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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSEABenchmarkeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSEABenchmarkeR_1.28.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GSEABenchmarkeR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSEABenchmarkeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABenchmarkeR’ version ‘1.28.1’
* 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 ‘GSEABenchmarkeR’ 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 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
evalRelevance: no visible binding for global variable ‘REL.SCORE’
Undefined global functions or variables:
  REL.SCORE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cacheResource.Rd: BiocFileCache-class
  evalRandomGS.Rd: sbeaMethods, nbeaMethods,
    SummarizedExperiment-class, sbea, nbea, BiocParallelParam-class,
    register
  evalRelevance.Rd: DataFrame-class, gsRanking
  evalTypeIError.Rd: sbeaMethods, nbeaMethods,
    SummarizedExperiment-class, sbea, nbea, BiocParallelParam-class,
    register
  loadEData.Rd: SummarizedExperiment-class, ExpressionSet-class
  maPreproc.Rd: ExpressionSet-class, BiocParallelParam-class,
    SummarizedExperiment-class
  readResults.Rd: sbeaMethods, nbeaMethods
  runDE.Rd: SummarizedExperiment-class, deAna, BiocParallelParam-class,
    rowData
  runEA.Rd: SummarizedExperiment-class, sbea, sbeaMethods, nbeaMethods,
    BiocParallelParam-class, nbea, register
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
evalTypeIError 34.195 24.142  69.035
loadEData      28.235  2.813  33.642
runEA          13.726 10.047  14.544
evalRandomGS   13.108  3.768  19.294
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/GSEABenchmarkeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GSEABenchmarkeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘GSEABenchmarkeR’ ...
** this is package ‘GSEABenchmarkeR’ version ‘1.28.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (GSEABenchmarkeR)