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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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.28.0’
* 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
plotMultiHeatmap 33.468  0.861  39.978
plotPbExprs      31.390  0.653  37.418
plotDiffHeatmap  29.449  0.966  35.725
sce2fcs          25.110  0.839  30.460
plotExprHeatmap  24.181  0.896  29.143
plotDR           22.684  0.698  26.990
plotClusterExprs 15.144  0.502  17.617
mergeClusters    14.704  0.569  20.234
clrDR            14.493  0.563  17.189
plotAbundances   14.537  0.468  16.903
plotMahal        14.488  0.214  17.500
plotCodes        13.994  0.546  16.794
plotFreqHeatmap  13.366  0.593  17.114
pbMDS            13.425  0.507  15.640
SCE-accessors    12.856  0.905  15.675
compCytof        13.133  0.462  15.322
plotYields       11.715  0.233  13.935
filterSCE        11.451  0.442  13.782
estCutoffs       11.024  0.204  12.703
plotScatter      10.730  0.233  12.755
cluster          10.354  0.391  12.118
plotSpillmat     10.539  0.166  12.116
extractClusters   9.935  0.543  11.792
adaptSpillmat     9.561  0.261  11.179
computeSpillmat   9.156  0.147  10.564
plotExprs         8.706  0.130  10.359
applyCutoffs      8.642  0.149   9.973
runDR             6.985  0.096   8.260
normCytof         6.004  0.082   6.832
plotEvents        5.774  0.077   6.914
assignPrelim      5.047  0.046   5.984
prepData          4.352  0.063   5.196
* 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.