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### Running command:
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###   /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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scBubbletree.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scBubbletree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scBubbletree’ version ‘1.12.0’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
* 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 ‘isTip’
compare_bubbletrees: no visible binding for global variable ‘Cells’
compare_bubbletrees: no visible binding for global variable ‘lab_short’
compare_bubbletrees: no visible binding for global variable ‘label’
compare_bubbletrees: no visible binding for global variable ‘JD’
compare_bubbletrees: no visible binding for global variable
  ‘intersection’
get_dendrogram: no visible binding for global variable ‘isTip’
get_dendrogram: no visible binding for global variable ‘Cells’
get_dendrogram: no visible binding for global variable ‘label’
get_dendrogram: no visible binding for global variable ‘lab_short’
get_dendrogram: no visible binding for global variable ‘lab_long’
get_num_cell_tiles: no visible binding for global variable ‘cluster’
ggplot_cat_tiles: no visible binding for global variable ‘feature’
ggplot_cat_tiles: no visible binding for global variable ‘cluster’
ggplot_cat_tiles: no visible binding for global variable ‘percent’
ggplot_num_cell_tiles: no visible binding for global variable ‘cluster’
ggplot_num_cell_tiles: no visible binding for global variable ‘f’
ggplot_num_tiles: no visible binding for global variable ‘feature’
ggplot_num_tiles: no visible binding for global variable ‘cluster’
ggplot_num_tiles: no visible binding for global variable ‘value’
ggplot_num_violins: no visible binding for global variable ‘cluster’
ggplot_num_violins: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Cells JD cluster f feature intersection isTip lab_long lab_short
  label percent value
* 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_bubbletree_comparison 67.289  0.557  76.305
get_bubbletree_kmeans     43.245  0.229  51.326
get_num_cell_tiles        43.242  0.227  52.666
get_num_tiles             43.276  0.189  55.424
get_bubbletree_graph      37.057  0.316  42.430
get_num_violins           35.332  0.186  48.643
get_cat_tiles             31.559  0.194  39.881
get_r                     29.039  0.457  38.362
get_bubbletree_dummy      22.020  0.123  25.036
get_gini_k                18.768  0.261  22.386
get_k                      4.318  0.056   5.137
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/scBubbletree.Rcheck/00check.log’
for details.