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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:miaViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings miaViz_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/miaViz.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-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 Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miaViz/DESCRIPTION’ ... OK
* this is package ‘miaViz’ version ‘1.13.0’
* 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 ‘miaViz’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.add_signif_to_vector_labels : <anonymous>: no visible global function
  definition for ‘italic’
.clean_tree_data: no visible global function definition for ‘all_of’
.get_prevalence_plot_matrix: no visible binding for global variable
  ‘ID’
.rda_plotter: no visible binding for global variable ‘color’
Undefined global functions or variables:
  ID all_of color italic
* checking Rd files ... NOTE
checkRd: (-1) plotAbundanceDensity.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:33-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAbundanceDensity.Rd:52-53: Lost braces in \itemize; meant \describe ?
* 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
plotTree             130.032  1.853 165.207
plotDMN               27.229  0.229  36.661
plotAbundanceDensity  22.236  3.541  40.077
plotPrevalence        19.926  0.224  26.220
plotAbundance         16.078  0.622  22.699
plotCCA               11.738  0.220  15.173
* 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-3.20-bioc/meat/miaViz.Rcheck/00check.log’
for details.