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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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Dune.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Dune/DESCRIPTION’ ... OK
* this is package ‘Dune’ version ‘1.18.0’
* 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              20.089  0.084  22.071
ARItrend          12.370  0.056  13.419
plotARIs          11.871  0.047  12.601
plotPrePost       11.817  0.070  12.832
ARIImp            11.585  0.265  13.023
plotNMIs          11.719  0.057  12.628
NMItrend          11.517  0.046  12.802
functionTracking  11.257  0.040  12.084
clusterConversion 10.972  0.081  12.209
intermediateMat   10.976  0.038  11.503
NMIImp            10.929  0.061  12.288
whenToStop        10.560  0.053  11.160
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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-x86_64/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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 0 | WARN 2 | SKIP 0 | PASS 452 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 452 ]
> 
> proc.time()
   user  system elapsed 
230.729   2.751 247.567