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This page was generated on 2025-08-21 11:41 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2013/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.18.1  (landing page)
Joshua David Campbell
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_21
git_last_commit: f519d00e
git_last_commit_date: 2025-07-01 15:40:07 -0400 (Tue, 01 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for singleCellTK on kjohnson1

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: 2.18.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.18.1.tar.gz
StartedAt: 2025-08-20 12:14:01 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 12:33:37 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 1176.0 seconds
RetCode: 0
Status:   OK  
CheckDir: singleCellTK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/singleCellTK.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.18.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 79 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘singleCellTK’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   1.5Mb
    shiny     2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dedupRowNames.Rd: SingleCellExperiment-class
  detectCellOutlier.Rd: colData
  diffAbundanceFET.Rd: colData
  downSampleCells.Rd: SingleCellExperiment-class
  downSampleDepth.Rd: SingleCellExperiment-class
  featureIndex.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  getBiomarker.Rd: SingleCellExperiment-class
  getDEGTopTable.Rd: SingleCellExperiment-class
  getEnrichRResult.Rd: SingleCellExperiment-class
  getFindMarkerTopTable.Rd: SingleCellExperiment-class
  getGenesetNamesFromCollection.Rd: SingleCellExperiment-class
  getPathwayResultNames.Rd: SingleCellExperiment-class
  getSampleSummaryStatsTable.Rd: SingleCellExperiment-class, assay,
    colData
  getSoupX.Rd: SingleCellExperiment-class
  getTSCANResults.Rd: SingleCellExperiment-class
  getTopHVG.Rd: SingleCellExperiment-class
  importAlevin.Rd: DelayedArray, readMM
  importAnnData.Rd: DelayedArray, readMM
  importBUStools.Rd: readMM
  importCellRanger.Rd: readMM, DelayedArray
  importCellRangerV2Sample.Rd: readMM, DelayedArray
  importCellRangerV3Sample.Rd: readMM, DelayedArray
  importDropEst.Rd: DelayedArray, readMM
  importExampleData.Rd: scRNAseq, Matrix, DelayedArray,
    ReprocessedFluidigmData, ReprocessedAllenData, NestorowaHSCData
  importFromFiles.Rd: readMM, DelayedArray, SingleCellExperiment-class
  importGeneSetsFromCollection.Rd: GeneSetCollection-class,
    SingleCellExperiment-class, GeneSetCollection, GSEABase, metadata
  importGeneSetsFromGMT.Rd: GeneSetCollection-class,
    SingleCellExperiment-class, getGmt, GSEABase, metadata
  importGeneSetsFromList.Rd: GeneSetCollection-class,
    SingleCellExperiment-class, GSEABase, metadata
  importGeneSetsFromMSigDB.Rd: SingleCellExperiment-class, msigdbr,
    GeneSetCollection-class, GSEABase, metadata
  importMitoGeneSet.Rd: SingleCellExperiment-class,
    GeneSetCollection-class, GSEABase, metadata
  importMultipleSources.Rd: DelayedArray
  importOptimus.Rd: readMM, DelayedArray
  importSEQC.Rd: readMM, DelayedArray
  importSTARsolo.Rd: readMM, DelayedArray
  iterateSimulations.Rd: SingleCellExperiment-class
  listSampleSummaryStatsTables.Rd: SingleCellExperiment-class, metadata
  plotBarcodeRankDropsResults.Rd: SingleCellExperiment-class
  plotBarcodeRankScatter.Rd: SingleCellExperiment-class
  plotBatchCorrCompare.Rd: SingleCellExperiment-class
  plotBatchVariance.Rd: SingleCellExperiment-class
  plotBcdsResults.Rd: SingleCellExperiment-class
  plotClusterAbundance.Rd: colData
  plotCxdsResults.Rd: SingleCellExperiment-class
  plotDEGHeatmap.Rd: SingleCellExperiment-class
  plotDEGRegression.Rd: SingleCellExperiment-class
  plotDEGViolin.Rd: SingleCellExperiment-class
  plotDEGVolcano.Rd: SingleCellExperiment-class
  plotDecontXResults.Rd: SingleCellExperiment-class
  plotDoubletFinderResults.Rd: SingleCellExperiment-class
  plotEmptyDropsResults.Rd: SingleCellExperiment-class
  plotEmptyDropsScatter.Rd: SingleCellExperiment-class
  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 58.135  0.641  58.985
plotDoubletFinderResults 50.143  0.230  50.575
runDoubletFinder         44.244  0.172  44.477
plotScDblFinderResults   38.866  0.827  39.875
runScDblFinder           27.789  0.474  28.271
importExampleData        18.720  1.344  22.440
plotBatchCorrCompare     16.409  0.140  16.617
plotScdsHybridResults    11.779  0.134  12.036
plotBcdsResults          10.802  0.221  11.182
plotDecontXResults       10.260  0.068  10.364
runDecontX                9.415  0.042   9.458
plotUMAP                  9.152  0.051   9.214
plotCxdsResults           9.099  0.067   9.193
runUMAP                   7.458  0.058   7.534
detectCellOutlier         6.624  0.131   6.807
plotEmptyDropsResults     6.667  0.036   6.715
runEmptyDrops             6.355  0.018   6.387
plotEmptyDropsScatter     6.002  0.019   6.043
convertSCEToSeurat        4.843  0.258   5.202
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.


Installation output

singleCellTK.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘singleCellTK’ ...
** this is package ‘singleCellTK’ version ‘2.18.1’
** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.146   0.042   0.198 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

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

Attaching package: 'MatrixGenerics'

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

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

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

Attaching package: 'generics'

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

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


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
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
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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  |======================================================================| 100%
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

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

Number of nodes: 390
Number of edges: 9849

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

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

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

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  |======================================================================| 100%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 22 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 22 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
356.770   7.198 377.391 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0040.006
SEG0.0030.0040.007
calcEffectSizes0.1870.0110.197
combineSCE0.7810.0240.806
computeZScore0.3030.0120.316
convertSCEToSeurat4.8430.2585.202
convertSeuratToSCE0.3360.0080.345
dedupRowNames0.0640.0040.067
detectCellOutlier6.6240.1316.807
diffAbundanceFET0.0810.0040.084
discreteColorPalette0.0070.0000.007
distinctColors0.0020.0000.003
downSampleCells0.6560.0790.739
downSampleDepth0.4950.0470.542
expData-ANY-character-method0.1410.0050.146
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.2030.0050.208
expData-set0.1610.0040.165
expData0.1480.0040.152
expDataNames-ANY-method0.1280.0090.137
expDataNames0.1300.0110.141
expDeleteDataTag0.0560.0040.060
expSetDataTag0.0550.0020.057
expTaggedData0.0440.0010.045
exportSCE0.0340.0030.038
exportSCEtoAnnData0.1340.0070.141
exportSCEtoFlatFile0.1310.0070.138
featureIndex0.0490.0070.056
generateSimulatedData0.0720.0080.079
getBiomarker0.0790.0100.088
getDEGTopTable0.7920.0620.865
getDiffAbundanceResults0.0730.0040.078
getEnrichRResult0.3490.0434.926
getFindMarkerTopTable1.5200.0741.603
getMSigDBTable0.0040.0040.009
getPathwayResultNames0.0360.0050.040
getSampleSummaryStatsTable0.2030.0050.207
getSoupX0.0000.0010.001
getTSCANResults1.2290.0661.326
getTopHVG0.8810.0160.900
importAnnData0.0020.0000.003
importBUStools0.1530.0040.158
importCellRanger0.7860.0370.828
importCellRangerV2Sample0.1410.0030.144
importCellRangerV3Sample0.3070.0140.322
importDropEst0.2160.0040.221
importExampleData18.720 1.34422.440
importGeneSetsFromCollection0.8320.0700.906
importGeneSetsFromGMT0.0780.0060.085
importGeneSetsFromList0.1290.0060.135
importGeneSetsFromMSigDB58.135 0.64158.985
importMitoGeneSet0.0690.0120.081
importOptimus0.0020.0010.003
importSEQC0.1690.0140.184
importSTARsolo0.1710.0160.187
iterateSimulations0.2200.0200.241
listSampleSummaryStatsTables0.3150.0240.339
mergeSCEColData0.3860.0370.474
mouseBrainSubsetSCE0.0550.0070.063
msigdb_table0.0020.0030.006
plotBarcodeRankDropsResults0.7430.0500.846
plotBarcodeRankScatter0.6690.0250.694
plotBatchCorrCompare16.409 0.14016.617
plotBatchVariance0.3410.0220.364
plotBcdsResults10.802 0.22111.182
plotBubble0.8650.0450.940
plotClusterAbundance0.8770.0110.895
plotCxdsResults9.0990.0679.193
plotDEGHeatmap2.2710.0472.336
plotDEGRegression3.3990.0543.487
plotDEGViolin4.1520.1234.356
plotDEGVolcano1.0200.0171.039
plotDecontXResults10.260 0.06810.364
plotDimRed0.3850.0250.419
plotDoubletFinderResults50.143 0.23050.575
plotEmptyDropsResults6.6670.0366.715
plotEmptyDropsScatter6.0020.0196.043
plotFindMarkerHeatmap3.9250.0323.959
plotMASTThresholdGenes1.3600.0351.416
plotPCA0.3600.0110.372
plotPathway0.6600.0130.677
plotRunPerCellQCResults2.1090.0262.143
plotSCEBarAssayData0.2410.0080.250
plotSCEBarColData0.1640.0100.176
plotSCEBatchFeatureMean0.2230.0050.228
plotSCEDensity0.2400.0080.249
plotSCEDensityAssayData0.2600.0080.268
plotSCEDensityColData0.2510.0070.257
plotSCEDimReduceColData0.5220.0120.539
plotSCEDimReduceFeatures0.2940.0110.305
plotSCEHeatmap0.4670.0080.477
plotSCEScatter0.3340.0090.345
plotSCEViolin0.2620.0090.270
plotSCEViolinAssayData0.2800.0090.288
plotSCEViolinColData0.2620.0080.271
plotScDblFinderResults38.866 0.82739.875
plotScanpyDotPlot0.0360.0100.047
plotScanpyEmbedding0.0370.0070.045
plotScanpyHVG0.0370.0070.044
plotScanpyHeatmap0.0340.0070.042
plotScanpyMarkerGenes0.0350.0040.040
plotScanpyMarkerGenesDotPlot0.0380.0020.040
plotScanpyMarkerGenesHeatmap0.0350.0020.037
plotScanpyMarkerGenesMatrixPlot0.0350.0020.036
plotScanpyMarkerGenesViolin0.0350.0020.037
plotScanpyMatrixPlot0.0370.0020.038
plotScanpyPCA0.0390.0020.041
plotScanpyPCAGeneRanking0.0350.0090.043
plotScanpyPCAVariance0.0350.0080.043
plotScanpyViolin0.0360.0080.044
plotScdsHybridResults11.779 0.13412.036
plotScrubletResults0.0360.0070.063
plotSeuratElbow0.0350.0010.036
plotSeuratHVG0.0350.0060.041
plotSeuratJackStraw0.0350.0030.038
plotSeuratReduction0.0370.0030.039
plotSoupXResults0.0010.0000.000
plotTSCANClusterDEG3.8770.0483.937
plotTSCANClusterPseudo1.0400.0231.073
plotTSCANDimReduceFeatures1.2820.0241.310
plotTSCANPseudotimeGenes1.4580.0211.482
plotTSCANPseudotimeHeatmap1.5040.0191.525
plotTSCANResults1.1110.0221.135
plotTSNE0.4000.0160.417
plotTopHVG0.5830.0120.599
plotUMAP9.1520.0519.214
readSingleCellMatrix0.0060.0010.008
reportCellQC0.0970.0060.103
reportDropletQC0.0350.0030.037
reportQCTool0.0980.0070.106
retrieveSCEIndex0.0410.0040.046
runBBKNN0.0000.0010.000
runBarcodeRankDrops0.2800.0100.293
runBcds1.8910.1852.101
runCellQC0.1050.0090.115
runClusterSummaryMetrics0.4190.0120.447
runComBatSeq0.5880.0270.638
runCxds0.3790.0080.388
runCxdsBcdsHybrid1.9200.0822.005
runDEAnalysis0.4320.0120.445
runDecontX9.4150.0429.458
runDimReduce0.3040.0080.313
runDoubletFinder44.244 0.17244.477
runDropletQC0.0370.0090.048
runEmptyDrops6.3550.0186.387
runEnrichR0.3290.0334.644
runFastMNN1.2880.0611.366
runFeatureSelection0.2600.0030.264
runFindMarker1.5560.0331.595
runGSVA0.8920.0560.961
runHarmony0.0430.0010.044
runKMeans0.2020.0090.211
runLimmaBC0.0820.0010.084
runMNNCorrect0.4700.0060.480
runModelGeneVar0.3270.0100.336
runNormalization3.2090.0613.273
runPerCellQC0.3920.0170.409
runSCANORAMA0.0010.0010.000
runSCMerge0.0050.0010.007
runScDblFinder27.789 0.47428.271
runScanpyFindClusters0.0410.0040.052
runScanpyFindHVG0.0360.0100.046
runScanpyFindMarkers0.0370.0100.048
runScanpyNormalizeData0.1150.0080.129
runScanpyPCA0.0360.0060.042
runScanpyScaleData0.0350.0040.040
runScanpyTSNE0.0350.0020.037
runScanpyUMAP0.0360.0030.039
runScranSNN0.3370.0120.350
runScrublet0.0360.0030.039
runSeuratFindClusters0.0350.0030.038
runSeuratFindHVG0.5180.0140.532
runSeuratHeatmap0.0380.0070.046
runSeuratICA0.0350.0020.037
runSeuratJackStraw0.0360.0020.037
runSeuratNormalizeData0.0360.0020.039
runSeuratPCA0.0360.0020.038
runSeuratSCTransform4.6590.1274.849
runSeuratScaleData0.0360.0050.041
runSeuratUMAP0.0360.0030.039
runSingleR0.0360.0030.040
runSoupX000
runTSCAN0.6770.0190.696
runTSCANClusterDEAnalysis0.7940.0180.813
runTSCANDEG0.8280.0290.857
runTSNE0.9380.0260.986
runUMAP7.4580.0587.534
runVAM0.1630.0070.170
runZINBWaVE0.0020.0010.002
sampleSummaryStats0.1350.0030.137
scaterCPM0.0760.0070.084
scaterPCA0.2610.0050.268
scaterlogNormCounts0.1730.0090.181
sce0.0120.0080.020
sctkListGeneSetCollections0.0890.0080.097
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv000
selectSCTKConda000
selectSCTKVirtualEnvironment000
setRowNames0.0920.0090.101
setSCTKDisplayRow0.2880.0080.297
singleCellTK0.0000.0010.001
subDiffEx0.2750.0270.304
subsetSCECols0.0570.0090.065
subsetSCERows0.1850.0110.197
summarizeSCE0.0730.0110.084
trimCounts0.2030.0230.226