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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:scTreeViz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings scTreeViz_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/scTreeViz.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scTreeViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scTreeViz’ version ‘1.6.0’
* 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 ‘scTreeViz’ 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 R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.generate_hierarchy_tree: no visible binding for global variable
  'otu_index'
.generate_leaf_of_table: no visible binding for global variable 'leaf'
.generate_leaf_of_table: no visible binding for global variable
  'otu_index'
.generate_leaf_of_table: no visible binding for global variable 'id'
.generate_node_ids : <anonymous>: no visible global function definition
  for '.'
.generate_node_ids : <anonymous>: no visible binding for global
  variable 'otu_index'
.generate_nodes_table: no visible binding for global variable 'id'
.generate_nodes_table: no visible binding for global variable 'lineage'
.generate_nodes_table: no visible binding for global variable
  'node_label'
.generate_nodes_table: no visible binding for global variable 'level'
.preprocessAndCreateTreeViz: no visible global function definition for
  'chracter'
getNodes,TreeIndex: no visible binding for global variable 'level'
getNodes,TreeIndex: no visible binding for global variable 'id'
splitAt,TreeIndex: no visible binding for global variable 'level'
splitAt,TreeIndex: no visible binding for global variable 'id'
splitAt,TreeIndex: no visible binding for global variable 'lineage'
splitAt,TreeIndex: no visible binding for global variable 'leaf'
splitAt,TreeIndex: no visible binding for global variable 'otu_index'
splitAt,TreeIndex: no visible global function definition for '.'
splitAt,TreeIndex: no visible binding for global variable 'node_label'
Undefined global functions or variables:
  . chracter id leaf level lineage node_label otu_index
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
TreeIndex-methods 20.255  0.418  20.442
createFromSCE      8.670  0.156   8.820
TreeIndex          8.302  0.288   8.452
TreeViz            8.428  0.108   8.416
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ExploreTreeViz.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/scTreeViz.Rcheck/00check.log’
for details.