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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 version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 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 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
.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
generateStatsSummary         8.047  0.136   8.357
visualizeGRN                 6.827  0.203   8.825
addConnections_TF_peak       5.942  0.724   8.240
loadExampleObject            6.326  0.288   7.522
plotDiagnosticPlots_peakGene 6.052  0.188   6.412
plotDiagnosticPlots_TFPeaks  5.910  0.176   6.265
nTFs                         5.537  0.247   6.009
plotPCA_all                  5.431  0.232   5.836
getGRNSummary                5.323  0.227   7.082
plot_stats_connectionSummary 5.225  0.227   6.773
plotCommunitiesStats         4.904  0.220   5.299
plotCommunitiesEnrichment    4.966  0.128   5.266
add_TF_gene_correlation      4.801  0.196   5.176
nGenes                       4.833  0.156   5.364
getTopNodes                  4.775  0.120   5.584
plotTFEnrichment             4.723  0.132   5.081
* 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.