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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 4.4.2 (2024-10-31)
* 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      30.574  1.384  31.623
plotMultiHeatmap 30.903  0.993  33.088
plotDiffHeatmap  27.553  1.190  30.602
sce2fcs          23.203  1.058  25.458
plotExprHeatmap  21.912  0.863  24.011
plotDR           21.340  0.792  23.296
plotClusterExprs 16.661  0.978  18.614
pbMDS            15.175  0.755  16.691
mergeClusters    14.424  0.598  15.710
plotAbundances   13.495  0.961  15.042
plotFreqHeatmap  13.644  0.753  15.055
plotCodes        13.529  0.754  14.921
plotMahal        13.597  0.129  14.015
clrDR            13.079  0.588  14.511
SCE-accessors    12.371  0.963  13.879
compCytof        11.628  0.297  12.594
filterSCE        11.266  0.645  12.538
cluster          10.724  0.569  11.948
extractClusters  10.496  0.692  11.746
plotYields       10.198  0.163  10.555
plotSpillmat      9.812  0.243  10.350
estCutoffs        9.757  0.215  10.934
plotScatter       9.734  0.207  10.350
computeSpillmat   9.462  0.231  10.463
adaptSpillmat     9.052  0.213   9.673
plotExprs         8.308  0.135   8.816
applyCutoffs      7.982  0.150   8.385
runDR             6.566  0.142   6.982
plotEvents        5.385  0.049   5.777
normCytof         5.278  0.074   5.596
assignPrelim      4.702  0.030   5.084
* 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.