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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scBubbletree.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings scBubbletree_1.9.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/scBubbletree.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.9.0'
* 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 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 30.63   0.63   31.25
get_num_tiles             22.66   0.26   22.95
get_num_cell_tiles        22.20   0.14   22.36
get_bubbletree_kmeans     20.31   0.25   20.56
get_num_violins           19.66   0.38   20.06
get_r                     18.78   1.03   19.83
get_bubbletree_graph      17.08   0.34   17.42
get_cat_tiles             14.28   0.20   14.49
get_gini_k                12.48   0.39   12.87
get_bubbletree_dummy       9.73   0.19    9.92
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/scBubbletree.Rcheck/00check.log'
for details.