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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:esetVis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings esetVis_1.29.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/esetVis.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘esetVis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esetVis’ version ‘1.29.2’
* 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 ‘esetVis’ 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 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
ggvisPlotEset: no visible global function definition for ‘:=’
ggvisPlotEset: no visible binding for global variable ‘fill’
ggvisPlotEset: no visible binding for global variable ‘shape’
ggvisPlotEset: no visible binding for global variable ‘size’
ggvisPlotEset: no visible binding for global variable ‘opacity’
Undefined global functions or variables:
  := fill opacity shape size
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'getCoordGeneSets.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'getTopElements.Rd':
  ‘returnTopElements’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
getGeneSetsForPlot 90.566  9.784 150.757
esetLda             9.850  0.391  11.801
esetPlotWrapper     7.557  0.368   9.092
esetSpectralMap     6.060  0.290   7.367
esetTsne            5.217  0.159   5.916
* 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/esetVis.Rcheck/00check.log’
for details.