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### Running command:
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###   set _R_CHECK_FORCE_SUGGESTS_=0&& F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:singleCellTK.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings singleCellTK_2.14.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'singleCellTK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'singleCellTK' version '2.14.0'
* 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 whether package 'singleCellTK' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    shiny     2.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
checkRd: (-1) dedupRowNames.Rd:10: Lost braces
    10 | \item{x}{A matrix like or /linkS4class{SingleCellExperiment} object, on which
       |                                       ^
checkRd: (-1) dedupRowNames.Rd:14: Lost braces
    14 | /linkS4class{SingleCellExperiment} object. When set to \code{TRUE}, will
       |             ^
checkRd: (-1) dedupRowNames.Rd:22: Lost braces
    22 | By default, a matrix or /linkS4class{SingleCellExperiment} object
       |                                     ^
checkRd: (-1) dedupRowNames.Rd:24: Lost braces
    24 | When \code{x} is a /linkS4class{SingleCellExperiment} and \code{as.rowData}
       |                                ^
checkRd: (-1) plotBubble.Rd:42: Lost braces
    42 | \item{scale}{Option to scale the data. Default: /code{FALSE}. Selected assay will not be scaled.}
       |                                                      ^
checkRd: (-1) runClusterSummaryMetrics.Rd:27: Lost braces
    27 | \item{scale}{Option to scale the data. Default: /code{FALSE}. Selected assay will not be scaled.}
       |                                                      ^
checkRd: (-1) runEmptyDrops.Rd:66: Lost braces
    66 | provided \\linkS4class{SingleCellExperiment} object.
       |                       ^
checkRd: (-1) runSCMerge.Rd:44: Lost braces
    44 | construct pseudo-replicates. The length of code{kmeansK} needs to be the same
       |                                                ^
* 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 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
importExampleData        19.40  29.49   50.17
plotScDblFinderResults   34.14  12.25   46.66
plotDoubletFinderResults 36.11   0.28   36.55
runDoubletFinder         33.01   0.25   33.31
runScDblFinder           21.53   0.69   22.22
plotBatchCorrCompare     12.00   0.18   12.14
plotEmptyDropsResults    11.52   0.07   11.59
plotEmptyDropsScatter    11.09   0.09   11.21
runEmptyDrops            10.95   0.06   11.01
plotScdsHybridResults    10.23   0.37   10.04
convertSCEToSeurat        4.81   5.57   12.11
plotBcdsResults           8.92   0.32    8.89
plotDecontXResults        7.92   0.22    8.17
detectCellOutlier         7.08   0.99    8.66
runUMAP                   7.51   0.13    7.64
runDecontX                7.12   0.16    7.28
plotUMAP                  7.19   0.08    7.27
plotCxdsResults           6.95   0.19    7.14
plotTSCANClusterDEG       6.36   0.54    6.91
runSeuratSCTransform      6.56   0.34    7.07
plotFindMarkerHeatmap     5.19   0.19    5.37
getFindMarkerTopTable     4.19   0.92    5.12
getEnrichRResult          0.31   0.37    5.14
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/singleCellTK.Rcheck/00check.log'
for details.