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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plaid.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plaid_0.99.19.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/plaid.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plaid/DESCRIPTION’ ... OK
* this is package ‘plaid’ version ‘0.99.19’
* 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 ‘plaid’ 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 plaid
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘plaid’ ...
** this is package ‘plaid’ version ‘0.99.19’
** using staged installation
** R
** inst
** 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 (plaid)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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(plaid)
> 
> test_check("plaid")
[plaid] No overlapping features.
[chunked_crossprod] chunked compute: chunk = 10
[replaid.scse] Converting data to linear scale (removing log2)...
[replaid.scse] Converting data to linear scale (removing log2)...
[replaid.scse] Converting data to linear scale (removing log2)...
FC testing using cor
single-sample testing using replaid.ssgsea
FC testing using rankcor
single-sample testing using replaid.ssgsea
FC testing using cor
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
FC testing using ztest
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
[fc_ttest] computing one-sample t-tests on logFC
[fc_ttest] computing one-sample t-tests on logFC
[fc_ttest] computing one-sample t-tests on logFC
[fc_ttest] computing one-sample t-tests on logFC
[gset.averageCLR] no overlapping features
gset has zero columns
matrix has missing values: computing column-wise reduced cor
FC testing using rankcor
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
FC testing using rankcor
single-sample testing using plaid
[ FAIL 0 | WARN 0 | SKIP 4 | PASS 333 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• BiocSet requires complex setup - error handling verified via code inspection
  (1): 'test-bioc-utils.R:233:3'
• BiocSet requires complex setup with tibbles and specific structure (1):
  'test-bioc-utils.R:224:3'
• Empty GMT lists are not supported by design (1): 'test-gmt-utils.R:480:3'
• Unnamed GMT lists can cause issues with name assignment after deduplication
  (1): 'test-gmt-utils.R:117:3'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 333 ]
> 
> proc.time()
   user  system elapsed 
  5.646   3.283   9.120