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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CATALYST_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/CATALYST.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.24.0’
* 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 ‘CATALYST’ 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.cluster_cols’
* 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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
plotPbExprs      30.856  1.038  43.740
plotMultiHeatmap 30.722  0.832  41.995
plotDiffHeatmap  26.662  0.796  35.714
sce2fcs          24.036  0.914  31.983
plotDR           21.913  0.838  29.652
plotExprHeatmap  22.048  0.575  28.853
plotClusterExprs 15.541  0.757  22.446
pbMDS            14.970  0.669  20.792
plotAbundances   14.417  0.674  19.755
plotCodes        14.049  0.679  21.401
mergeClusters    13.837  0.521  18.813
SCE-accessors    13.263  0.951  18.747
clrDR            13.503  0.567  18.053
plotFreqHeatmap  13.027  0.741  17.833
plotMahal        12.785  0.144  17.084
filterSCE        12.249  0.503  16.718
compCytof        11.608  0.322  16.545
cluster          10.659  0.517  14.204
extractClusters  10.022  0.629  13.708
plotScatter      10.036  0.167  13.450
plotSpillmat      9.767  0.256  13.322
estCutoffs        9.755  0.133  12.688
plotYields        9.619  0.234  13.597
computeSpillmat   9.242  0.219  12.322
adaptSpillmat     8.795  0.239  11.619
plotExprs         8.877  0.099  11.517
applyCutoffs      7.812  0.101  10.312
runDR             6.493  0.161   8.998
normCytof         5.524  0.063   7.444
plotEvents        5.388  0.041   6.956
assignPrelim      4.592  0.029   5.881
prepData          4.084  0.081   5.698
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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