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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_1.2.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/GRaNIE.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.2.6’
* 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 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 ... OK
* 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           16.374  0.590  17.221
getGRNConnections               9.751  0.940  11.133
getCounts                       9.572  0.701  10.652
addConnections_TF_peak          8.990  1.031  17.782
plotGeneralGraphStats           6.316  0.580   7.164
plotDiagnosticPlots_peakGene    6.541  0.307   7.060
plotCommunitiesEnrichment       6.094  0.470   6.756
plotTFEnrichment                5.775  0.536   6.562
plotCommunitiesStats            5.892  0.386   6.481
visualizeGRN                    5.374  0.444   6.051
calculateCommunitiesEnrichment  5.415  0.383   6.014
plot_stats_connectionSummary    5.350  0.319   5.878
plotDiagnosticPlots_TFPeaks     5.224  0.380   5.799
build_eGRN_graph                5.176  0.368   5.759
plotGeneralEnrichment           5.125  0.352   5.732
filterGRNAndConnectGenes        4.969  0.393   5.581
calculateTFEnrichment           5.006  0.326   5.561
calculateCommunitiesStats       4.871  0.427   6.487
getTopNodes                     4.796  0.426   5.412
filterData                      4.807  0.350   5.370
deleteIntermediateData          4.691  0.385   5.314
add_TF_gene_correlation         4.549  0.361   5.120
nGenes                          4.450  0.446   5.096
nTFs                            4.526  0.349   5.074
plotPCA_all                     4.491  0.368   5.088
nPeaks                          4.459  0.384   5.053
overlapPeaksAndTFBS             4.514  0.317   5.040
loadExampleObject               4.488  0.331   5.016
calculateGeneralEnrichment      4.379  0.425   5.063
changeOutputDirectory           4.447  0.328   5.001
* 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: OK

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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/4.2/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)