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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSABenchmark.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSABenchmark_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/GSABenchmark.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* 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: 2026-04-30 00:08:29 UTC
* using option ‘--no-vignettes’
* checking for file ‘GSABenchmark/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSABenchmark’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘GSABenchmark’ 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 ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GSABenchmark
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘GSABenchmark’ ...
** this is package ‘GSABenchmark’ version ‘1.0.0’
** 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 (GSABenchmark)

R version 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(GSABenchmark)
> 
> test_check("GSABenchmark")
Running AddModuleScore...
Running AUCell...
Running CSOA...
Running GSVA...
Running JASMINE...
Running MDT...
Running MLM...
Running ORA...
Running Pagoda2...
Running PLAGE...
Running Singscore...
Running SiPSiC...
Running ssGSEA...
Running UCell...
Running UDT...
Running VAM...
Running Zscore...
Shuffling genes: gene loss = 20%, noise = 20%, replicate = 1.
Running CSOA...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
3 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
1 overlap will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Shuffling genes: gene loss = 20%, noise = 20%, replicate = 2.
Running CSOA...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
5 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
3 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Shuffling genes: gene loss = 20%, noise = 20%, replicate = 3.
Running CSOA...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
4 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
1 overlap will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Averaging replicates...
Computing cosine distance matrix...
Computing silhouette for identity class: label...
Computing identity class-normalized silhouette...
Computing PCA-based distance matrix...
Running class determination boundary benchmark...
Running MCC benchmark...
Constructing binary predictions...
Running global evaluation benchmark...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
 17.622   0.771  18.211