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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
addConnections_TF_peak         10.351  1.536  14.122
generateStatsSummary           10.532  0.445  11.224
addSNPData                      7.498  0.514  10.826
plotDiagnosticPlots_TFPeaks     6.955  0.381   7.537
plotDiagnosticPlots_peakGene    6.427  0.348   6.955
plotCommunitiesEnrichment       6.310  0.408   6.905
plotGeneralGraphStats           6.356  0.303   6.853
plotCommunitiesStats            6.334  0.308   6.839
plotPCA_all                     6.149  0.354   6.685
getGRNSummary                   5.778  0.311   6.257
add_TF_gene_correlation         5.649  0.409   6.284
plot_stats_connectionSummary    5.580  0.382   6.164
plotCorrelations                5.638  0.313   6.130
plotGeneralEnrichment           5.352  0.262   5.778
addConnections_peak_gene        5.119  0.407   5.785
filterData                      5.176  0.314   5.662
visualizeGRN                    5.182  0.287   5.637
filterGRNAndConnectGenes        5.112  0.319   5.639
calculateTFEnrichment           5.117  0.288   5.586
plotTFEnrichment                5.073  0.263   5.494
deleteIntermediateData          5.001  0.284   5.481
getCounts                       4.982  0.285   5.456
calculateGeneralEnrichment      4.977  0.286   5.433
calculateCommunitiesEnrichment  4.910  0.341   5.466
overlapPeaksAndTFBS             4.945  0.287   5.688
filterConnectionsForPlotting    4.920  0.288   5.386
changeOutputDirectory           4.905  0.291   5.375
getGRNConnections               4.898  0.291   5.366
getTopNodes                     4.873  0.303   5.359
getParameters                   4.860  0.269   5.319
nTFs                            4.823  0.283   5.296
nGenes                          4.820  0.267   5.266
nPeaks                          4.816  0.260   5.254
build_eGRN_graph                4.689  0.352   5.268
calculateCommunitiesStats       4.702  0.265   5.148
* 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.

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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
** 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)