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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lefser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lefser_1.17.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/lefser.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lefser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lefser’ version ‘1.17.2’
* 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 ‘lefser’ 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘BiocGenerics’ ‘ape’ ‘ggrepel’ ‘mia’ ‘purrr’ ‘tidyselect’ ‘treeio’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
lefserPlot: no visible binding for global variable ‘.’
lefserPlotClad: no visible binding for global variable ‘node’
lefserPlotClad: no visible binding for global variable ‘showNodeLabs’
lefserPlotFeat: no visible binding for global variable ‘abundance’
lefserPlotFeat: no visible binding for global variable ‘classCol’
lefserPlotFeat: no visible binding for global variable ‘subclassCol’
lefserPlotFeat: no visible binding for global variable ‘x1’
lefserPlotFeat: no visible binding for global variable ‘x2’
lefserPlotFeat: no visible binding for global variable ‘mean1’
lefserPlotFeat: no visible binding for global variable ‘mean2’
lefserPlotFeat: no visible binding for global variable ‘median1’
lefserPlotFeat: no visible binding for global variable ‘median2’
Undefined global functions or variables:
  . abundance classCol mean1 mean2 median1 median2 node showNodeLabs
  subclassCol x1 x2
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lefser.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/lefser.Rcheck/00check.log’
for details.