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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBubbletree_1.7.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scBubbletree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scBubbletree’ version ‘1.7.7’
* 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 ‘scBubbletree’ 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 ... NOTE
compare_bubbletrees: no visible binding for global variable ‘JD’
compare_bubbletrees: no visible binding for global variable
  ‘intersection’
get_bubbletree_dummy: no visible global function definition for
  ‘as.dist’
get_bubbletree_dummy: no visible global function definition for
  ‘hclust’
get_bubbletree_graph: no visible global function definition for
  ‘as.dist’
get_bubbletree_graph: no visible global function definition for
  ‘hclust’
get_bubbletree_kmeans: no visible global function definition for
  ‘kmeans’
get_bubbletree_kmeans: no visible global function definition for
  ‘as.dist’
get_bubbletree_kmeans: no visible global function definition for
  ‘hclust’
get_gap_k : get_Wk: no visible global function definition for ‘kmeans’
get_gap_k : <anonymous>: no visible global function definition for
  ‘runif’
get_gap_k: no visible binding for global variable ‘var’
get_gap_r : <anonymous>: no visible global function definition for
  ‘runif’
get_gap_r: no visible binding for global variable ‘var’
get_gap_r_k1 : <anonymous>: no visible global function definition for
  ‘runif’
get_gap_r_k1: no visible binding for global variable ‘var’
get_k: no visible binding for global variable ‘kmeans’
get_k: no visible binding for global variable ‘var’
get_r: no visible binding for global variable ‘var’
Undefined global functions or variables:
  JD as.dist hclust intersection kmeans runif var
Consider adding
  importFrom("stats", "as.dist", "hclust", "kmeans", "runif", "var")
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 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
get_r      10.350  0.178  10.583
get_gini_k  7.179  0.186   7.510
* 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:
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 477 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-input-get-num-tiles.R:341:3'): btd argument ──────────────────
  `get_bubbletree_graph(...)` did not produce any warnings.
  ── Failure ('test-input-get-num-tiles.R:397:3'): btd argument ──────────────────
  `get_num_tiles(...)` did not throw an error.
  ── Failure ('test-input-get-num-violins.R:159:3'): btd argument ────────────────
  `get_bubbletree_graph(...)` did not produce any warnings.
  ── Failure ('test-input-get-num-violins.R:192:3'): btd argument ────────────────
  `get_num_violins(...)` did not throw an error.
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 477 ]
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scBubbletree
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘scBubbletree’ ...
** using staged installation
** R
** data
** 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 (scBubbletree)

R version 4.4.0 Patched (2024-04-24 r86482) -- "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(scBubbletree)
> 
> test_check("scBubbletree")
Tests input rules of get_bubbletree_graph 
Tests input rules of get_bubbletree_kmeans 
Tests input rules of get_cat_tiles 
Tests input rules of get_gini_k 
Tests input rules of get_gini 
Tests input rules of get_k 
Tests input rules of get_num_tiles 
Tests input rules of get_num_violins 
Tests input rules of get_r 
Tests input rules of util 
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 477 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-input-get-num-tiles.R:341:3'): btd argument ──────────────────
`get_bubbletree_graph(...)` did not produce any warnings.
── Failure ('test-input-get-num-tiles.R:397:3'): btd argument ──────────────────
`get_num_tiles(...)` did not throw an error.
── Failure ('test-input-get-num-violins.R:159:3'): btd argument ────────────────
`get_bubbletree_graph(...)` did not produce any warnings.
── Failure ('test-input-get-num-violins.R:192:3'): btd argument ────────────────
`get_num_violins(...)` did not throw an error.

[ FAIL 4 | WARN 1 | SKIP 0 | PASS 477 ]
Error: Test failures
Execution halted