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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_1.30.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CATALYST.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.30.2’
* 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) plotDiffHeatmap.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotDiffHeatmap.Rd:88: 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 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      30.405  1.436  33.519
plotMultiHeatmap 30.512  1.276  32.258
plotDiffHeatmap  28.506  1.499  30.614
sce2fcs          23.065  1.551  25.076
plotDR           21.795  2.240  24.558
plotExprHeatmap  21.464  1.224  23.120
plotClusterExprs 15.575  1.236  17.214
plotFreqHeatmap  14.371  1.929  16.458
pbMDS            13.757  1.754  15.671
clrDR            13.980  1.075  15.238
plotAbundances   13.150  1.234  14.658
mergeClusters    13.066  0.943  14.446
plotMahal        13.540  0.144  13.772
SCE-accessors    12.434  1.203  14.018
plotCodes        12.444  0.857  13.555
compCytof        12.484  0.506  13.180
extractClusters  10.658  1.270  12.044
cluster          10.688  0.975  11.890
filterSCE        10.117  1.138  11.370
plotYields       10.192  0.191  10.525
plotSpillmat      9.868  0.240  10.381
estCutoffs        9.722  0.175   9.967
plotScatter       9.625  0.179   9.890
adaptSpillmat     8.983  0.252   9.299
computeSpillmat   8.656  0.227   9.268
plotExprs         8.336  0.108   8.511
applyCutoffs      8.044  0.161   8.323
runDR             6.743  0.185   7.001
normCytof         5.359  0.159   5.561
plotEvents        5.426  0.056   5.528
* 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-3.20-bioc/meat/CATALYST.Rcheck/00check.log’
for details.