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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_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CATALYST.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.29.0’
* 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 32.260  0.865  39.492
plotPbExprs      31.039  0.815  37.115
plotDiffHeatmap  28.401  1.013  34.151
sce2fcs          25.475  1.022  34.254
plotDR           23.036  0.860  27.765
plotExprHeatmap  22.203  0.568  25.690
plotClusterExprs 15.959  0.493  19.640
mergeClusters    14.532  0.595  21.958
pbMDS            13.983  0.760  17.050
plotMahal        13.888  0.173  16.405
clrDR            13.346  0.618  16.800
plotAbundances   13.350  0.566  16.426
SCE-accessors    12.579  1.068  15.214
plotFreqHeatmap  12.836  0.719  15.532
plotCodes        12.718  0.514  15.462
compCytof        12.013  0.329  14.120
estCutoffs       11.608  0.224  13.724
cluster          11.024  0.468  13.332
filterSCE        11.015  0.457  13.450
plotScatter      10.488  0.194  13.510
plotYields       10.444  0.173  13.025
plotSpillmat     10.206  0.271  13.944
extractClusters   9.571  0.576  11.998
plotExprs         9.359  0.223  10.683
adaptSpillmat     9.181  0.335   9.992
computeSpillmat   9.029  0.196  10.619
applyCutoffs      8.271  0.206   8.730
runDR             6.717  0.135   8.947
normCytof         5.922  0.089   7.097
plotEvents        5.645  0.063   6.292
assignPrelim      5.001  0.084   5.383
prepData          4.252  0.066   5.571
* 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.