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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/singleCellTK.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 ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.16.1’
* 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 ‘singleCellTK’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   1.5Mb
    shiny     2.9Mb
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'importGeneSetsFromMSigDB.Rd':
  ‘[msigdbr]{msigdbr_show_species}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotScDblFinderResults   56.972  0.969  61.085
plotDoubletFinderResults 42.205  0.264  42.869
runDoubletFinder         37.227  0.194  37.840
runScDblFinder           34.933  0.457  35.897
importExampleData        20.837  2.094  30.721
plotBatchCorrCompare     13.728  0.131  14.071
plotScdsHybridResults    12.320  0.114  13.026
plotBcdsResults          11.106  0.297  12.368
plotDecontXResults       10.189  0.125  10.496
plotEmptyDropsResults     9.925  0.056  10.023
plotDEGViolin             9.664  0.165   9.898
plotFindMarkerHeatmap     9.683  0.069   9.949
plotEmptyDropsScatter     9.720  0.026   9.778
runEmptyDrops             9.388  0.027   9.522
convertSCEToSeurat        8.665  0.296   9.065
plotTSCANClusterDEG       8.511  0.084   8.973
runSeuratSCTransform      8.179  0.246   8.583
plotCxdsResults           8.132  0.126   8.766
plotDEGRegression         7.934  0.107   8.171
runDecontX                7.557  0.059   7.971
runUMAP                   7.446  0.079   7.642
detectCellOutlier         7.299  0.170   7.521
plotUMAP                  6.963  0.057   7.303
plotDEGHeatmap            5.228  0.130   5.633
getEnrichRResult          0.773  0.117   6.778
runEnrichR                0.692  0.048   8.883
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.