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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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CATALYST.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.28.0’
* 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 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      32.700  0.866  37.138
plotMultiHeatmap 32.302  0.714  36.899
plotDiffHeatmap  29.686  1.017  32.681
sce2fcs          24.857  0.926  28.801
plotExprHeatmap  22.766  0.783  25.432
plotDR           22.435  0.715  25.137
plotClusterExprs 16.121  0.624  17.981
pbMDS            14.957  0.714  16.965
plotAbundances   14.460  0.581  15.972
plotFreqHeatmap  14.180  0.663  16.024
SCE-accessors    13.704  0.988  15.905
mergeClusters    13.898  0.525  16.762
plotCodes        13.757  0.638  15.685
plotMahal        14.050  0.211  15.219
clrDR            13.537  0.551  15.403
filterSCE        12.241  0.520  14.036
compCytof        12.117  0.274  13.347
estCutoffs       11.815  0.179  12.954
cluster          11.248  0.520  12.833
extractClusters  10.529  0.638  12.308
plotScatter      10.582  0.229  12.053
plotYields       10.587  0.184  12.041
plotSpillmat     10.270  0.181  11.688
adaptSpillmat     9.407  0.292  10.616
computeSpillmat   9.126  0.203   9.875
plotExprs         8.477  0.127   9.271
applyCutoffs      8.441  0.153   9.269
runDR             6.957  0.114   7.870
normCytof         5.974  0.096   6.668
plotEvents        5.679  0.057   5.994
assignPrelim      4.971  0.038   5.460
* 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.