Build/check report for BioC 3.22 - CHECK results for singleCellTK on nebbiolo2

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"	4888
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 nebbiolo2

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: 2.20.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings singleCellTK_2.20.1.tar.gz

StartedAt: 2026-02-04 04:45:33 -0500 (Wed, 04 Feb 2026)

EndedAt: 2026-02-04 05:12:25 -0500 (Wed, 04 Feb 2026)

EllapsedTime: 1611.2 seconds

RetCode: 0

Status: OK

CheckDir: singleCellTK.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings singleCellTK_2.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.20.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
 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  7.0Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   1.6Mb
    shiny     3.0Mb
* 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 loading without being on the library search path ... 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 44.944  0.713  45.659
plotDoubletFinderResults 42.960  0.339  43.379
runDoubletFinder         37.498  0.371  37.871
plotScDblFinderResults   30.002  0.653  30.699
runSeuratSCTransform     29.826  0.297  30.124
runScDblFinder           18.087  0.441  18.472
plotBatchCorrCompare     14.288  0.075  14.548
importExampleData        10.410  0.300  11.134
plotDecontXResults        9.272  0.073   9.346
plotUMAP                  8.459  0.169   8.707
runDecontX                8.320  0.118   8.438
plotCxdsResults           8.131  0.101   8.313
plotScdsHybridResults     7.965  0.070   8.114
runUMAP                   7.702  0.157   7.939
plotBcdsResults           6.987  0.072   7.138
plotDEGViolin             6.822  0.126   6.942
plotEmptyDropsResults     6.684  0.027   6.710
plotEmptyDropsScatter     6.553  0.040   6.593
runEmptyDrops             6.244  0.003   6.247
detectCellOutlier         6.063  0.169   6.233
plotTSCANClusterDEG       5.139  0.017   5.157
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.

Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘singleCellTK’ ...
** this is package ‘singleCellTK’ version ‘2.20.1’
** 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 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.149   0.039   0.175

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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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%
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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 46 | SKIP 0 | PASS 223 ]

[ FAIL 0 | WARN 46 | SKIP 0 | PASS 223 ]
> 
> proc.time()
   user  system elapsed 
307.711   5.640 317.338

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

name	user	system	elapsed
MitoGenes	0.002	0.000	0.003
SEG	0.001	0.001	0.002
calcEffectSizes	0.191	0.002	0.193
combineSCE	0.748	0.004	0.752
computeZScore	0.237	0.009	0.246
convertSCEToSeurat	4.603	0.091	4.695
convertSeuratToSCE	0.347	0.003	0.350
dedupRowNames	0.056	0.001	0.057
detectCellOutlier	6.063	0.169	6.233
diffAbundanceFET	0.054	0.002	0.056
discreteColorPalette	0.005	0.001	0.006
distinctColors	0.002	0.000	0.002
downSampleCells	0.468	0.055	0.523
downSampleDepth	0.379	0.005	0.385
expData-ANY-character-method	0.119	0.009	0.129
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method	0.157	0.010	0.167
expData-set	0.141	0.002	0.143
expData	0.120	0.002	0.122
expDataNames-ANY-method	0.123	0.004	0.127
expDataNames	0.112	0.010	0.121
expDeleteDataTag	0.032	0.001	0.033
expSetDataTag	0.024	0.000	0.024
expTaggedData	0.022	0.002	0.024
exportSCE	0.021	0.001	0.022
exportSCEtoAnnData	0.089	0.008	0.097
exportSCEtoFlatFile	0.086	0.011	0.097
featureIndex	0.034	0.002	0.036
generateSimulatedData	0.071	0.008	0.079
getBiomarker	0.059	0.000	0.059
getDEGTopTable	0.639	0.020	0.659
getDiffAbundanceResults	0.046	0.001	0.047
getEnrichRResult	0.451	0.035	3.126
getFindMarkerTopTable	1.461	0.040	1.502
getMSigDBTable	0.004	0.000	0.003
getPathwayResultNames	0.018	0.004	0.021
getSampleSummaryStatsTable	0.191	0.000	0.190
getSoupX	0	0	0
getTSCANResults	0.961	0.008	0.970
getTopHVG	0.852	0.008	0.861
importAnnData	0.002	0.000	0.002
importBUStools	0.141	0.000	0.142
importCellRanger	0.724	0.005	0.731
importCellRangerV2Sample	0.141	0.001	0.142
importCellRangerV3Sample	0.280	0.006	0.285
importDropEst	1.361	0.066	1.428
importExampleData	10.410	0.300	11.134
importGeneSetsFromCollection	1.815	0.025	1.842
importGeneSetsFromGMT	0.064	0.000	0.064
importGeneSetsFromList	0.126	0.001	0.126
importGeneSetsFromMSigDB	44.944	0.713	45.659
importMitoGeneSet	0.051	0.007	0.058
importOptimus	0.002	0.000	0.001
importSEQC	0.139	0.024	0.163
importSTARsolo	0.150	0.024	0.174
iterateSimulations	0.197	0.021	0.218
listSampleSummaryStatsTables	0.254	0.030	0.284
mergeSCEColData	0.366	0.015	0.381
mouseBrainSubsetSCE	0.037	0.000	0.037
msigdb_table	0.001	0.001	0.001
plotBarcodeRankDropsResults	0.864	0.005	0.869
plotBarcodeRankScatter	0.833	0.003	0.835
plotBatchCorrCompare	14.288	0.075	14.548
plotBatchVariance	0.472	0.003	0.475
plotBcdsResults	6.987	0.072	7.138
plotBubble	0.834	0.002	0.837
plotClusterAbundance	1.346	0.039	1.384
plotCxdsResults	8.131	0.101	8.313
plotDEGHeatmap	2.100	0.005	2.106
plotDEGRegression	4.443	0.053	4.491
plotDEGViolin	6.822	0.126	6.942
plotDEGVolcano	0.949	0.005	0.954
plotDecontXResults	9.272	0.073	9.346
plotDimRed	0.289	0.002	0.290
plotDoubletFinderResults	42.960	0.339	43.379
plotEmptyDropsResults	6.684	0.027	6.710
plotEmptyDropsScatter	6.553	0.040	6.593
plotFindMarkerHeatmap	3.879	0.047	3.926
plotMASTThresholdGenes	1.252	0.009	1.262
plotPCA	0.351	0.002	0.354
plotPathway	0.674	0.001	0.676
plotRunPerCellQCResults	3.002	0.008	3.011
plotSCEBarAssayData	0.326	0.001	0.327
plotSCEBarColData	0.229	0.000	0.229
plotSCEBatchFeatureMean	0.379	0.002	0.381
plotSCEDensity	0.32	0.00	0.32
plotSCEDensityAssayData	0.322	0.002	0.324
plotSCEDensityColData	0.304	0.000	0.305
plotSCEDimReduceColData	0.757	0.001	0.758
plotSCEDimReduceFeatures	0.459	0.001	0.460
plotSCEHeatmap	0.440	0.003	0.443
plotSCEScatter	0.373	0.001	0.374
plotSCEViolin	0.456	0.012	0.469
plotSCEViolinAssayData	0.405	0.001	0.406
plotSCEViolinColData	0.382	0.001	0.383
plotScDblFinderResults	30.002	0.653	30.699
plotScanpyDotPlot	0.023	0.000	0.023
plotScanpyEmbedding	0.022	0.000	0.022
plotScanpyHVG	0.022	0.000	0.022
plotScanpyHeatmap	0.022	0.000	0.022
plotScanpyMarkerGenes	0.022	0.000	0.022
plotScanpyMarkerGenesDotPlot	0.022	0.000	0.022
plotScanpyMarkerGenesHeatmap	0.023	0.000	0.023
plotScanpyMarkerGenesMatrixPlot	0.023	0.000	0.023
plotScanpyMarkerGenesViolin	0.023	0.000	0.023
plotScanpyMatrixPlot	0.023	0.001	0.024
plotScanpyPCA	0.023	0.000	0.023
plotScanpyPCAGeneRanking	0.024	0.000	0.024
plotScanpyPCAVariance	0.023	0.000	0.023
plotScanpyViolin	0.022	0.001	0.022
plotScdsHybridResults	7.965	0.070	8.114
plotScrubletResults	0.024	0.000	0.024
plotSeuratElbow	0.024	0.000	0.024
plotSeuratHVG	0.021	0.001	0.022
plotSeuratJackStraw	0.020	0.002	0.022
plotSeuratReduction	0.021	0.001	0.022
plotSoupXResults	0	0	0
plotTSCANClusterDEG	5.139	0.017	5.157
plotTSCANClusterPseudo	1.445	0.002	1.447
plotTSCANDimReduceFeatures	1.297	0.003	1.300
plotTSCANPseudotimeGenes	1.635	0.007	1.643
plotTSCANPseudotimeHeatmap	1.390	0.001	1.391
plotTSCANResults	1.193	0.002	1.196
plotTSNE	0.371	0.000	0.371
plotTopHVG	0.691	0.000	0.691
plotUMAP	8.459	0.169	8.707
readSingleCellMatrix	0.006	0.000	0.005
reportCellQC	0.080	0.000	0.081
reportDropletQC	0.020	0.003	0.023
reportQCTool	0.082	0.001	0.083
retrieveSCEIndex	0.029	0.000	0.029
runBBKNN	0	0	0
runBarcodeRankDrops	0.231	0.001	0.231
runBcds	0.085	0.000	0.086
runCellQC	0.082	0.001	0.084
runClusterSummaryMetrics	0.387	0.002	0.389
runComBatSeq	0.459	0.002	0.461
runCxds	0.392	0.001	0.392
runCxdsBcdsHybrid	0.084	0.000	0.083
runDEAnalysis	0.409	0.011	0.419
runDecontX	8.320	0.118	8.438
runDimReduce	0.308	0.001	0.309
runDoubletFinder	37.498	0.371	37.871
runDropletQC	0.020	0.002	0.022
runEmptyDrops	6.244	0.003	6.247
runEnrichR	0.542	0.030	2.774
runFastMNN	1.683	0.066	1.750
runFeatureSelection	0.207	0.000	0.207
runFindMarker	1.378	0.005	1.383
runGSVA	0.822	0.011	0.833
runHarmony	0.039	0.000	0.039
runKMeans	0.170	0.003	0.172
runLimmaBC	0.076	0.000	0.075
runMNNCorrect	0.403	0.001	0.403
runModelGeneVar	0.295	0.000	0.295
runNormalization	2.508	0.012	2.520
runPerCellQC	0.317	0.000	0.317
runSCANORAMA	0	0	0
runSCMerge	0.002	0.002	0.004
runScDblFinder	18.087	0.441	18.472
runScanpyFindClusters	0.024	0.000	0.024
runScanpyFindHVG	0.022	0.000	0.022
runScanpyFindMarkers	0.021	0.001	0.022
runScanpyNormalizeData	0.105	0.000	0.105
runScanpyPCA	0.023	0.000	0.022
runScanpyScaleData	0.021	0.001	0.022
runScanpyTSNE	0.021	0.000	0.021
runScanpyUMAP	0.022	0.000	0.022
runScranSNN	0.290	0.001	0.291
runScrublet	0.022	0.001	0.023
runSeuratFindClusters	0.022	0.000	0.023
runSeuratFindHVG	0.469	0.001	0.470
runSeuratHeatmap	0.023	0.000	0.023
runSeuratICA	0.023	0.000	0.023
runSeuratJackStraw	0.022	0.000	0.023
runSeuratNormalizeData	0.022	0.000	0.022
runSeuratPCA	0.022	0.000	0.021
runSeuratSCTransform	29.826	0.297	30.124
runSeuratScaleData	0.023	0.000	0.024
runSeuratUMAP	0.023	0.000	0.023
runSingleR	0.040	0.001	0.041
runSoupX	0.001	0.000	0.000
runTSCAN	0.716	0.004	0.720
runTSCANClusterDEAnalysis	0.812	0.000	0.813
runTSCANDEG	0.754	0.001	0.756
runTSNE	0.739	0.001	0.740
runUMAP	7.702	0.157	7.939
runVAM	0.294	0.000	0.294
runZINBWaVE	0.004	0.000	0.004
sampleSummaryStats	0.156	0.001	0.157
scaterCPM	0.132	0.006	0.138
scaterPCA	0.443	0.001	0.444
scaterlogNormCounts	0.229	0.005	0.234
sce	0.021	0.000	0.021
sctkListGeneSetCollections	0.078	0.002	0.080
sctkPythonInstallConda	0.000	0.000	0.001
sctkPythonInstallVirtualEnv	0	0	0
selectSCTKConda	0.000	0.000	0.001
selectSCTKVirtualEnvironment	0	0	0
setRowNames	0.085	0.001	0.086
setSCTKDisplayRow	0.416	0.001	0.417
singleCellTK	0	0	0
subDiffEx	0.322	0.002	0.324
subsetSCECols	0.079	0.002	0.081
subsetSCERows	0.264	0.000	0.264
summarizeSCE	0.068	0.000	0.068
trimCounts	0.198	0.007	0.205