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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GRaNIE.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.10.0’
* 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 code 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 whether 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'
Undefined global functions or variables:
  adj_pvalue
* 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 ... OK
* 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           11.712  0.182  12.983
addSNPData                      8.847  0.426  24.857
plotDiagnosticPlots_peakGene    8.318  0.163   9.832
addConnections_TF_peak          6.855  1.314   9.699
plotDiagnosticPlots_TFPeaks     6.173  0.147   7.425
plotCommunitiesEnrichment       5.819  0.194   7.347
getGRNSummary                   5.310  0.116   6.030
plot_stats_connectionSummary    5.228  0.135   6.091
plotCommunitiesStats            5.145  0.084   5.990
calculateCommunitiesEnrichment  4.965  0.211   6.139
plotGeneralGraphStats           4.826  0.088   5.760
visualizeGRN                    4.571  0.146   5.188
plotCorrelations                4.521  0.149   6.036
plotPCA_all                     4.257  0.174   5.145
plotTFEnrichment                4.275  0.077   5.020
calculateCommunitiesStats       4.098  0.137   5.463
addConnections_peak_gene        4.011  0.092   5.226
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRaNIE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)