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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_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CATALYST.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 ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.27.0’
* 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      29.704  0.819  34.003
plotMultiHeatmap 29.826  0.631  33.905
plotDiffHeatmap  26.577  0.713  31.215
sce2fcs          23.792  0.818  27.560
plotDR           21.719  0.603  25.168
plotExprHeatmap  21.195  0.676  25.253
pbMDS            15.696  0.749  18.713
plotAbundances   15.393  0.693  17.958
clrDR            14.301  0.675  16.872
plotClusterExprs 14.216  0.501  16.627
plotCodes        14.021  0.557  15.883
mergeClusters    13.885  0.574  16.228
plotFreqHeatmap  13.610  0.777  17.513
SCE-accessors    12.388  0.974  14.980
plotMahal        12.566  0.161  14.310
cluster          11.850  0.603  15.072
filterSCE        11.434  0.662  12.724
compCytof        11.513  0.287  13.172
extractClusters  10.404  0.583  12.170
plotScatter      10.005  0.201  11.458
plotSpillmat      9.727  0.204  11.381
estCutoffs        9.741  0.174  11.117
computeSpillmat   9.522  0.227  10.940
plotYields        9.476  0.150  10.901
adaptSpillmat     8.935  0.283  10.305
plotExprs         8.807  0.187  10.343
applyCutoffs      7.965  0.163   8.927
runDR             6.583  0.100   7.422
normCytof         5.756  0.140   7.384
plotEvents        5.497  0.061   6.475
assignPrelim      4.754  0.041   5.178
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/CATALYST.Rcheck/00check.log’
for details.