Build/check report for BioC 3.23 - CHECK results for singleCellTK on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4818
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 nebbiolo1

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: 2.21.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings singleCellTK_2.21.0.tar.gz

StartedAt: 2025-11-06 03:57:46 -0500 (Thu, 06 Nov 2025)

EndedAt: 2025-11-06 04:14:54 -0500 (Thu, 06 Nov 2025)

EllapsedTime: 1028.1 seconds

RetCode: 0

Status: OK

CheckDir: singleCellTK.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings singleCellTK_2.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/singleCellTK.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘2.21.0’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    shiny   2.3Mb
* 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 46.494  1.612  48.110
plotDoubletFinderResults 39.520  0.454  39.974
runDoubletFinder         35.685  0.257  35.943
plotScDblFinderResults   30.161  0.746  30.601
runSeuratSCTransform     28.509  1.065  29.578
runScDblFinder           20.603  1.580  21.848
plotBatchCorrCompare     13.360  0.325  13.685
importExampleData        11.384  1.400  13.147
plotScdsHybridResults    11.786  0.101  11.060
plotBcdsResults           8.835  0.157   8.217
plotDecontXResults        8.171  0.204   8.375
runDecontX                7.441  0.110   7.552
plotCxdsResults           7.337  0.182   7.520
plotUMAP                  7.307  0.149   7.459
runUMAP                   7.243  0.181   7.423
plotEmptyDropsResults     6.683  0.058   6.741
plotEmptyDropsScatter     6.567  0.045   6.613
runEmptyDrops             6.249  0.014   6.263
detectCellOutlier         5.483  0.174   5.657
plotDEGViolin             5.254  0.079   5.327
plotTSCANClusterDEG       5.152  0.013   5.165
* 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-3.23-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.

Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘singleCellTK’ ...
** this is package ‘singleCellTK’ version ‘2.21.0’
** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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 
  0.144   0.037   0.167

singleCellTK.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

  |                                                                            
  |                                                                      |   0%
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  |======================================================================| 100%
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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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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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 
314.647  10.240 328.838

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

name	user	system	elapsed
MitoGenes	0.002	0.000	0.002
SEG	0.002	0.001	0.003
calcEffectSizes	0.158	0.010	0.168
combineSCE	0.714	0.036	0.751
computeZScore	0.227	0.013	0.240
convertSCEToSeurat	4.230	0.130	4.361
convertSeuratToSCE	0.303	0.012	0.315
dedupRowNames	0.056	0.003	0.059
detectCellOutlier	5.483	0.174	5.657
diffAbundanceFET	0.052	0.000	0.053
discreteColorPalette	0.005	0.000	0.006
distinctColors	0.002	0.000	0.002
downSampleCells	0.484	0.048	0.532
downSampleDepth	0.388	0.005	0.393
expData-ANY-character-method	0.114	0.002	0.116
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method	0.156	0.000	0.157
expData-set	0.140	0.003	0.143
expData	0.121	0.001	0.122
expDataNames-ANY-method	0.119	0.001	0.121
expDataNames	0.127	0.001	0.127
expDeleteDataTag	0.033	0.000	0.034
expSetDataTag	0.024	0.000	0.023
expTaggedData	0.024	0.001	0.024
exportSCE	0.020	0.001	0.021
exportSCEtoAnnData	0.090	0.008	0.097
exportSCEtoFlatFile	0.092	0.005	0.098
featureIndex	0.036	0.013	0.048
generateSimulatedData	0.049	0.005	0.054
getBiomarker	0.058	0.003	0.061
getDEGTopTable	0.667	0.105	0.773
getDiffAbundanceResults	0.047	0.001	0.047
getEnrichRResult	0.542	0.029	2.855
getFindMarkerTopTable	1.464	0.082	1.547
getMSigDBTable	0.004	0.000	0.004
getPathwayResultNames	0.021	0.001	0.022
getSampleSummaryStatsTable	0.178	0.013	0.190
getSoupX	0	0	0
getTSCANResults	1.024	0.102	1.126
getTopHVG	0.767	0.028	0.795
importAnnData	0.001	0.000	0.001
importBUStools	0.176	0.002	0.179
importCellRanger	0.669	0.020	0.690
importCellRangerV2Sample	0.150	0.005	0.155
importCellRangerV3Sample	0.362	0.012	0.376
importDropEst	0.189	0.006	0.196
importExampleData	11.384	1.400	13.147
importGeneSetsFromCollection	0.651	0.036	0.687
importGeneSetsFromGMT	0.060	0.001	0.060
importGeneSetsFromList	0.117	0.001	0.118
importGeneSetsFromMSigDB	46.494	1.612	48.110
importMitoGeneSet	0.051	0.004	0.056
importOptimus	0.002	0.000	0.001
importSEQC	0.146	0.010	0.157
importSTARsolo	0.142	0.023	0.165
iterateSimulations	0.176	0.024	0.201
listSampleSummaryStatsTables	0.239	0.033	0.272
mergeSCEColData	0.376	0.035	0.410
mouseBrainSubsetSCE	0.035	0.001	0.036
msigdb_table	0.000	0.001	0.002
plotBarcodeRankDropsResults	0.857	0.007	0.863
plotBarcodeRankScatter	0.807	0.000	0.807
plotBatchCorrCompare	13.360	0.325	13.685
plotBatchVariance	0.468	0.007	0.474
plotBcdsResults	8.835	0.157	8.217
plotBubble	0.744	0.016	0.760
plotClusterAbundance	1.300	0.031	1.331
plotCxdsResults	7.337	0.182	7.520
plotDEGHeatmap	2.034	0.062	2.096
plotDEGRegression	4.449	0.009	4.453
plotDEGViolin	5.254	0.079	5.327
plotDEGVolcano	0.920	0.014	0.934
plotDecontXResults	8.171	0.204	8.375
plotDimRed	0.275	0.002	0.277
plotDoubletFinderResults	39.520	0.454	39.974
plotEmptyDropsResults	6.683	0.058	6.741
plotEmptyDropsScatter	6.567	0.045	6.613
plotFindMarkerHeatmap	3.775	0.064	3.840
plotMASTThresholdGenes	1.228	0.010	1.237
plotPCA	0.348	0.003	0.352
plotPathway	0.670	0.004	0.675
plotRunPerCellQCResults	2.888	0.007	2.896
plotSCEBarAssayData	0.266	0.000	0.265
plotSCEBarColData	0.254	0.002	0.256
plotSCEBatchFeatureMean	0.363	0.001	0.364
plotSCEDensity	0.291	0.001	0.292
plotSCEDensityAssayData	0.261	0.002	0.263
plotSCEDensityColData	0.328	0.001	0.329
plotSCEDimReduceColData	0.720	0.004	0.725
plotSCEDimReduceFeatures	0.405	0.001	0.406
plotSCEHeatmap	0.404	0.006	0.411
plotSCEScatter	0.352	0.002	0.354
plotSCEViolin	0.354	0.003	0.358
plotSCEViolinAssayData	0.415	0.001	0.415
plotSCEViolinColData	0.347	0.001	0.348
plotScDblFinderResults	30.161	0.746	30.601
plotScanpyDotPlot	0.022	0.000	0.022
plotScanpyEmbedding	0.020	0.001	0.022
plotScanpyHVG	0.020	0.002	0.022
plotScanpyHeatmap	0.021	0.000	0.021
plotScanpyMarkerGenes	0.021	0.000	0.022
plotScanpyMarkerGenesDotPlot	0.021	0.001	0.023
plotScanpyMarkerGenesHeatmap	0.023	0.000	0.022
plotScanpyMarkerGenesMatrixPlot	0.020	0.002	0.022
plotScanpyMarkerGenesViolin	0.019	0.003	0.021
plotScanpyMatrixPlot	0.021	0.000	0.021
plotScanpyPCA	0.021	0.000	0.021
plotScanpyPCAGeneRanking	0.022	0.000	0.021
plotScanpyPCAVariance	0.021	0.000	0.021
plotScanpyViolin	0.021	0.001	0.022
plotScdsHybridResults	11.786	0.101	11.060
plotScrubletResults	0.022	0.000	0.023
plotSeuratElbow	0.020	0.002	0.022
plotSeuratHVG	0.021	0.001	0.022
plotSeuratJackStraw	0.024	0.000	0.024
plotSeuratReduction	0.023	0.000	0.023
plotSoupXResults	0.001	0.000	0.000
plotTSCANClusterDEG	5.152	0.013	5.165
plotTSCANClusterPseudo	1.385	0.007	1.392
plotTSCANDimReduceFeatures	1.411	0.005	1.416
plotTSCANPseudotimeGenes	1.672	0.009	1.680
plotTSCANPseudotimeHeatmap	1.303	0.006	1.309
plotTSCANResults	1.228	0.003	1.230
plotTSNE	0.362	0.005	0.368
plotTopHVG	0.625	0.002	0.626
plotUMAP	7.307	0.149	7.459
readSingleCellMatrix	0.005	0.000	0.005
reportCellQC	0.072	0.004	0.076
reportDropletQC	0.022	0.000	0.022
reportQCTool	0.074	0.002	0.077
retrieveSCEIndex	0.028	0.000	0.028
runBBKNN	0	0	0
runBarcodeRankDrops	0.218	0.002	0.219
runBcds	1.935	0.019	1.158
runCellQC	0.078	0.001	0.079
runClusterSummaryMetrics	0.352	0.003	0.355
runComBatSeq	0.415	0.003	0.419
runCxds	0.304	0.000	0.305
runCxdsBcdsHybrid	2.050	0.076	1.280
runDEAnalysis	0.423	0.008	0.431
runDecontX	7.441	0.110	7.552
runDimReduce	0.267	0.001	0.268
runDoubletFinder	35.685	0.257	35.943
runDropletQC	0.022	0.001	0.023
runEmptyDrops	6.249	0.014	6.263
runEnrichR	0.424	0.063	2.639
runFastMNN	1.757	0.148	1.905
runFeatureSelection	0.218	0.019	0.237
runFindMarker	1.468	0.105	1.573
runGSVA	0.709	0.084	0.793
runHarmony	0.040	0.003	0.043
runKMeans	0.252	0.069	0.321
runLimmaBC	0.083	0.002	0.085
runMNNCorrect	0.410	0.062	0.471
runModelGeneVar	0.296	0.035	0.331
runNormalization	2.676	0.636	3.311
runPerCellQC	0.325	0.003	0.329
runSCANORAMA	0.000	0.000	0.001
runSCMerge	0.004	0.000	0.004
runScDblFinder	20.603	1.580	21.848
runScanpyFindClusters	0.020	0.002	0.023
runScanpyFindHVG	0.021	0.001	0.022
runScanpyFindMarkers	0.020	0.001	0.022
runScanpyNormalizeData	0.091	0.004	0.095
runScanpyPCA	0.022	0.000	0.022
runScanpyScaleData	0.020	0.002	0.021
runScanpyTSNE	0.022	0.000	0.022
runScanpyUMAP	0.021	0.001	0.022
runScranSNN	0.278	0.001	0.278
runScrublet	0.023	0.000	0.022
runSeuratFindClusters	0.023	0.000	0.023
runSeuratFindHVG	0.432	0.006	0.437
runSeuratHeatmap	0.022	0.000	0.021
runSeuratICA	0.021	0.000	0.021
runSeuratJackStraw	0.020	0.001	0.021
runSeuratNormalizeData	0.021	0.000	0.022
runSeuratPCA	0.019	0.002	0.022
runSeuratSCTransform	28.509	1.065	29.578
runSeuratScaleData	0.020	0.002	0.023
runSeuratUMAP	0.021	0.001	0.022
runSingleR	0.036	0.002	0.039
runSoupX	0.000	0.000	0.001
runTSCAN	0.635	0.022	0.658
runTSCANClusterDEAnalysis	0.719	0.029	0.748
runTSCANDEG	0.715	0.048	0.763
runTSNE	0.709	0.026	0.735
runUMAP	7.243	0.181	7.423
runVAM	0.278	0.002	0.280
runZINBWaVE	0.003	0.001	0.004
sampleSummaryStats	0.149	0.014	0.163
scaterCPM	0.135	0.002	0.137
scaterPCA	0.416	0.005	0.420
scaterlogNormCounts	0.232	0.005	0.237
sce	0.018	0.003	0.022
sctkListGeneSetCollections	0.076	0.002	0.078
sctkPythonInstallConda	0	0	0
sctkPythonInstallVirtualEnv	0.001	0.000	0.000
selectSCTKConda	0	0	0
selectSCTKVirtualEnvironment	0.000	0.000	0.001
setRowNames	0.081	0.000	0.082
setSCTKDisplayRow	0.413	0.003	0.416
singleCellTK	0	0	0
subDiffEx	0.300	0.011	0.310
subsetSCECols	0.082	0.001	0.083
subsetSCERows	0.256	0.011	0.268
summarizeSCE	0.065	0.001	0.066
trimCounts	0.194	0.009	0.203