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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microbiomeExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microbiomeExplorer_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/microbiomeExplorer.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microbiomeExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘microbiomeExplorer’ version ‘1.14.0’
* 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 ‘microbiomeExplorer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
    shiny     2.9Mb
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) plotBeta.Rd:46: Lost braces
    46 | \item{plotTitle}{Plot title. By default, becomes PCoA (code{dist.method}).}
       |                                                            ^
* 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
plotHeatmap         2.138  0.112  95.991
corrAnalysisUI      0.977  0.098  42.692
corrFeature         0.731  0.084  67.289
plotAbundance       0.747  0.058  28.815
corrPhenotype       0.433  0.050  27.562
plotAvgAbundance    0.441  0.040  27.439
plotLongFeature     0.351  0.054  47.187
plotAlpha           0.313  0.041  30.692
plotSingleFeature   0.310  0.044  28.756
aggFeatures         0.311  0.029  51.725
plotBeta            0.272  0.040  27.522
makeQCPlot          0.219  0.037  22.417
plotlyHistogram     0.167  0.037  30.700
plotlySampleBarplot 0.155  0.039  28.425
aggregationTabUI    0.042  0.006  22.738
* 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-3.19-bioc/meat/microbiomeExplorer.Rcheck/00check.log’
for details.