Multiple platform build/check report for BioC 3.22 - CHECK results for singleCellTK on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4873
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4654
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4600
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for singleCellTK on merida1

To the developers/maintainers of the singleCellTK package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singleCellTK.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: singleCellTK

Version: 2.20.0

Command: /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_2.20.0.tar.gz

StartedAt: 2025-11-21 11:52:45 -0500 (Fri, 21 Nov 2025)

EndedAt: 2025-11-21 12:24:13 -0500 (Fri, 21 Nov 2025)

EllapsedTime: 1887.7 seconds

RetCode: 0

Status: OK

CheckDir: singleCellTK.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘2.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 80 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... INFO
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dedupRowNames.Rd: SingleCellExperiment-class
  detectCellOutlier.Rd: colData
  diffAbundanceFET.Rd: colData
  downSampleCells.Rd: SingleCellExperiment-class
  downSampleDepth.Rd: SingleCellExperiment-class
  featureIndex.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  getBiomarker.Rd: SingleCellExperiment-class
  getDEGTopTable.Rd: SingleCellExperiment-class
  getEnrichRResult.Rd: SingleCellExperiment-class
  getFindMarkerTopTable.Rd: SingleCellExperiment-class
  getGenesetNamesFromCollection.Rd: SingleCellExperiment-class
  getPathwayResultNames.Rd: SingleCellExperiment-class
  getSampleSummaryStatsTable.Rd: SingleCellExperiment-class, assay,
    colData
  getSoupX.Rd: SingleCellExperiment-class
  getTSCANResults.Rd: SingleCellExperiment-class
  getTopHVG.Rd: SingleCellExperiment-class
  importAlevin.Rd: DelayedArray, readMM
  importAnnData.Rd: DelayedArray, readMM
  importBUStools.Rd: readMM
  importCellRanger.Rd: readMM, DelayedArray
  importCellRangerV2Sample.Rd: readMM, DelayedArray
  importCellRangerV3Sample.Rd: readMM, DelayedArray
  importDropEst.Rd: DelayedArray, readMM
  importExampleData.Rd: scRNAseq, Matrix, DelayedArray,
    ReprocessedFluidigmData, ReprocessedAllenData, NestorowaHSCData
  importFromFiles.Rd: readMM, DelayedArray, SingleCellExperiment-class
  importGeneSetsFromCollection.Rd: GeneSetCollection-class,
    SingleCellExperiment-class, GeneSetCollection, GSEABase, metadata
  importGeneSetsFromGMT.Rd: GeneSetCollection-class,
    SingleCellExperiment-class, getGmt, GSEABase, metadata
  importGeneSetsFromList.Rd: GeneSetCollection-class,
    SingleCellExperiment-class, GSEABase, metadata
  importGeneSetsFromMSigDB.Rd: SingleCellExperiment-class, msigdbr,
    GeneSetCollection-class, GSEABase, metadata
  importMitoGeneSet.Rd: SingleCellExperiment-class,
    GeneSetCollection-class, GSEABase, metadata
  importMultipleSources.Rd: DelayedArray
  importOptimus.Rd: readMM, DelayedArray
  importSEQC.Rd: readMM, DelayedArray
  importSTARsolo.Rd: readMM, DelayedArray
  iterateSimulations.Rd: SingleCellExperiment-class
  listSampleSummaryStatsTables.Rd: SingleCellExperiment-class, metadata
  plotBarcodeRankDropsResults.Rd: SingleCellExperiment-class
  plotBarcodeRankScatter.Rd: SingleCellExperiment-class
  plotBatchCorrCompare.Rd: SingleCellExperiment-class
  plotBatchVariance.Rd: SingleCellExperiment-class
  plotBcdsResults.Rd: SingleCellExperiment-class
  plotClusterAbundance.Rd: colData
  plotCxdsResults.Rd: SingleCellExperiment-class
  plotDEGHeatmap.Rd: SingleCellExperiment-class
  plotDEGRegression.Rd: SingleCellExperiment-class
  plotDEGViolin.Rd: SingleCellExperiment-class
  plotDEGVolcano.Rd: SingleCellExperiment-class
  plotDecontXResults.Rd: SingleCellExperiment-class
  plotDoubletFinderResults.Rd: SingleCellExperiment-class
  plotEmptyDropsResults.Rd: SingleCellExperiment-class
  plotEmptyDropsScatter.Rd: SingleCellExperiment-class
  plotEnrichR.Rd: SingleCellExperiment-class
  plotFindMarkerHeatmap.Rd: SingleCellExperiment-class
  plotPCA.Rd: SingleCellExperiment-class
  plotPathway.Rd: SingleCellExperiment-class
  plotRunPerCellQCResults.Rd: SingleCellExperiment-class
  plotSCEBarAssayData.Rd: SingleCellExperiment-class
  plotSCEBarColData.Rd: SingleCellExperiment-class
  plotSCEBatchFeatureMean.Rd: SingleCellExperiment-class
  plotSCEDensity.Rd: SingleCellExperiment-class
  plotSCEDensityAssayData.Rd: SingleCellExperiment-class
  plotSCEDensityColData.Rd: SingleCellExperiment-class
  plotSCEDimReduceColData.Rd: SingleCellExperiment-class
  plotSCEDimReduceFeatures.Rd: SingleCellExperiment-class
  plotSCEHeatmap.Rd: SingleCellExperiment-class
  plotSCEScatter.Rd: SingleCellExperiment-class
  plotSCEViolin.Rd: SingleCellExperiment-class
  plotSCEViolinAssayData.Rd: SingleCellExperiment-class
  plotSCEViolinColData.Rd: SingleCellExperiment-class
  plotScDblFinderResults.Rd: SingleCellExperiment-class
  plotScdsHybridResults.Rd: SingleCellExperiment-class
  plotScrubletResults.Rd: SingleCellExperiment-class
  plotSoupXResults.Rd: SingleCellExperiment-class
  plotTSCANClusterDEG.Rd: SingleCellExperiment-class
  plotTSCANClusterPseudo.Rd: SingleCellExperiment-class
  plotTSCANDimReduceFeatures.Rd: SingleCellExperiment-class
  plotTSCANPseudotimeGenes.Rd: SingleCellExperiment-class
  plotTSCANPseudotimeHeatmap.Rd: SingleCellExperiment-class
  plotTSCANResults.Rd: SingleCellExperiment-class
  plotTSNE.Rd: SingleCellExperiment-class
  plotUMAP.Rd: SingleCellExperiment-class
  readSingleCellMatrix.Rd: DelayedArray
  reportCellQC.Rd: SingleCellExperiment-class
  reportClusterAbundance.Rd: colData
  reportDiffAbundanceFET.Rd: colData
  retrieveSCEIndex.Rd: SingleCellExperiment-class
  runBBKNN.Rd: SingleCellExperiment-class
  runBarcodeRankDrops.Rd: SingleCellExperiment-class, colData
  runBcds.Rd: SingleCellExperiment-class, colData
  runCellQC.Rd: colData
  runComBatSeq.Rd: SingleCellExperiment-class
  runCxds.Rd: SingleCellExperiment-class, colData
  runCxdsBcdsHybrid.Rd: colData
  runDEAnalysis.Rd: SingleCellExperiment-class
  runDecontX.Rd: colData
  runDimReduce.Rd: SingleCellExperiment-class
  runDoubletFinder.Rd: SingleCellExperiment-class
  runDropletQC.Rd: colData
  runEmptyDrops.Rd: SingleCellExperiment-class, colData
  runEnrichR.Rd: SingleCellExperiment-class
  runFastMNN.Rd: SingleCellExperiment-class, BiocParallelParam-class
  runFeatureSelection.Rd: SingleCellExperiment-class
  runFindMarker.Rd: SingleCellExperiment-class
  runGSVA.Rd: SingleCellExperiment-class
  runHarmony.Rd: SingleCellExperiment-class
  runKMeans.Rd: SingleCellExperiment-class, colData
  runLimmaBC.Rd: SingleCellExperiment-class, assay
  runMNNCorrect.Rd: SingleCellExperiment-class, assay,
    BiocParallelParam-class
  runModelGeneVar.Rd: SingleCellExperiment-class
  runPerCellQC.Rd: SingleCellExperiment-class, BiocParallelParam,
    colData
  runSCANORAMA.Rd: SingleCellExperiment-class, assay
  runSCMerge.Rd: SingleCellExperiment-class, colData, assay,
    BiocParallelParam-class
  runScDblFinder.Rd: SingleCellExperiment-class, colData
  runScranSNN.Rd: SingleCellExperiment-class, reducedDim, assay,
    altExp, colData, igraph
  runScrublet.Rd: SingleCellExperiment-class, colData
  runSingleR.Rd: SingleCellExperiment-class
  runSoupX.Rd: SingleCellExperiment-class
  runTSCAN.Rd: SingleCellExperiment-class
  runTSCANClusterDEAnalysis.Rd: SingleCellExperiment-class
  runTSCANDEG.Rd: SingleCellExperiment-class
  runTSNE.Rd: SingleCellExperiment-class
  runUMAP.Rd: SingleCellExperiment-class, BiocParallelParam-class
  runVAM.Rd: SingleCellExperiment-class
  runZINBWaVE.Rd: SingleCellExperiment-class, colData,
    BiocParallelParam-class
  sampleSummaryStats.Rd: SingleCellExperiment-class, assay, colData
  scaterPCA.Rd: SingleCellExperiment-class, BiocParallelParam-class
  scaterlogNormCounts.Rd: logNormCounts
  sctkListGeneSetCollections.Rd: GeneSetCollection-class
  sctkPythonInstallConda.Rd: conda_install, reticulate, conda_create
  sctkPythonInstallVirtualEnv.Rd: virtualenv_install, reticulate,
    virtualenv_create
  selectSCTKConda.Rd: reticulate
  selectSCTKVirtualEnvironment.Rd: reticulate
  setRowNames.Rd: SingleCellExperiment-class
  setSCTKDisplayRow.Rd: SingleCellExperiment-class
  singleCellTK.Rd: SingleCellExperiment-class
  subsetSCECols.Rd: SingleCellExperiment-class
  subsetSCERows.Rd: SingleCellExperiment-class, altExp
  summarizeSCE.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
importGeneSetsFromMSigDB 90.178  0.758  91.688
plotDoubletFinderResults 54.455  0.266  56.454
plotScDblFinderResults   51.690  1.082  56.592
runDoubletFinder         47.750  0.182  48.545
runScDblFinder           34.196  0.506  35.025
importExampleData        21.562  2.295  25.172
plotBatchCorrCompare     19.346  0.170  19.537
plotScdsHybridResults    15.714  0.204  16.449
plotBcdsResults          14.784  0.235  15.053
plotDecontXResults       13.764  0.098  14.013
plotDEGViolin            12.973  0.166  13.207
plotDEGRegression        12.259  0.092  12.462
plotTSCANClusterDEG      12.203  0.125  13.453
plotCxdsResults          12.023  0.099  12.309
plotEmptyDropsResults    10.386  0.043  11.157
plotEmptyDropsScatter    10.220  0.052  10.903
plotFindMarkerHeatmap     9.962  0.055  10.743
runDecontX                9.659  0.062   9.855
runUMAP                   9.406  0.093   9.545
convertSCEToSeurat        9.135  0.358   9.768
runEmptyDrops             9.412  0.031   9.708
plotUMAP                  9.256  0.087   9.846
detectCellOutlier         8.591  0.161   8.908
plotRunPerCellQCResults   7.513  0.042   7.922
runSeuratSCTransform      7.151  0.124   7.329
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.

Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘singleCellTK’ ...
** this is package ‘singleCellTK’ version ‘2.20.0’
** using staged installation
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (singleCellTK)

Tests output

singleCellTK.Rcheck/tests/spelling.Rout


R version 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.352   0.113   0.436

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(singleCellTK)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: SingleCellExperiment
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

The following object is masked from 'package:abind':

    abind

The following object is masked from 'package:base':

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    apply, scale, sweep


Attaching package: 'singleCellTK'

The following object is masked from 'package:BiocGenerics':

    plotPCA

> 
> test_check("singleCellTK")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 0 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Uploading data to Enrichr... Done.
  Querying HDSigDB_Human_2021... Done.
Parsing results... Done.
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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  |======================================================================| 100%
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 390
Number of edges: 9849

Running Louvain algorithm...
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8351
Number of communities: 7
Elapsed time: 0 seconds
Using method 'umap'
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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  |======================================================================| 100%

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  |======================================================================| 100%
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 21 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
557.601   9.771 582.894

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

name	user	system	elapsed
MitoGenes	0.004	0.006	0.011
SEG	0.004	0.005	0.009
calcEffectSizes	0.451	0.025	0.478
combineSCE	1.631	0.025	1.759
computeZScore	0.404	0.019	0.449
convertSCEToSeurat	9.135	0.358	9.768
convertSeuratToSCE	0.781	0.012	0.810
dedupRowNames	0.130	0.007	0.146
detectCellOutlier	8.591	0.161	8.908
diffAbundanceFET	0.097	0.006	0.103
discreteColorPalette	0.010	0.001	0.010
distinctColors	0.003	0.001	0.004
downSampleCells	1.062	0.128	1.198
downSampleDepth	0.889	0.071	0.967
expData-ANY-character-method	0.281	0.010	0.296
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method	0.386	0.016	0.418
expData-set	0.350	0.007	0.359
expData	0.288	0.012	0.302
expDataNames-ANY-method	0.276	0.014	0.295
expDataNames	0.279	0.030	0.328
expDeleteDataTag	0.057	0.007	0.068
expSetDataTag	0.045	0.005	0.054
expTaggedData	0.045	0.006	0.054
exportSCE	0.039	0.008	0.050
exportSCEtoAnnData	0.120	0.007	0.132
exportSCEtoFlatFile	0.122	0.008	0.133
featureIndex	0.069	0.009	0.082
generateSimulatedData	0.094	0.010	0.112
getBiomarker	0.113	0.017	0.133
getDEGTopTable	1.596	0.129	1.743
getDiffAbundanceResults	0.087	0.004	0.092
getEnrichRResult	0.700	0.058	2.745
getFindMarkerTopTable	3.379	0.091	3.520
getMSigDBTable	0.008	0.007	0.014
getPathwayResultNames	0.040	0.007	0.048
getSampleSummaryStatsTable	0.405	0.007	0.415
getSoupX	0.000	0.000	0.001
getTSCANResults	2.269	0.063	2.347
getTopHVG	1.869	0.027	1.914
importAnnData	0.002	0.001	0.004
importBUStools	0.345	0.007	0.353
importCellRanger	1.663	0.048	1.726
importCellRangerV2Sample	0.350	0.004	0.357
importCellRangerV3Sample	0.619	0.022	0.650
importDropEst	0.469	0.008	0.478
importExampleData	21.562	2.295	25.172
importGeneSetsFromCollection	2.839	0.157	3.017
importGeneSetsFromGMT	0.129	0.008	0.140
importGeneSetsFromList	0.302	0.009	0.316
importGeneSetsFromMSigDB	90.178	0.758	91.688
importMitoGeneSet	0.118	0.018	0.136
importOptimus	0.003	0.001	0.004
importSEQC	0.335	0.023	0.361
importSTARsolo	0.360	0.029	0.391
iterateSimulations	0.369	0.032	0.402
listSampleSummaryStatsTables	0.523	0.056	0.580
mergeSCEColData	0.839	0.050	0.893
mouseBrainSubsetSCE	0.068	0.007	0.075
msigdb_table	0.002	0.005	0.007
plotBarcodeRankDropsResults	1.978	0.044	2.029
plotBarcodeRankScatter	2.033	0.019	2.056
plotBatchCorrCompare	19.346	0.170	19.537
plotBatchVariance	1.084	0.024	1.111
plotBcdsResults	14.784	0.235	15.053
plotBubble	1.854	0.016	1.875
plotClusterAbundance	3.499	0.032	3.546
plotCxdsResults	12.023	0.099	12.309
plotDEGHeatmap	4.873	0.038	4.919
plotDEGRegression	12.259	0.092	12.462
plotDEGViolin	12.973	0.166	13.207
plotDEGVolcano	1.991	0.018	2.013
plotDecontXResults	13.764	0.098	14.013
plotDimRed	0.665	0.010	0.686
plotDoubletFinderResults	54.455	0.266	56.454
plotEmptyDropsResults	10.386	0.043	11.157
plotEmptyDropsScatter	10.220	0.052	10.903
plotFindMarkerHeatmap	9.962	0.055	10.743
plotMASTThresholdGenes	3.240	0.048	3.705
plotPCA	0.890	0.015	0.993
plotPathway	1.649	0.016	1.757
plotRunPerCellQCResults	7.513	0.042	7.922
plotSCEBarAssayData	0.727	0.009	0.742
plotSCEBarColData	0.550	0.009	0.563
plotSCEBatchFeatureMean	0.943	0.008	0.953
plotSCEDensity	0.755	0.009	0.768
plotSCEDensityAssayData	0.731	0.010	0.754
plotSCEDensityColData	0.754	0.011	0.815
plotSCEDimReduceColData	1.927	0.019	2.055
plotSCEDimReduceFeatures	0.888	0.011	0.936
plotSCEHeatmap	0.991	0.010	1.047
plotSCEScatter	0.884	0.013	0.986
plotSCEViolin	0.958	0.012	1.019
plotSCEViolinAssayData	0.918	0.012	0.949
plotSCEViolinColData	0.884	0.013	0.985
plotScDblFinderResults	51.690	1.082	56.592
plotScanpyDotPlot	0.048	0.005	0.054
plotScanpyEmbedding	0.041	0.004	0.047
plotScanpyHVG	0.042	0.005	0.050
plotScanpyHeatmap	0.046	0.004	0.050
plotScanpyMarkerGenes	0.039	0.005	0.044
plotScanpyMarkerGenesDotPlot	0.042	0.005	0.048
plotScanpyMarkerGenesHeatmap	0.043	0.006	0.049
plotScanpyMarkerGenesMatrixPlot	0.042	0.008	0.050
plotScanpyMarkerGenesViolin	0.041	0.006	0.048
plotScanpyMatrixPlot	0.040	0.005	0.045
plotScanpyPCA	0.040	0.004	0.044
plotScanpyPCAGeneRanking	0.045	0.003	0.049
plotScanpyPCAVariance	0.041	0.005	0.046
plotScanpyViolin	0.039	0.004	0.044
plotScdsHybridResults	15.714	0.204	16.449
plotScrubletResults	0.043	0.004	0.048
plotSeuratElbow	0.040	0.005	0.049
plotSeuratHVG	0.039	0.003	0.046
plotSeuratJackStraw	0.039	0.004	0.046
plotSeuratReduction	0.039	0.004	0.049
plotSoupXResults	0.000	0.000	0.001
plotTSCANClusterDEG	12.203	0.125	13.453
plotTSCANClusterPseudo	3.317	0.050	3.937
plotTSCANDimReduceFeatures	3.408	0.033	3.469
plotTSCANPseudotimeGenes	4.246	0.037	4.494
plotTSCANPseudotimeHeatmap	3.147	0.042	3.608
plotTSCANResults	3.074	0.034	3.213
plotTSNE	0.918	0.016	0.958
plotTopHVG	1.415	0.024	1.470
plotUMAP	9.256	0.087	9.846
readSingleCellMatrix	0.010	0.001	0.022
reportCellQC	0.180	0.007	0.207
reportDropletQC	0.040	0.005	0.046
reportQCTool	0.177	0.008	0.217
retrieveSCEIndex	0.054	0.005	0.067
runBBKNN	0.000	0.001	0.001
runBarcodeRankDrops	0.481	0.008	0.561
runBcds	3.415	0.051	3.889
runCellQC	0.178	0.006	0.213
runClusterSummaryMetrics	0.900	0.016	1.032
runComBatSeq	0.998	0.019	1.145
runCxds	0.689	0.017	0.747
runCxdsBcdsHybrid	3.460	0.108	3.734
runDEAnalysis	0.930	0.068	1.040
runDecontX	9.659	0.062	9.855
runDimReduce	0.643	0.008	0.655
runDoubletFinder	47.750	0.182	48.545
runDropletQC	0.039	0.004	0.043
runEmptyDrops	9.412	0.031	9.708
runEnrichR	0.658	0.051	3.869
runFastMNN	4.031	0.074	4.149
runFeatureSelection	0.457	0.007	0.466
runFindMarker	3.294	0.047	3.407
runGSVA	1.551	0.051	1.613
runHarmony	0.094	0.002	0.097
runKMeans	0.510	0.025	0.537
runLimmaBC	0.187	0.002	0.190
runMNNCorrect	0.892	0.006	0.903
runModelGeneVar	0.693	0.009	0.707
runNormalization	3.573	0.061	3.650
runPerCellQC	0.761	0.014	0.829
runSCANORAMA	0	0	0
runSCMerge	0.007	0.002	0.009
runScDblFinder	34.196	0.506	35.025
runScanpyFindClusters	0.041	0.004	0.044
runScanpyFindHVG	0.040	0.005	0.046
runScanpyFindMarkers	0.041	0.010	0.051
runScanpyNormalizeData	0.222	0.005	0.228
runScanpyPCA	0.040	0.007	0.047
runScanpyScaleData	0.040	0.006	0.047
runScanpyTSNE	0.038	0.004	0.042
runScanpyUMAP	0.041	0.004	0.044
runScranSNN	0.646	0.020	0.671
runScrublet	0.041	0.003	0.044
runSeuratFindClusters	0.040	0.007	0.047
runSeuratFindHVG	1.071	0.016	1.090
runSeuratHeatmap	0.043	0.005	0.048
runSeuratICA	0.053	0.005	0.058
runSeuratJackStraw	0.040	0.004	0.044
runSeuratNormalizeData	0.040	0.004	0.043
runSeuratPCA	0.040	0.003	0.044
runSeuratSCTransform	7.151	0.124	7.329
runSeuratScaleData	0.041	0.005	0.045
runSeuratUMAP	0.041	0.007	0.049
runSingleR	0.084	0.004	0.089
runSoupX	0	0	0
runTSCAN	1.531	0.019	1.595
runTSCANClusterDEAnalysis	1.726	0.024	1.770
runTSCANDEG	1.671	0.036	1.752
runTSNE	1.295	0.018	1.316
runUMAP	9.406	0.093	9.545
runVAM	0.693	0.010	0.707
runZINBWaVE	0.006	0.002	0.008
sampleSummaryStats	0.354	0.008	0.363
scaterCPM	0.213	0.008	0.224
scaterPCA	1.042	0.013	1.075
scaterlogNormCounts	0.426	0.008	0.437
sce	0.038	0.008	0.045
sctkListGeneSetCollections	0.178	0.009	0.187
sctkPythonInstallConda	0.000	0.000	0.001
sctkPythonInstallVirtualEnv	0.001	0.001	0.001
selectSCTKConda	0.000	0.001	0.001
selectSCTKVirtualEnvironment	0.000	0.001	0.001
setRowNames	0.192	0.009	0.202
setSCTKDisplayRow	1.005	0.025	1.035
singleCellTK	0.001	0.000	0.001
subDiffEx	0.672	0.038	0.714
subsetSCECols	0.185	0.009	0.195
subsetSCERows	0.586	0.032	0.622
summarizeSCE	0.136	0.008	0.145
trimCounts	0.343	0.016	0.363