Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2026-01-08 11:59 -0500 (Thu, 08 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4671
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

Package 2033/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.20.0  (landing page)
Joshua David Campbell
Snapshot Date: 2026-01-05 13:45 -0500 (Mon, 05 Jan 2026)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_22
git_last_commit: c1aa93d
git_last_commit_date: 2025-12-30 13:54:56 -0500 (Tue, 30 Dec 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for singleCellTK on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: singleCellTK
Version: 2.20.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings singleCellTK_2.20.0.tar.gz
StartedAt: 2026-01-06 15:30:22 -0000 (Tue, 06 Jan 2026)
EndedAt: 2026-01-06 15:52:28 -0000 (Tue, 06 Jan 2026)
EllapsedTime: 1325.6 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings singleCellTK_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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  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 50.912  1.129  52.142
runSeuratSCTransform     43.569  0.877  44.609
plotDoubletFinderResults 42.822  0.239  43.285
runDoubletFinder         38.727  0.269  39.095
plotScDblFinderResults   34.480  0.428  34.966
runScDblFinder           22.784  0.789  23.481
importExampleData        14.330  1.333  21.363
plotBatchCorrCompare     13.931  0.200  14.500
plotScdsHybridResults    11.771  0.038  11.164
plotBcdsResults          10.641  0.124  10.127
plotDecontXResults       10.012  0.108  10.139
plotCxdsResults           8.472  0.143   8.765
plotDEGViolin             8.077  0.041   8.133
runUMAP                   7.768  0.197   8.115
runDecontX                7.843  0.040   7.902
plotUMAP                  7.608  0.188   7.945
plotTSCANClusterDEG       7.471  0.044   7.538
convertSCEToSeurat        5.753  1.340   7.113
plotDEGRegression         6.949  0.081   7.049
plotEmptyDropsResults     5.830  0.047   5.887
plotFindMarkerHeatmap     5.798  0.056   5.867
detectCellOutlier         5.468  0.358   5.847
plotEmptyDropsScatter     5.694  0.028   5.730
runEmptyDrops             5.256  0.005   5.271
getEnrichRResult          0.412  0.078   9.756
runEnrichR                0.397  0.043  59.041
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.


Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  0.202   0.023   0.210 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

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

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

  |                                                                            
  |                                                                      |   0%
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  |======================================================================| 100%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 21 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 21 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
376.161   9.272 404.046 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0000.003
SEG0.0030.0000.003
calcEffectSizes0.2270.0160.243
combineSCE1.0380.0441.084
computeZScore0.2790.0200.300
convertSCEToSeurat5.7531.3407.113
convertSeuratToSCE0.4380.0000.439
dedupRowNames0.0730.0080.081
detectCellOutlier5.4680.3585.847
diffAbundanceFET0.0650.0000.065
discreteColorPalette0.0070.0000.007
distinctColors0.0030.0000.003
downSampleCells0.7280.0560.786
downSampleDepth0.5820.0200.603
expData-ANY-character-method0.1630.0000.163
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.2090.0120.220
expData-set0.2100.0000.211
expData0.1800.0040.185
expDataNames-ANY-method0.1690.0080.178
expDataNames0.1450.0040.149
expDeleteDataTag0.0380.0000.039
expSetDataTag0.0270.0000.027
expTaggedData0.0280.0000.028
exportSCE0.0250.0000.025
exportSCEtoAnnData0.0690.0080.077
exportSCEtoFlatFile0.0720.0120.084
featureIndex0.0410.0040.045
generateSimulatedData0.0620.0040.066
getBiomarker0.0730.0000.073
getDEGTopTable0.9670.1041.073
getDiffAbundanceResults0.0530.0000.054
getEnrichRResult0.4120.0789.756
getFindMarkerTopTable2.0480.1872.240
getMSigDBTable0.0040.0000.004
getPathwayResultNames0.0240.0000.024
getSampleSummaryStatsTable0.2620.0110.274
getSoupX000
getTSCANResults1.4880.0831.575
getTopHVG1.1220.0521.178
importAnnData0.0020.0000.001
importBUStools0.3830.0360.421
importCellRanger1.0070.0641.079
importCellRangerV2Sample0.1980.0080.207
importCellRangerV3Sample0.4290.0440.473
importDropEst0.2630.0190.285
importExampleData14.330 1.33321.363
importGeneSetsFromCollection1.9270.1602.090
importGeneSetsFromGMT0.0860.0000.087
importGeneSetsFromList0.1890.0000.190
importGeneSetsFromMSigDB50.912 1.12952.142
importMitoGeneSet0.0680.0040.071
importOptimus0.0020.0000.002
importSEQC0.1920.0200.214
importSTARsolo0.2060.0270.235
iterateSimulations0.2350.0200.255
listSampleSummaryStatsTables0.3240.0280.352
mergeSCEColData0.5460.0320.580
mouseBrainSubsetSCE0.0410.0000.041
msigdb_table0.0010.0000.002
plotBarcodeRankDropsResults1.2220.0241.248
plotBarcodeRankScatter1.2460.0081.256
plotBatchCorrCompare13.931 0.20014.500
plotBatchVariance0.7420.0000.743
plotBcdsResults10.641 0.12410.127
plotBubble1.1140.0161.133
plotClusterAbundance2.0060.0042.015
plotCxdsResults8.4720.1438.765
plotDEGHeatmap3.0030.0083.022
plotDEGRegression6.9490.0817.049
plotDEGViolin8.0770.0418.133
plotDEGVolcano1.2550.0201.278
plotDecontXResults10.012 0.10810.139
plotDimRed0.4210.0030.425
plotDoubletFinderResults42.822 0.23943.285
plotEmptyDropsResults5.8300.0475.887
plotEmptyDropsScatter5.6940.0285.730
plotFindMarkerHeatmap5.7980.0565.867
plotMASTThresholdGenes1.8890.0361.930
plotPCA0.5300.0000.531
plotPathway1.0390.0041.047
plotRunPerCellQCResults4.7010.0214.732
plotSCEBarAssayData0.5270.0070.537
plotSCEBarColData0.3500.0040.355
plotSCEBatchFeatureMean0.6090.0050.615
plotSCEDensity0.4720.0040.477
plotSCEDensityAssayData0.4990.0040.504
plotSCEDensityColData0.4330.0040.438
plotSCEDimReduceColData1.1210.0041.128
plotSCEDimReduceFeatures0.6400.0000.641
plotSCEHeatmap0.6210.0000.624
plotSCEScatter0.5370.0000.538
plotSCEViolin0.6420.0040.647
plotSCEViolinAssayData0.5620.0040.568
plotSCEViolinColData0.5270.0040.533
plotScDblFinderResults34.480 0.42834.966
plotScanpyDotPlot0.0230.0000.024
plotScanpyEmbedding0.0190.0040.023
plotScanpyHVG0.0230.0000.023
plotScanpyHeatmap0.0230.0000.023
plotScanpyMarkerGenes0.0230.0000.023
plotScanpyMarkerGenesDotPlot0.0230.0000.023
plotScanpyMarkerGenesHeatmap0.0240.0000.024
plotScanpyMarkerGenesMatrixPlot0.0240.0000.024
plotScanpyMarkerGenesViolin0.0240.0000.024
plotScanpyMatrixPlot0.0190.0040.023
plotScanpyPCA0.0240.0000.024
plotScanpyPCAGeneRanking0.0190.0040.023
plotScanpyPCAVariance0.0230.0000.023
plotScanpyViolin0.0230.0000.024
plotScdsHybridResults11.771 0.03811.164
plotScrubletResults0.0250.0000.025
plotSeuratElbow0.0250.0000.025
plotSeuratHVG0.0240.0000.025
plotSeuratJackStraw0.0240.0000.024
plotSeuratReduction0.0250.0000.025
plotSoupXResults000
plotTSCANClusterDEG7.4710.0447.538
plotTSCANClusterPseudo2.0250.0362.067
plotTSCANDimReduceFeatures2.0890.0122.107
plotTSCANPseudotimeGenes2.4760.0042.487
plotTSCANPseudotimeHeatmap1.9820.0162.005
plotTSCANResults1.9380.0431.988
plotTSNE0.5430.0000.544
plotTopHVG1.0050.0001.007
plotUMAP7.6080.1887.945
readSingleCellMatrix0.0060.0000.006
reportCellQC0.1050.0000.106
reportDropletQC0.0240.0000.024
reportQCTool0.1080.0000.109
retrieveSCEIndex0.0360.0000.037
runBBKNN000
runBarcodeRankDrops0.2960.0040.300
runBcds0.1080.0000.108
runCellQC0.1020.0040.106
runClusterSummaryMetrics0.5470.0040.552
runComBatSeq0.7000.0000.701
runCxds0.4370.0000.439
runCxdsBcdsHybrid0.1040.0000.104
runDEAnalysis0.5030.0080.512
runDecontX7.8430.0407.902
runDimReduce0.3920.0000.394
runDoubletFinder38.727 0.26939.095
runDropletQC0.0260.0000.026
runEmptyDrops5.2560.0055.271
runEnrichR 0.397 0.04359.041
runFastMNN2.4040.2552.672
runFeatureSelection0.3080.0080.318
runFindMarker2.0420.1862.237
runGSVA1.3590.1081.472
runHarmony0.0580.0000.059
runKMeans0.2280.0160.245
runLimmaBC0.1170.0120.130
runMNNCorrect0.5490.0590.610
runModelGeneVar0.4190.0440.465
runNormalization2.9250.3543.291
runPerCellQC0.4690.0120.482
runSCANORAMA000
runSCMerge0.0040.0000.005
runScDblFinder22.784 0.78923.481
runScanpyFindClusters0.0210.0040.026
runScanpyFindHVG0.0250.0000.024
runScanpyFindMarkers0.0250.0000.024
runScanpyNormalizeData0.1320.0040.137
runScanpyPCA0.0240.0000.025
runScanpyScaleData0.0240.0000.024
runScanpyTSNE0.0240.0000.024
runScanpyUMAP0.0240.0000.024
runScranSNN0.4170.0000.419
runScrublet0.0230.0000.024
runSeuratFindClusters0.0240.0000.024
runSeuratFindHVG0.6590.0040.665
runSeuratHeatmap0.0160.0080.024
runSeuratICA0.0250.0000.025
runSeuratJackStraw0.0230.0000.023
runSeuratNormalizeData0.0240.0000.024
runSeuratPCA0.0240.0000.024
runSeuratSCTransform43.569 0.87744.609
runSeuratScaleData0.0240.0000.024
runSeuratUMAP0.0230.0000.023
runSingleR0.0490.0040.053
runSoupX000
runTSCAN0.9640.0230.993
runTSCANClusterDEAnalysis1.0810.0071.093
runTSCANDEG1.0570.0401.102
runTSNE1.0090.0121.024
runUMAP7.7680.1978.115
runVAM0.4240.0160.442
runZINBWaVE0.0040.0000.004
sampleSummaryStats0.2430.0000.244
scaterCPM0.1450.0040.150
scaterPCA0.6840.0080.693
scaterlogNormCounts0.2880.0000.288
sce0.030.000.03
sctkListGeneSetCollections0.1180.0000.119
sctkPythonInstallConda0.0000.0000.001
sctkPythonInstallVirtualEnv000
selectSCTKConda0.0000.0010.000
selectSCTKVirtualEnvironment000
setRowNames0.1290.0010.130
setSCTKDisplayRow0.6230.0200.645
singleCellTK000
subDiffEx0.4890.0080.499
subsetSCECols0.1240.0030.128
subsetSCERows0.4040.0040.409
summarizeSCE0.0890.0040.094
trimCounts0.2240.0000.225