Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4902
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4668
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2033/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.20.0  (landing page)
Joshua David Campbell
Snapshot Date: 2025-11-11 13:45 -0500 (Tue, 11 Nov 2025)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: RELEASE_3_22
git_last_commit: e2bff7b
git_last_commit_date: 2025-10-29 11:29:49 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
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: 2025-11-11 14:56:12 -0000 (Tue, 11 Nov 2025)
EndedAt: 2025-11-11 15:22:56 -0000 (Tue, 11 Nov 2025)
EllapsedTime: 1603.5 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 49.268  1.093  58.628
runSeuratSCTransform     43.706  0.805  48.933
plotDoubletFinderResults 42.890  0.247  51.849
runDoubletFinder         35.637  0.241  40.876
plotScDblFinderResults   33.730  0.434  41.808
runScDblFinder           22.182  0.659  26.982
importExampleData        13.960  1.051  30.149
plotBatchCorrCompare     13.212  0.180  20.084
plotScdsHybridResults    11.945  0.053  13.018
plotBcdsResults          10.753  0.112  13.688
plotDecontXResults        9.863  0.059  11.197
plotDEGViolin             9.456  0.107  10.625
plotCxdsResults           8.271  0.088  10.114
runDecontX                7.473  0.027   8.253
runUMAP                   7.220  0.084   8.769
plotUMAP                  7.121  0.168  10.227
plotTSCANClusterDEG       7.273  0.016   9.188
plotDEGRegression         6.593  0.092   8.661
detectCellOutlier         6.006  0.264   9.563
convertSCEToSeurat        5.564  0.339   6.485
plotEmptyDropsResults     5.817  0.016   6.557
plotFindMarkerHeatmap     5.683  0.063   7.185
plotEmptyDropsScatter     5.684  0.012   6.084
runEmptyDrops             5.289  0.000   5.982
getEnrichRResult          0.458  0.048  33.379
runEnrichR                0.408  0.047  70.192
* 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 
  0.204   0.030   0.452 

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

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

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

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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
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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 
367.266   7.977 493.854 

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0000.003
SEG0.0000.0030.003
calcEffectSizes0.2650.0270.294
combineSCE1.1030.1621.352
computeZScore0.2690.0310.305
convertSCEToSeurat5.5640.3396.485
convertSeuratToSCE0.4760.0080.485
dedupRowNames0.0740.0000.074
detectCellOutlier6.0060.2649.563
diffAbundanceFET0.0680.0000.141
discreteColorPalette0.0080.0000.016
distinctColors0.0030.0000.006
downSampleCells0.7230.0470.896
downSampleDepth0.5860.0150.627
expData-ANY-character-method0.1470.0160.172
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.2120.0040.378
expData-set0.1890.0040.192
expData0.1520.0040.156
expDataNames-ANY-method0.1450.0000.145
expDataNames0.1370.0040.141
expDeleteDataTag0.0380.0000.038
expSetDataTag0.0230.0040.027
expTaggedData0.0270.0000.027
exportSCE0.0240.0000.024
exportSCEtoAnnData0.0730.0030.077
exportSCEtoFlatFile0.0760.0000.076
featureIndex0.0370.0040.041
generateSimulatedData0.0480.0200.067
getBiomarker0.0630.0040.067
getDEGTopTable0.9520.0401.140
getDiffAbundanceResults0.0520.0030.055
getEnrichRResult 0.458 0.04833.379
getFindMarkerTopTable2.1350.1202.508
getMSigDBTable0.0000.0040.005
getPathwayResultNames0.0230.0000.022
getSampleSummaryStatsTable0.2380.0280.266
getSoupX0.0010.0000.000
getTSCANResults1.4200.1271.573
getTopHVG1.2190.0711.297
importAnnData0.0020.0000.002
importBUStools0.2380.0160.312
importCellRanger1.0880.0641.349
importCellRangerV2Sample0.2040.0000.205
importCellRangerV3Sample0.4000.0160.433
importDropEst0.2740.0150.313
importExampleData13.960 1.05130.149
importGeneSetsFromCollection1.9890.0922.094
importGeneSetsFromGMT0.0870.0000.092
importGeneSetsFromList0.1840.0000.185
importGeneSetsFromMSigDB49.268 1.09358.628
importMitoGeneSet0.0610.0080.070
importOptimus0.0020.0000.002
importSEQC0.1800.0320.307
importSTARsolo0.2130.0160.253
iterateSimulations0.2210.0280.250
listSampleSummaryStatsTables0.3100.0480.358
mergeSCEColData0.5460.0240.924
mouseBrainSubsetSCE0.0380.0040.081
msigdb_table0.0010.0000.006
plotBarcodeRankDropsResults1.2440.0202.059
plotBarcodeRankScatter1.2720.0082.123
plotBatchCorrCompare13.212 0.18020.084
plotBatchVariance0.6590.0040.664
plotBcdsResults10.753 0.11213.688
plotBubble1.1410.0041.259
plotClusterAbundance1.9530.0072.076
plotCxdsResults 8.271 0.08810.114
plotDEGHeatmap2.9570.0273.466
plotDEGRegression6.5930.0928.661
plotDEGViolin 9.456 0.10710.625
plotDEGVolcano1.2780.0041.776
plotDecontXResults 9.863 0.05911.197
plotDimRed0.4080.0030.429
plotDoubletFinderResults42.890 0.24751.849
plotEmptyDropsResults5.8170.0166.557
plotEmptyDropsScatter5.6840.0126.084
plotFindMarkerHeatmap5.6830.0637.185
plotMASTThresholdGenes1.8720.0111.941
plotPCA0.5460.0000.564
plotPathway1.0500.0081.202
plotRunPerCellQCResults4.6050.0684.811
plotSCEBarAssayData0.4640.0040.491
plotSCEBarColData0.3240.0000.325
plotSCEBatchFeatureMean0.5840.0000.586
plotSCEDensity0.4650.0000.542
plotSCEDensityAssayData0.4670.0000.468
plotSCEDensityColData0.4310.0000.448
plotSCEDimReduceColData1.0920.0121.214
plotSCEDimReduceFeatures0.6290.0080.639
plotSCEHeatmap0.6440.0000.729
plotSCEScatter0.5300.0000.531
plotSCEViolin0.6010.0040.690
plotSCEViolinAssayData0.5390.0000.541
plotSCEViolinColData0.5270.0000.560
plotScDblFinderResults33.730 0.43441.808
plotScanpyDotPlot0.0250.0000.025
plotScanpyEmbedding0.0220.0000.022
plotScanpyHVG0.0220.0000.022
plotScanpyHeatmap0.0230.0000.023
plotScanpyMarkerGenes0.0220.0000.022
plotScanpyMarkerGenesDotPlot0.0230.0000.023
plotScanpyMarkerGenesHeatmap0.0230.0000.023
plotScanpyMarkerGenesMatrixPlot0.0190.0040.023
plotScanpyMarkerGenesViolin0.0230.0000.023
plotScanpyMatrixPlot0.0230.0000.023
plotScanpyPCA0.0230.0000.022
plotScanpyPCAGeneRanking0.0230.0000.024
plotScanpyPCAVariance0.0240.0000.024
plotScanpyViolin0.0240.0000.023
plotScdsHybridResults11.945 0.05313.018
plotScrubletResults0.0270.0000.027
plotSeuratElbow0.0270.0000.027
plotSeuratHVG0.0270.0000.027
plotSeuratJackStraw0.0270.0000.027
plotSeuratReduction0.0280.0000.052
plotSoupXResults000
plotTSCANClusterDEG7.2730.0169.188
plotTSCANClusterPseudo1.9670.0402.637
plotTSCANDimReduceFeatures2.0780.0242.885
plotTSCANPseudotimeGenes2.5530.0202.633
plotTSCANPseudotimeHeatmap1.9090.0442.134
plotTSCANResults1.7390.0281.903
plotTSNE0.5160.0040.612
plotTopHVG0.9550.0080.985
plotUMAP 7.121 0.16810.227
readSingleCellMatrix0.0060.0000.007
reportCellQC0.1030.0000.104
reportDropletQC0.0230.0000.024
reportQCTool0.1040.0000.104
retrieveSCEIndex0.0320.0000.032
runBBKNN000
runBarcodeRankDrops0.2830.0000.285
runBcds3.1280.0363.156
runCellQC0.1130.0000.114
runClusterSummaryMetrics0.5170.0080.526
runComBatSeq0.6710.0041.167
runCxds0.4200.0040.522
runCxdsBcdsHybrid2.4980.0534.003
runDEAnalysis0.6380.0011.236
runDecontX7.4730.0278.253
runDimReduce0.3850.0080.394
runDoubletFinder35.637 0.24140.876
runDropletQC0.0300.0000.029
runEmptyDrops5.2890.0005.982
runEnrichR 0.408 0.04770.192
runFastMNN2.4170.2352.706
runFeatureSelection0.3010.0080.310
runFindMarker2.0380.1602.399
runGSVA1.0410.0761.135
runHarmony0.0520.0040.057
runKMeans0.3570.0280.386
runLimmaBC0.1250.0000.125
runMNNCorrect0.6450.0121.198
runModelGeneVar0.4720.0240.614
runNormalization2.8740.3003.378
runPerCellQC0.4730.0521.036
runSCANORAMA0.0000.0000.001
runSCMerge0.0050.0000.009
runScDblFinder22.182 0.65926.982
runScanpyFindClusters0.0280.0000.028
runScanpyFindHVG0.0270.0000.027
runScanpyFindMarkers0.0270.0000.027
runScanpyNormalizeData0.1320.0000.132
runScanpyPCA0.0270.0000.027
runScanpyScaleData0.0270.0000.027
runScanpyTSNE0.0270.0000.027
runScanpyUMAP0.0270.0000.027
runScranSNN0.3930.0040.446
runScrublet0.0260.0000.027
runSeuratFindClusters0.0270.0000.027
runSeuratFindHVG0.6420.0080.651
runSeuratHeatmap0.0260.0000.026
runSeuratICA0.0260.0000.026
runSeuratJackStraw0.0260.0000.025
runSeuratNormalizeData0.0260.0000.026
runSeuratPCA0.0220.0040.026
runSeuratSCTransform43.706 0.80548.933
runSeuratScaleData0.0210.0040.027
runSeuratUMAP0.0210.0040.025
runSingleR0.0540.0000.054
runSoupX000
runTSCAN0.9890.0081.213
runTSCANClusterDEAnalysis1.0410.0281.107
runTSCANDEG1.0560.0121.071
runTSNE1.0070.0001.097
runUMAP7.2200.0848.769
runVAM0.3910.0040.396
runZINBWaVE0.0050.0000.004
sampleSummaryStats0.2040.0000.205
scaterCPM0.1290.0040.132
scaterPCA0.5940.0000.595
scaterlogNormCounts0.2670.0000.268
sce0.0200.0000.021
sctkListGeneSetCollections0.10.00.1
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv0.0000.0000.001
selectSCTKConda000
selectSCTKVirtualEnvironment000
setRowNames0.1030.0040.107
setSCTKDisplayRow0.5530.0000.553
singleCellTK0.0010.0000.000
subDiffEx0.4210.0040.425
subsetSCECols0.1140.0080.122
subsetSCERows0.3910.0080.401
summarizeSCE0.0820.0040.086
trimCounts0.2090.0040.212