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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      30.473  1.438  33.028
plotMultiHeatmap 30.455  1.352  32.669
plotDiffHeatmap  28.102  1.521  30.095
sce2fcs          22.479  1.603  24.386
plotDR           21.324  1.430  23.346
plotExprHeatmap  21.232  1.034  22.458
plotClusterExprs 15.885  1.148  17.269
mergeClusters    15.318  1.268  16.789
plotAbundances   14.334  1.248  15.808
pbMDS            13.977  1.368  15.909
plotFreqHeatmap  13.505  1.682  15.586
clrDR            13.968  0.904  15.080
plotCodes        13.437  1.253  15.000
extractClusters  12.298  1.432  13.873
SCE-accessors    12.467  1.110  13.787
plotMahal        13.359  0.159  13.625
compCytof        12.542  0.560  13.527
filterSCE        10.365  1.107  11.620
plotYields       11.032  0.267  11.438
cluster           9.996  0.825  10.993
estCutoffs        9.723  0.202  10.033
plotScatter       9.677  0.169   9.989
plotSpillmat      9.544  0.293  10.045
adaptSpillmat     8.973  0.197   9.320
computeSpillmat   8.559  0.201   8.967
plotExprs         8.462  0.115   8.649
applyCutoffs      7.897  0.153   8.347
runDR             6.581  0.091   6.744
plotEvents        5.360  0.047   5.438
normCytof         5.204  0.093   5.346
* 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.