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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:scBubbletree.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scBubbletree_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scBubbletree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scBubbletree’ version ‘1.8.0’
* 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 loading without being on the library search path ... 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 37.803  0.467  38.344
get_num_cell_tiles        26.252  0.084  26.402
get_num_tiles             25.621  0.427  26.151
get_bubbletree_kmeans     24.223  0.060  24.328
get_num_violins           21.159  0.212  21.414
get_bubbletree_graph      21.033  0.079  21.200
get_r                     18.744  0.105  18.978
get_cat_tiles             18.769  0.044  18.850
get_bubbletree_dummy      14.031  0.088  14.146
get_gini_k                13.117  0.052  13.193
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scBubbletree.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scBubbletree
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 0 | WARN 0 | SKIP 0 | PASS 477 ]
> 
> proc.time()
   user  system elapsed 
323.990   1.518 326.510