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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_2.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.4.0’
* 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 ‘singleCellTK’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    shiny     2.8Mb
* 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 R 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 ... NOTE
Namespaces in Imports field not imported from:
  'AnnotationDbi' 'RColorBrewer'
  All declared Imports should be used.
* 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 ... 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 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   32.604  0.538  33.176
importExampleData        27.459  2.170  31.255
plotDoubletFinderResults 27.785  0.144  27.949
runDoubletFinder         19.573  0.049  19.632
runScDblFinder           15.900  0.356  16.272
plotBatchCorrCompare     12.134  0.107  12.237
plotMarkerDiffExp        11.670  0.040  11.723
plotScdsHybridResults    11.305  0.124  11.436
plotBcdsResults          10.362  0.255  10.620
findMarkerTopTable       10.215  0.047  10.274
findMarkerDiffExp         9.982  0.090  10.079
plotDEGHeatmap            9.637  0.090   9.736
plotEmptyDropsResults     9.609  0.026   9.649
runDESeq2                 9.588  0.042   9.642
plotEmptyDropsScatter     9.586  0.017   9.613
plotDecontXResults        9.441  0.064   9.517
runEmptyDrops             9.135  0.017   9.161
runDecontX                7.865  0.026   7.896
plotCxdsResults           7.726  0.051   7.773
plotDEGViolin             7.407  0.152   7.571
runMAST                   7.226  0.042   7.272
detectCellOutlier         6.853  0.240   7.103
plotUMAP                  6.427  0.046   6.476
importGeneSetsFromMSigDB  6.102  0.331   6.442
plotDEGRegression         6.062  0.042   6.113
seuratSCTransform         4.927  0.091   5.030
enrichRSCE                0.725  0.031   6.832
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.