Multiple platform build/check report for BioC 3.21 - CHECK results for singleCellTK on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4827
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4608
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4549
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4581
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for singleCellTK on kunpeng2

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: 2.18.1

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_2.18.1.tar.gz

StartedAt: 2025-09-19 14:53:04 -0000 (Fri, 19 Sep 2025)

EndedAt: 2025-09-19 15:13:01 -0000 (Fri, 19 Sep 2025)

EllapsedTime: 1196.8 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_2.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/singleCellTK.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* 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  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
  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
runSeuratSCTransform     44.566  0.719  45.417
plotScDblFinderResults   42.204  0.485  43.028
plotDoubletFinderResults 41.068  0.291  41.586
runDoubletFinder         37.453  0.178  37.715
runScDblFinder           29.153  0.682  29.901
importExampleData        15.084  1.180  26.404
plotBatchCorrCompare     13.425  0.216  14.020
plotScdsHybridResults    11.201  0.097  10.426
plotBcdsResults          10.298  0.181   9.549
plotDecontXResults        8.980  0.188   9.192
runUMAP                   7.643  0.117   7.905
runDecontX                7.624  0.000   7.642
plotCxdsResults           7.514  0.060   7.724
plotUMAP                  7.287  0.030   7.465
plotFindMarkerHeatmap     7.202  0.065   7.284
detectCellOutlier         6.458  0.016   6.487
plotDEGViolin             5.865  0.096   5.977
convertSCEToSeurat        5.528  0.091   5.631
plotEmptyDropsResults     5.543  0.029   5.584
plotEmptyDropsScatter     5.471  0.004   5.485
plotTSCANClusterDEG       5.138  0.124   5.276
runEmptyDrops             5.196  0.012   5.218
getEnrichRResult          0.439  0.243  20.378
runEnrichR                0.387  0.061   8.248
* 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-3.21-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-devel_2025-02-19/site-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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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)
NULL
> 
> proc.time()
   user  system elapsed 
  0.198   0.036   0.220

singleCellTK.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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: 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
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

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

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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 
325.361   7.982 347.175

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

name	user	system	elapsed
MitoGenes	0.003	0.000	0.004
SEG	0.002	0.000	0.002
calcEffectSizes	0.282	0.012	0.293
combineSCE	1.140	0.008	1.150
computeZScore	0.293	0.004	0.298
convertSCEToSeurat	5.528	0.091	5.631
convertSeuratToSCE	0.470	0.004	0.475
dedupRowNames	0.075	0.000	0.075
detectCellOutlier	6.458	0.016	6.487
diffAbundanceFET	0.066	0.000	0.066
discreteColorPalette	0.007	0.000	0.007
distinctColors	0.003	0.000	0.003
downSampleCells	0.734	0.044	0.779
downSampleDepth	0.626	0.008	0.636
expData-ANY-character-method	0.163	0.004	0.168
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method	0.213	0.000	0.214
expData-set	0.208	0.000	0.209
expData	0.169	0.000	0.171
expDataNames-ANY-method	0.161	0.000	0.162
expDataNames	0.157	0.000	0.158
expDeleteDataTag	0.038	0.004	0.042
expSetDataTag	0.032	0.000	0.032
expTaggedData	0.033	0.000	0.033
exportSCE	0.028	0.000	0.028
exportSCEtoAnnData	0.079	0.000	0.079
exportSCEtoFlatFile	0.072	0.008	0.080
featureIndex	0.048	0.000	0.049
generateSimulatedData	0.068	0.000	0.069
getBiomarker	0.076	0.000	0.075
getDEGTopTable	0.956	0.036	0.994
getDiffAbundanceResults	0.058	0.000	0.058
getEnrichRResult	0.439	0.243	20.378
getFindMarkerTopTable	2.139	0.651	2.797
getMSigDBTable	0.000	0.004	0.004
getPathwayResultNames	0.03	0.00	0.03
getSampleSummaryStatsTable	0.281	0.004	0.286
getSoupX	0	0	0
getTSCANResults	1.453	0.191	1.649
getTopHVG	1.186	0.060	1.249
importAnnData	0.000	0.002	0.001
importBUStools	0.230	0.004	0.237
importCellRanger	1.088	0.044	1.139
importCellRangerV2Sample	0.218	0.004	0.223
importCellRangerV3Sample	0.398	0.032	0.431
importDropEst	0.345	0.004	0.352
importExampleData	15.084	1.180	26.404
importGeneSetsFromCollection	2.266	0.047	2.319
importGeneSetsFromGMT	0.083	0.000	0.084
importGeneSetsFromList	0.17	0.00	0.17
importGeneSetsFromMSigDB	1.393	0.116	1.519
importMitoGeneSet	0.066	0.012	0.078
importOptimus	0.001	0.000	0.001
importSEQC	0.202	0.039	0.243
importSTARsolo	0.267	0.033	0.303
iterateSimulations	0.249	0.000	0.250
listSampleSummaryStatsTables	0.332	0.003	0.336
mergeSCEColData	0.483	0.012	0.497
mouseBrainSubsetSCE	0.043	0.000	0.043
msigdb_table	0.002	0.000	0.001
plotBarcodeRankDropsResults	0.823	0.016	0.841
plotBarcodeRankScatter	0.999	0.012	1.014
plotBatchCorrCompare	13.425	0.216	14.020
plotBatchVariance	0.452	0.004	0.457
plotBcdsResults	10.298	0.181	9.549
plotBubble	0.970	0.024	0.996
plotClusterAbundance	1.228	0.016	1.247
plotCxdsResults	7.514	0.060	7.724
plotDEGHeatmap	3.021	0.029	3.057
plotDEGRegression	4.826	0.033	4.871
plotDEGViolin	5.865	0.096	5.977
plotDEGVolcano	1.111	0.000	1.115
plotDecontXResults	8.980	0.188	9.192
plotDimRed	0.265	0.000	0.266
plotDoubletFinderResults	41.068	0.291	41.586
plotEmptyDropsResults	5.543	0.029	5.584
plotEmptyDropsScatter	5.471	0.004	5.485
plotFindMarkerHeatmap	7.202	0.065	7.284
plotMASTThresholdGenes	1.883	0.060	1.947
plotPCA	0.440	0.004	0.445
plotPathway	0.778	0.000	0.782
plotRunPerCellQCResults	2.882	0.008	2.898
plotSCEBarAssayData	0.268	0.000	0.269
plotSCEBarColData	0.250	0.000	0.251
plotSCEBatchFeatureMean	0.335	0.000	0.335
plotSCEDensity	0.306	0.000	0.307
plotSCEDensityAssayData	0.248	0.012	0.261
plotSCEDensityColData	0.302	0.000	0.302
plotSCEDimReduceColData	0.706	0.016	0.724
plotSCEDimReduceFeatures	0.397	0.020	0.419
plotSCEHeatmap	0.613	0.036	0.651
plotSCEScatter	0.369	0.000	0.370
plotSCEViolin	0.353	0.004	0.358
plotSCEViolinAssayData	0.381	0.000	0.382
plotSCEViolinColData	0.352	0.004	0.357
plotScDblFinderResults	42.204	0.485	43.028
plotScanpyDotPlot	0.027	0.004	0.029
plotScanpyEmbedding	0.028	0.000	0.029
plotScanpyHVG	0.023	0.008	0.031
plotScanpyHeatmap	0.031	0.000	0.031
plotScanpyMarkerGenes	0.03	0.00	0.03
plotScanpyMarkerGenesDotPlot	0.031	0.000	0.031
plotScanpyMarkerGenesHeatmap	0.03	0.00	0.03
plotScanpyMarkerGenesMatrixPlot	0.029	0.000	0.030
plotScanpyMarkerGenesViolin	0.032	0.000	0.031
plotScanpyMatrixPlot	0.031	0.000	0.031
plotScanpyPCA	0.026	0.004	0.031
plotScanpyPCAGeneRanking	0.030	0.000	0.031
plotScanpyPCAVariance	0.031	0.000	0.031
plotScanpyViolin	0.027	0.000	0.026
plotScdsHybridResults	11.201	0.097	10.426
plotScrubletResults	0.025	0.000	0.025
plotSeuratElbow	0.020	0.003	0.024
plotSeuratHVG	0.024	0.000	0.024
plotSeuratJackStraw	0.024	0.000	0.025
plotSeuratReduction	0.025	0.000	0.025
plotSoupXResults	0	0	0
plotTSCANClusterDEG	5.138	0.124	5.276
plotTSCANClusterPseudo	1.665	0.012	1.681
plotTSCANDimReduceFeatures	1.724	0.008	1.737
plotTSCANPseudotimeGenes	1.978	0.004	1.988
plotTSCANPseudotimeHeatmap	1.903	0.036	1.944
plotTSCANResults	1.645	0.016	1.665
plotTSNE	0.426	0.008	0.435
plotTopHVG	0.725	0.008	0.735
plotUMAP	7.287	0.030	7.465
readSingleCellMatrix	0.007	0.000	0.006
reportCellQC	0.101	0.004	0.105
reportDropletQC	0.024	0.000	0.024
reportQCTool	0.105	0.000	0.105
retrieveSCEIndex	0.032	0.000	0.032
runBBKNN	0	0	0
runBarcodeRankDrops	0.283	0.000	0.285
runBcds	3.043	0.032	1.987
runCellQC	0.11	0.00	0.11
runClusterSummaryMetrics	0.495	0.008	0.505
runComBatSeq	0.650	0.004	0.656
runCxds	0.403	0.004	0.408
runCxdsBcdsHybrid	2.932	0.048	1.931
runDEAnalysis	0.534	0.000	0.536
runDecontX	7.624	0.000	7.642
runDimReduce	0.387	0.004	0.392
runDoubletFinder	37.453	0.178	37.715
runDropletQC	0.026	0.000	0.026
runEmptyDrops	5.196	0.012	5.218
runEnrichR	0.387	0.061	8.248
runFastMNN	2.358	0.222	2.591
runFeatureSelection	0.319	0.000	0.320
runFindMarker	2.072	0.163	2.242
runGSVA	1.187	0.163	1.354
runHarmony	0.062	0.000	0.061
runKMeans	0.235	0.019	0.256
runLimmaBC	0.116	0.008	0.124
runMNNCorrect	0.578	0.056	0.636
runModelGeneVar	0.424	0.052	0.477
runNormalization	2.706	0.370	3.083
runPerCellQC	0.474	0.008	0.483
runSCANORAMA	0	0	0
runSCMerge	0.005	0.000	0.004
runScDblFinder	29.153	0.682	29.901
runScanpyFindClusters	0.025	0.000	0.024
runScanpyFindHVG	0.025	0.000	0.024
runScanpyFindMarkers	0.024	0.000	0.024
runScanpyNormalizeData	0.127	0.000	0.128
runScanpyPCA	0.024	0.000	0.024
runScanpyScaleData	0.023	0.000	0.023
runScanpyTSNE	0.024	0.000	0.024
runScanpyUMAP	0.023	0.000	0.024
runScranSNN	0.385	0.000	0.386
runScrublet	0.024	0.000	0.025
runSeuratFindClusters	0.024	0.000	0.024
runSeuratFindHVG	0.630	0.004	0.636
runSeuratHeatmap	0.026	0.000	0.027
runSeuratICA	0.026	0.000	0.026
runSeuratJackStraw	0.023	0.004	0.026
runSeuratNormalizeData	0.028	0.000	0.027
runSeuratPCA	0.026	0.000	0.026
runSeuratSCTransform	44.566	0.719	45.417
runSeuratScaleData	0.024	0.000	0.025
runSeuratUMAP	0.026	0.008	0.034
runSingleR	0.051	0.000	0.050
runSoupX	0	0	0
runTSCAN	0.902	0.016	0.920
runTSCANClusterDEAnalysis	0.974	0.028	1.004
runTSCANDEG	0.950	0.008	0.961
runTSNE	1.039	0.016	1.058
runUMAP	7.643	0.117	7.905
runVAM	0.416	0.000	0.417
runZINBWaVE	0.004	0.000	0.004
sampleSummaryStats	0.222	0.000	0.223
scaterCPM	0.134	0.008	0.143
scaterPCA	0.660	0.000	0.662
scaterlogNormCounts	0.292	0.004	0.297
sce	0.025	0.000	0.025
sctkListGeneSetCollections	0.090	0.012	0.102
sctkPythonInstallConda	0	0	0
sctkPythonInstallVirtualEnv	0	0	0
selectSCTKConda	0	0	0
selectSCTKVirtualEnvironment	0	0	0
setRowNames	0.114	0.000	0.114
setSCTKDisplayRow	0.413	0.016	0.430
singleCellTK	0	0	0
subDiffEx	0.434	0.000	0.436
subsetSCECols	0.107	0.004	0.112
subsetSCERows	0.360	0.004	0.364
summarizeSCE	0.086	0.000	0.086
trimCounts	0.243	0.000	0.243