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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings GRaNIE_1.2.7.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/GRaNIE.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GRaNIE/DESCRIPTION' ... OK
* this is package 'GRaNIE' version '1.2.7'
* 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 whether package 'GRaNIE' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
See 'F:/biocbuild/bbs-3.16-bioc/meat/GRaNIE.Rcheck/00install.out' for details.
* 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 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 ... 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 ... 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   7.00   0.20    7.65
addConnections_TF_peak 5.08   1.23    7.64
* 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: 4 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/GRaNIE.Rcheck/00check.log'
for details.