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### Running command:
###
###   /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           13.914  0.979  15.104
addConnections_TF_peak          9.924  1.798  14.499
plotDiagnosticPlots_peakGene    9.412  0.964  11.495
add_TF_gene_correlation         8.380  0.763  10.955
plotCommunitiesStats            7.730  0.938   9.251
getGRNSummary                   7.261  0.983   8.352
getCounts                       7.452  0.714   8.816
genes-methods                   6.924  0.937   7.991
plotTFEnrichment                6.894  0.858   8.360
plot_stats_connectionSummary    6.955  0.796   8.705
plotPCA_all                     6.654  0.887   8.953
loadExampleObject               6.745  0.738   7.716
getGRNConnections               6.360  0.764   8.738
getParameters                   6.358  0.719   7.251
plotDiagnosticPlots_TFPeaks     6.048  0.776   6.929
plotCommunitiesEnrichment       6.177  0.644   6.928
getTopNodes                     6.234  0.582   7.099
addConnections_peak_gene        6.090  0.590   7.322
nGenes                          5.887  0.731   7.911
nPeaks                          5.853  0.656   7.626
filterData                      5.652  0.736   6.496
build_eGRN_graph                5.898  0.444   7.863
calculateCommunitiesEnrichment  5.585  0.624   6.314
plotGeneralGraphStats           5.546  0.660   6.314
calculateTFEnrichment           4.879  0.879   5.864
visualizeGRN                    5.001  0.484   5.591
calculateCommunitiesStats       4.758  0.589   5.453
filterGRNAndConnectGenes        4.585  0.660   5.351
nTFs                            4.580  0.611   5.297
calculateGeneralEnrichment      4.521  0.552   5.178
overlapPeaksAndTFBS             4.487  0.456   5.050
* 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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GRaNIE
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)