichment      6.026  0.421   7.280
plotDiagnosticPlots_peakGene   6.148  0.254   6.605
add_TF_gene_correlation        5.866  0.434   8.512
getGRNSummary                  5.814  0.425   8.148
plotPCA_all                    5.455  0.333   5.991
plot_stats_connectionSummary   5.337  0.353   5.917
getTopNodes                    5.295  0.318   7.076
getParameters                  5.026  0.537   7.087
getGRNConnections              5.115  0.430   7.619
plotDiagnosticPlots_TFPeaks    5.218  0.322   5.738
nGenes                         4.956  0.581   6.990
loadExampleObject              5.191  0.295   6.900
build_eGRN_graph               4.928  0.388   6.581
plotTFEnrichment               4.810  0.346   5.393
calculateGeneralEnrichment     4.650  0.345   6.303
calculateCommunitiesStats      4.473  0.359   6.492
nPeaks                         4.383  0.440   5.993
calculateTFEnrichment          4.442  0.288   5.100
overlapPeaksAndTFBS            4.237  0.357   6.186
nTFs                           4.180  0.413   6.014
peaks-methods                  4.158  0.322   5.752
* 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 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.