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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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.8.0’
* 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 ... WARNING
Missing or unexported object: 'AnnotationHub::getAnnotationHub'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getAnnotationHub: no visible global function definition for 'is'
.performIHW: no visible binding for global variable 'adj_pvalue'
.retrieveAnnotationData: no visible global function definition for 'is'
Undefined global functions or variables:
  adj_pvalue is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                             ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                   ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                           ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                        ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                                                                            ^
checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup?
    36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end 
       |                                                                                                                        ^
* 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           12.898  0.281  15.865
addConnections_TF_peak          8.255  1.407  11.588
addSNPData                      9.054  0.376  28.398
plotDiagnosticPlots_peakGene    7.850  0.193   9.721
plotCommunitiesStats            6.707  0.195   8.407
plotDiagnosticPlots_TFPeaks     6.545  0.151   8.337
visualizeGRN                    6.475  0.167   8.070
plotGeneralGraphStats           6.211  0.121   7.929
plotCommunitiesEnrichment       6.040  0.214   7.664
plotPCA_all                     5.704  0.180   7.179
calculateCommunitiesEnrichment  4.930  0.171   6.098
calculateTFEnrichment           4.818  0.104   5.907
plotTFEnrichment                4.330  0.101   5.801
plot_stats_connectionSummary    4.280  0.133   5.449
getGRNSummary                   4.207  0.120   5.372
addConnections_peak_gene        4.098  0.091   5.125
getParameters                   3.955  0.115   5.149
filterData                      3.561  0.110   5.269
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /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)