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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GSEABenchmarkeR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GSEABenchmarkeR_1.27.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GSEABenchmarkeR.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GSEABenchmarkeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABenchmarkeR' version '1.27.0'
* 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 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
loadEData      25.62   4.25   71.83
evalTypeIError 28.74   0.35   33.00
runEA          12.67   0.53   13.21
evalRandomGS    8.66   0.50   11.36
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/GSEABenchmarkeR.Rcheck/00check.log'
for details.