##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/GSEABenchmarkeR.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-22 23:52:42 UTC
* using option ‘--no-vignettes’
* checking for file ‘GSEABenchmarkeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABenchmarkeR’ version ‘1.33.1’
* 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.
* 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 11.969  7.148  23.375
loadEData       7.634  0.734   8.184
runEA           4.094  2.711   4.413
evalRandomGS    3.666  1.085   5.163
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.24-bioc/meat/GSEABenchmarkeR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GSEABenchmarkeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘GSEABenchmarkeR’ ...
** this is package ‘GSEABenchmarkeR’ version ‘1.33.1’
** 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)