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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scBubbletree.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scBubbletree_1.7.7.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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    7   0.06    7.06
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck/00check.log'
for details.