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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Dune.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Dune_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Dune.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Dune/DESCRIPTION’ ... OK
* this is package ‘Dune’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... NOTE
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* 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 ‘Dune’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.metricTrend: no visible binding for global variable ‘.’
.metricTrend: no visible binding for global variable ‘step’
.metricTrend: no visible binding for global variable ‘change’
.metricTrend: no visible binding for global variable ‘value’
.plotMetric: no visible binding for global variable ‘label2’
.plotMetric: no visible binding for global variable ‘metric’
.plotMetric: no visible binding for global variable ‘label1’
ARIImp : f: no visible binding for global variable ‘cells’
ConfusionEvolution : <anonymous>: no visible binding for global
  variable ‘Freq’
ConfusionEvolution : <anonymous>: no visible binding for global
  variable ‘total_x’
ConfusionEvolution : <anonymous>: no visible binding for global
  variable ‘total_y’
ConfusionEvolution: no visible binding for global variable ‘overlap’
ConfusionEvolution: no visible binding for global variable ‘Freq’
ConfusionEvolution: no visible binding for global variable ‘step’
ConfusionPlot: no visible binding for global variable ‘Freq’
ConfusionPlot: no visible binding for global variable ‘total_x’
ConfusionPlot: no visible binding for global variable ‘total_y’
ConfusionPlot: no visible binding for global variable ‘overlap’
NMIImp : f: no visible binding for global variable ‘cells’
intermediateMat: no visible binding for global variable ‘cells’
plotPrePost: no visible binding for global variable ‘Nb’
Undefined global functions or variables:
  . Freq Nb cells change label1 label2 metric overlap step total_x
  total_y value
Consider adding
  importFrom("stats", "step")
to your NAMESPACE file.
* 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:
  ARItrend.Rd: ggplot
  ConfusionEvolution.Rd: transition_states, animate
  ConfusionPlot.Rd: ggplot
  Dune.Rd: SummarizedExperiment
  NMItrend.Rd: ggplot
  plotARIs.Rd: ggplot
  plotNMIs.Rd: ggplot
  plotPrePost.Rd: ggplot
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected`: TRUE 
  ── Failure ('test-Main-Dune.R:59:7'): Dune correctly picks the best cluster for NMI ──
  mean((final_ARI - init_ARI)[upper.tri(init_ARI)]) <= ... is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-Main-Dune.R:59:7'): Dune correctly picks the best cluster for NMI ──
  mean((final_ARI - init_ARI)[upper.tri(init_ARI)]) <= ... is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 6 | WARN 4 | SKIP 0 | PASS 446 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/Dune.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Dune
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘Dune’ ...
** this is package ‘Dune’ version ‘1.21.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (Dune)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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.

> library(testthat)
> library(Dune)
Dune now uses the Normalized Mutual Informationinstead of the adjusted Rand Index. You can restore the old option bysetting metric'ARI' in the Dune function.
> 
> test_check("Dune")
[ FAIL 6 | WARN 4 | SKIP 0 | PASS 446 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Main-Dune.R:37:7'): Dune correctly picks the best cluster for ARI ──
mean((final_ARI - init_ARI)[upper.tri(init_ARI)]) <= ... is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-Main-Dune.R:37:7'): Dune correctly picks the best cluster for ARI ──
mean((final_ARI - init_ARI)[upper.tri(init_ARI)]) <= ... is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-Main-Dune.R:37:7'): Dune correctly picks the best cluster for ARI ──
mean((final_ARI - init_ARI)[upper.tri(init_ARI)]) <= ... is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-Main-Dune.R:37:7'): Dune correctly picks the best cluster for ARI ──
mean((final_ARI - init_ARI)[upper.tri(init_ARI)]) <= ... is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-Main-Dune.R:59:7'): Dune correctly picks the best cluster for NMI ──
mean((final_ARI - init_ARI)[upper.tri(init_ARI)]) <= ... is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-Main-Dune.R:59:7'): Dune correctly picks the best cluster for NMI ──
mean((final_ARI - init_ARI)[upper.tri(init_ARI)]) <= ... is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 6 | WARN 4 | SKIP 0 | PASS 446 ]
Error: Test failures
Execution halted