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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_1.3.34.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GRaNIE.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.3.34’
* 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 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
.getFinalListOfTFs: no visible binding for global variable
  ‘external_gene_name’
.getFinalListOfTFs: no visible binding for global variable
  ‘ensembl_gene_id’
.getFinalListOfTFs: no visible binding for global variable ‘SYMBOL’
.makeObjectCompatible: no visible binding for global variable ‘TF.name’
.performIHW: no visible binding for global variable ‘adj_pvalue’
.printGene: no visible binding for global variable ‘gene.ENSEMBL’
.printTF: no visible binding for global variable ‘TF.ID’
getGRNSummary: no visible binding for global variable ‘pval’
Undefined global functions or variables:
  SYMBOL TF.ID TF.name adj_pvalue ensembl_gene_id external_gene_name
  gene.ENSEMBL pval
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotCorrelations':
  ‘peak_gene_max_adjP’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
plotCommunitiesEnrichment      10.478  0.751  13.375
generateStatsSummary            9.266  0.536   9.982
plotPCA_all                     7.968  0.864   9.899
plotCommunitiesStats            8.144  0.615   9.761
calculateCommunitiesEnrichment  7.452  0.628   8.305
addConnections_TF_peak          7.219  0.692   9.626
add_TF_gene_correlation         7.242  0.616   8.413
nPeaks                          6.788  0.564   8.993
plotCorrelations                6.694  0.608   7.982
loadExampleObject               6.659  0.640   8.504
getGRNSummary                   6.657  0.600   8.758
plotDiagnosticPlots_peakGene    6.602  0.552   7.334
getTopNodes                     6.583  0.508   7.402
getParameters                   6.445  0.515   7.967
calculateTFEnrichment           6.392  0.551   8.244
overlapPeaksAndTFBS             6.252  0.364   8.019
nGenes                          6.050  0.560   6.887
calculateGeneralEnrichment      6.197  0.360   7.216
build_eGRN_graph                5.980  0.419   6.781
nTFs                            5.886  0.499   7.776
plotDiagnosticPlots_TFPeaks     5.863  0.464   6.507
visualizeGRN                    5.814  0.476   6.467
calculateCommunitiesStats       5.175  0.460   5.990
plotGeneralEnrichment           4.802  0.540   5.513
plotTFEnrichment                4.905  0.384   5.465
plotGeneralGraphStats           4.756  0.420   5.357
filterData                      4.588  0.484   5.245
plot_stats_connectionSummary    4.594  0.400   5.166
filterGRNAndConnectGenes        4.528  0.400   5.100
deleteIntermediateData          4.446  0.396   5.014
* 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: 1 WARNING, 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
** 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)