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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GRaNIE_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GRaNIE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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           8.867  0.499   9.473
add_TF_gene_correlation        7.622  1.083  10.812
plotDiagnosticPlots_peakGene   7.526  0.772   8.447
plotCommunitiesEnrichment      7.311  0.804   8.223
getGRNSummary                  7.108  0.867   8.087
addConnections_TF_peak         6.645  1.236   9.134
loadExampleObject              6.654  0.766   7.544
calculateCommunitiesEnrichment 6.662  0.693   7.619
getParameters                  6.560  0.707   7.863
plot_stats_connectionSummary   6.524  0.695   7.411
nPeaks                         6.244  0.808   7.161
calculateGeneralEnrichment     6.311  0.716   7.891
getTopNodes                    6.402  0.472   8.526
getGRNConnections              6.240  0.608   7.172
nGenes                         5.924  0.631   7.174
plotDiagnosticPlots_TFPeaks    5.874  0.676   6.657
nTFs                           5.707  0.707   7.656
plotPCA_all                    5.650  0.676   6.433
overlapPeaksAndTFBS            5.674  0.651   7.602
plotGeneralGraphStats          5.568  0.604   6.278
peaks-methods                  5.688  0.471   7.491
calculateCommunitiesStats      5.485  0.637   7.543
filterData                     5.214  0.844   6.163
plotTFEnrichment               5.248  0.604   5.958
plotGeneralEnrichment          5.092  0.435   5.721
plotCommunitiesStats           5.035  0.467   5.609
build_eGRN_graph               4.955  0.514   5.984
visualizeGRN                   4.790  0.489   5.386
calculateTFEnrichment          4.578  0.532   5.216
getCounts                      4.561  0.548   5.214
plotCorrelations               4.580  0.452   5.139
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GRaNIE_packageDetails.Rmd’ using ‘UTF-8’... OK
  ‘GRaNIE_singleCell_eGRNs.Rmd’ using ‘UTF-8’... OK
  ‘GRaNIE_workflow.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.