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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/meat/GRaNIE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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           13.966  0.203  18.105
plotDiagnosticPlots_peakGene    8.931  0.171  12.129
addConnections_TF_peak          6.904  1.351  11.231
plotDiagnosticPlots_TFPeaks     6.392  0.214   8.773
plotCommunitiesEnrichment       6.107  0.353   8.286
visualizeGRN                    6.085  0.164   8.681
calculateCommunitiesEnrichment  5.749  0.156   7.696
plotPCA_all                     5.634  0.241   8.905
plotCommunitiesStats            5.413  0.170   7.378
getGRNSummary                   5.143  0.117   7.400
plotGeneralGraphStats           5.142  0.106   7.828
plotTFEnrichment                4.902  0.109   7.405
plot_stats_connectionSummary    4.372  0.130   6.405
loadExampleObject               4.127  0.078   5.724
overlapPeaksAndTFBS             3.966  0.082   5.096
addConnections_peak_gene        3.931  0.096   5.798
changeOutputDirectory           3.911  0.084   5.447
plotCorrelations                3.827  0.163   5.353
calculateTFEnrichment           3.810  0.095   5.343
filterData                      3.631  0.089   5.022
calculateGeneralEnrichment      3.536  0.127   5.126
plotGeneralEnrichment           3.524  0.081   5.280
* 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/meat/GRaNIE.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRaNIE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘GRaNIE’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GRaNIE)