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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_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GRaNIE.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.6.1’
* 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'
Undefined global functions or variables:
  adj_pvalue
* checking Rd files ... OK
* checking Rd metadata ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
generateStatsSummary           12.480  0.600  13.442
addConnections_TF_peak         11.276  1.560  14.529
addSNPData                      7.017  0.649  10.238
plotCommunitiesEnrichment       6.770  0.430   7.440
plotDiagnosticPlots_peakGene    6.676  0.340   7.257
plotGeneralGraphStats           6.457  0.389   7.077
visualizeGRN                    6.426  0.386   7.038
plotCommunitiesStats            6.308  0.338   6.856
plotTFEnrichment                6.187  0.369   6.752
plot_stats_connectionSummary    6.106  0.309   6.599
add_TF_gene_correlation         5.770  0.411   6.451
getGRNSummary                   5.713  0.312   6.220
plotCorrelations                5.658  0.366   6.230
filterData                      5.594  0.353   6.210
plotDiagnosticPlots_TFPeaks     5.582  0.343   6.144
calculateGeneralEnrichment      5.338  0.372   5.987
nPeaks                          5.365  0.344   5.926
calculateTFEnrichment           5.375  0.323   5.916
getTopNodes                     5.364  0.324   5.917
filterGRNAndConnectGenes        5.171  0.349   5.791
overlapPeaksAndTFBS             5.153  0.321   5.705
getGRNConnections               5.199  0.270   5.660
nGenes                          5.139  0.323   5.695
loadExampleObject               5.132  0.294   5.661
addConnections_peak_gene        5.056  0.356   5.652
calculateCommunitiesEnrichment  5.019  0.388   5.711
nTFs                            5.092  0.315   5.632
deleteIntermediateData          5.089  0.309   5.608
filterConnectionsForPlotting    5.083  0.313   5.612
calculateCommunitiesStats       5.015  0.334   5.610
plotPCA_all                     5.002  0.325   5.518
getParameters                   5.020  0.296   5.515
changeOutputDirectory           4.990  0.314   5.502
plotGeneralEnrichment           4.705  0.276   5.183
build_eGRN_graph                4.584  0.366   5.212
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.