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### Running command:
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###   /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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Dune.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Dune/DESCRIPTION’ ... OK
* this is package ‘Dune’ version ‘1.16.0’
* 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 ... 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 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Dune             6.216  0.051   9.387
ARItrend         4.122  0.040   6.380
plotARIs         3.935  0.045   6.193
ARIImp           3.759  0.102   5.872
plotNMIs         3.787  0.037   5.828
NMItrend         3.704  0.036   5.674
functionTracking 3.639  0.031   5.550
plotPrePost      3.627  0.034   5.383
intermediateMat  3.492  0.031   5.244
NMIImp           3.429  0.033   5.419
* 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 2 | 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-arm64/Resources/library’
* installing *source* package ‘Dune’ ...
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 2 | 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 2 | SKIP 0 | PASS 446 ]
Error: Test failures
Execution halted