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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_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GRaNIE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.4.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GRaNIE’ can be installed ... 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 startup messages can be suppressed ... 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
.performIHW: no visible binding for global variable 'adj_pvalue'
getGRNSummary: no visible binding for global variable 'pval'
Undefined global functions or variables:
  adj_pvalue 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
generateStatsSummary           11.799  0.299  20.230
addConnections_TF_peak          9.647  1.589  17.446
plotDiagnosticPlots_peakGene    8.835  0.290  14.177
plotCommunitiesEnrichment       6.808  0.303  11.446
plotDiagnosticPlots_TFPeaks     6.754  0.298  10.015
add_TF_gene_correlation         6.518  0.251   9.847
plotTFEnrichment                6.478  0.224  10.419
plotCommunitiesStats            6.422  0.275  10.184
plotGeneralGraphStats           6.428  0.213  10.301
visualizeGRN                    6.291  0.228  10.125
plotPCA_all                     6.136  0.236   9.979
plot_stats_connectionSummary    6.028  0.247   9.889
calculateCommunitiesEnrichment  5.746  0.250   9.125
getGRNSummary                   5.699  0.215   9.222
filterData                      5.523  0.223   9.121
calculateTFEnrichment           5.480  0.212   8.641
plotGeneralEnrichment           5.470  0.211   8.759
calculateGeneralEnrichment      5.334  0.205   8.427
getParameters                   5.174  0.210   9.537
filterGRNAndConnectGenes        5.164  0.213   9.731
getGRNConnections               5.131  0.207   8.273
getCounts                       5.077  0.213   8.216
genes-methods                   5.081  0.189   8.215
overlapPeaksAndTFBS             5.039  0.217   9.507
deleteIntermediateData          5.026  0.221   8.206
changeOutputDirectory           5.029  0.212   8.205
nPeaks                          5.023  0.202   7.989
nTFs                            5.008  0.209   8.692
nGenes                          4.977  0.201   7.543
peaks-methods                   4.934  0.207   9.323
getTopNodes                     4.888  0.220   9.244
addConnections_peak_gene        4.872  0.223   7.697
build_eGRN_graph                4.714  0.204   7.528
plotCorrelations                4.659  0.236   6.754
loadExampleObject               4.220  0.214   6.045
calculateCommunitiesStats       4.197  0.204   6.868
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GRaNIE.Rcheck/00check.log’
for details.