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"	4824
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R 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*

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: 2025-08-19 14:09:40 -0000 (Tue, 19 Aug 2025)

EndedAt: 2025-08-19 14:29:31 -0000 (Tue, 19 Aug 2025)

EllapsedTime: 1190.2 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     45.285  0.337  45.719
plotScDblFinderResults   41.313  0.223  41.735
plotDoubletFinderResults 41.288  0.240  41.742
runDoubletFinder         37.524  0.221  37.834
runScDblFinder           30.220  0.451  30.717
importExampleData        15.261  1.229  22.070
plotBatchCorrCompare     13.444  0.069  13.872
plotScdsHybridResults    11.317  0.062  10.420
plotBcdsResults          10.461  0.121   9.643
plotDecontXResults        8.908  0.136   9.064
runDecontX                7.749  0.032   7.809
plotCxdsResults           7.470  0.084   7.700
runUMAP                   7.470  0.038   7.645
plotUMAP                  7.410  0.077   7.660
plotFindMarkerHeatmap     7.062  0.080   7.156
detectCellOutlier         6.617  0.215   6.846
plotDEGViolin             5.784  0.077   5.876
convertSCEToSeurat        5.507  0.244   5.763
plotEmptyDropsResults     5.547  0.033   5.591
plotEmptyDropsScatter     5.488  0.020   5.517
plotTSCANClusterDEG       5.213  0.115   5.341
runEmptyDrops             5.195  0.004   5.204
runEnrichR                0.430  0.134   9.328
getEnrichRResult          0.405  0.076   8.675
* 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 
  0.185   0.038   0.210

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
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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'
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 
329.466   9.101 356.413

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

name	user	system	elapsed
MitoGenes	0.003	0.000	0.003
SEG	0.003	0.000	0.003
calcEffectSizes	0.270	0.016	0.287
combineSCE	1.084	0.020	1.107
computeZScore	0.271	0.020	0.292
convertSCEToSeurat	5.507	0.244	5.763
convertSeuratToSCE	0.484	0.008	0.492
dedupRowNames	0.076	0.000	0.076
detectCellOutlier	6.617	0.215	6.846
diffAbundanceFET	0.076	0.000	0.075
discreteColorPalette	0.008	0.000	0.008
distinctColors	0.003	0.000	0.003
downSampleCells	0.738	0.072	0.812
downSampleDepth	0.624	0.004	0.630
expData-ANY-character-method	0.182	0.000	0.182
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method	0.239	0.000	0.240
expData-set	0.217	0.004	0.221
expData	0.171	0.000	0.171
expDataNames-ANY-method	0.162	0.000	0.162
expDataNames	0.158	0.000	0.158
expDeleteDataTag	0.043	0.000	0.043
expSetDataTag	0.03	0.00	0.03
expTaggedData	0.031	0.000	0.031
exportSCE	0.026	0.000	0.026
exportSCEtoAnnData	0.074	0.004	0.078
exportSCEtoFlatFile	0.079	0.000	0.078
featureIndex	0.041	0.004	0.044
generateSimulatedData	0.066	0.000	0.066
getBiomarker	0.071	0.000	0.070
getDEGTopTable	0.945	0.044	0.991
getDiffAbundanceResults	0.061	0.012	0.074
getEnrichRResult	0.405	0.076	8.675
getFindMarkerTopTable	2.108	0.197	2.310
getMSigDBTable	0.004	0.000	0.005
getPathwayResultNames	0.037	0.004	0.041
getSampleSummaryStatsTable	0.266	0.016	0.282
getSoupX	0	0	0
getTSCANResults	1.505	0.151	1.661
getTopHVG	1.189	0.060	1.251
importAnnData	0.001	0.000	0.002
importBUStools	0.210	0.016	0.228
importCellRanger	1.091	0.108	1.206
importCellRangerV2Sample	0.214	0.020	0.235
importCellRangerV3Sample	0.420	0.028	0.449
importDropEst	0.306	0.036	0.343
importExampleData	15.261	1.229	22.070
importGeneSetsFromCollection	2.341	0.100	2.446
importGeneSetsFromGMT	0.078	0.003	0.082
importGeneSetsFromList	0.164	0.000	0.164
importGeneSetsFromMSigDB	1.226	0.112	1.341
importMitoGeneSet	0.058	0.004	0.062
importOptimus	0.002	0.000	0.002
importSEQC	0.180	0.016	0.198
importSTARsolo	0.261	0.008	0.271
iterateSimulations	0.232	0.003	0.236
listSampleSummaryStatsTables	0.332	0.000	0.332
mergeSCEColData	0.510	0.008	0.519
mouseBrainSubsetSCE	0.043	0.004	0.047
msigdb_table	0.001	0.000	0.002
plotBarcodeRankDropsResults	0.840	0.004	0.847
plotBarcodeRankScatter	0.970	0.016	0.988
plotBatchCorrCompare	13.444	0.069	13.872
plotBatchVariance	0.450	0.008	0.459
plotBcdsResults	10.461	0.121	9.643
plotBubble	0.944	0.020	0.966
plotClusterAbundance	1.249	0.008	1.260
plotCxdsResults	7.470	0.084	7.700
plotDEGHeatmap	3.015	0.017	3.039
plotDEGRegression	4.698	0.032	4.742
plotDEGViolin	5.784	0.077	5.876
plotDEGVolcano	1.069	0.008	1.079
plotDecontXResults	8.908	0.136	9.064
plotDimRed	0.254	0.008	0.262
plotDoubletFinderResults	41.288	0.240	41.742
plotEmptyDropsResults	5.547	0.033	5.591
plotEmptyDropsScatter	5.488	0.020	5.517
plotFindMarkerHeatmap	7.062	0.080	7.156
plotMASTThresholdGenes	1.838	0.020	1.862
plotPCA	0.430	0.004	0.435
plotPathway	0.739	0.012	0.753
plotRunPerCellQCResults	2.828	0.036	2.869
plotSCEBarAssayData	0.261	0.000	0.261
plotSCEBarColData	0.244	0.003	0.247
plotSCEBatchFeatureMean	0.325	0.000	0.327
plotSCEDensity	0.301	0.004	0.306
plotSCEDensityAssayData	0.239	0.000	0.239
plotSCEDensityColData	0.3	0.0	0.3
plotSCEDimReduceColData	0.712	0.004	0.717
plotSCEDimReduceFeatures	0.401	0.000	0.401
plotSCEHeatmap	0.593	0.003	0.598
plotSCEScatter	0.347	0.001	0.347
plotSCEViolin	0.352	0.000	0.353
plotSCEViolinAssayData	0.369	0.000	0.370
plotSCEViolinColData	0.348	0.000	0.348
plotScDblFinderResults	41.313	0.223	41.735
plotScanpyDotPlot	0.028	0.000	0.028
plotScanpyEmbedding	0.028	0.000	0.028
plotScanpyHVG	0.027	0.000	0.028
plotScanpyHeatmap	0.029	0.000	0.029
plotScanpyMarkerGenes	0.029	0.000	0.029
plotScanpyMarkerGenesDotPlot	0.025	0.000	0.025
plotScanpyMarkerGenesHeatmap	0.025	0.000	0.024
plotScanpyMarkerGenesMatrixPlot	0.025	0.000	0.025
plotScanpyMarkerGenesViolin	0.024	0.000	0.024
plotScanpyMatrixPlot	0.024	0.000	0.025
plotScanpyPCA	0.028	0.000	0.028
plotScanpyPCAGeneRanking	0.025	0.000	0.025
plotScanpyPCAVariance	0.024	0.000	0.025
plotScanpyViolin	0.024	0.000	0.025
plotScdsHybridResults	11.317	0.062	10.420
plotScrubletResults	0.025	0.000	0.026
plotSeuratElbow	0.026	0.000	0.026
plotSeuratHVG	0.025	0.000	0.025
plotSeuratJackStraw	0.025	0.000	0.025
plotSeuratReduction	0.026	0.000	0.026
plotSoupXResults	0	0	0
plotTSCANClusterDEG	5.213	0.115	5.341
plotTSCANClusterPseudo	1.682	0.001	1.687
plotTSCANDimReduceFeatures	1.770	0.004	1.777
plotTSCANPseudotimeGenes	1.932	0.028	1.964
plotTSCANPseudotimeHeatmap	1.858	0.016	1.879
plotTSCANResults	1.537	0.004	1.545
plotTSNE	0.423	0.000	0.424
plotTopHVG	0.705	0.000	0.706
plotUMAP	7.410	0.077	7.660
readSingleCellMatrix	0.002	0.005	0.006
reportCellQC	0.117	0.000	0.117
reportDropletQC	0.032	0.000	0.032
reportQCTool	0.118	0.000	0.118
retrieveSCEIndex	0.041	0.000	0.040
runBBKNN	0	0	0
runBarcodeRankDrops	0.308	0.000	0.309
runBcds	3.022	0.012	1.987
runCellQC	0.108	0.000	0.109
runClusterSummaryMetrics	0.526	0.000	0.533
runComBatSeq	0.664	0.008	0.673
runCxds	0.434	0.000	0.435
runCxdsBcdsHybrid	3.063	0.032	2.025
runDEAnalysis	0.543	0.028	0.574
runDecontX	7.749	0.032	7.809
runDimReduce	0.407	0.000	0.408
runDoubletFinder	37.524	0.221	37.834
runDropletQC	0.027	0.000	0.027
runEmptyDrops	5.195	0.004	5.204
runEnrichR	0.430	0.134	9.328
runFastMNN	2.524	0.268	2.797
runFeatureSelection	0.304	0.022	0.334
runFindMarker	2.065	0.155	2.228
runGSVA	1.254	0.100	1.356
runHarmony	0.057	0.004	0.061
runKMeans	0.264	0.008	0.273
runLimmaBC	0.108	0.016	0.124
runMNNCorrect	0.600	0.035	0.636
runModelGeneVar	0.445	0.032	0.479
runNormalization	2.700	0.180	2.884
runPerCellQC	0.452	0.008	0.461
runSCANORAMA	0.001	0.000	0.000
runSCMerge	0.005	0.000	0.005
runScDblFinder	30.220	0.451	30.717
runScanpyFindClusters	0.029	0.000	0.029
runScanpyFindHVG	0.029	0.000	0.028
runScanpyFindMarkers	0.029	0.000	0.030
runScanpyNormalizeData	0.141	0.000	0.141
runScanpyPCA	0.027	0.000	0.027
runScanpyScaleData	0.028	0.000	0.028
runScanpyTSNE	0.027	0.000	0.027
runScanpyUMAP	0.024	0.004	0.029
runScranSNN	0.399	0.000	0.399
runScrublet	0.029	0.000	0.029
runSeuratFindClusters	0.029	0.000	0.029
runSeuratFindHVG	0.658	0.004	0.663
runSeuratHeatmap	0.028	0.000	0.028
runSeuratICA	0.029	0.000	0.029
runSeuratJackStraw	0.029	0.000	0.029
runSeuratNormalizeData	0.03	0.00	0.03
runSeuratPCA	0.028	0.000	0.028
runSeuratSCTransform	45.285	0.337	45.719
runSeuratScaleData	0.027	0.000	0.027
runSeuratUMAP	0.025	0.000	0.025
runSingleR	0.048	0.000	0.049
runSoupX	0	0	0
runTSCAN	0.887	0.016	0.905
runTSCANClusterDEAnalysis	0.991	0.004	0.997
runTSCANDEG	0.956	0.016	0.974
runTSNE	1.041	0.004	1.046
runUMAP	7.470	0.038	7.645
runVAM	0.4	0.0	0.4
runZINBWaVE	0.004	0.000	0.005
sampleSummaryStats	0.221	0.000	0.222
scaterCPM	0.131	0.008	0.139
scaterPCA	0.642	0.004	0.647
scaterlogNormCounts	0.274	0.004	0.279
sce	0.020	0.004	0.024
sctkListGeneSetCollections	0.097	0.000	0.097
sctkPythonInstallConda	0.001	0.000	0.000
sctkPythonInstallVirtualEnv	0	0	0
selectSCTKConda	0	0	0
selectSCTKVirtualEnvironment	0.000	0.000	0.001
setRowNames	0.105	0.000	0.106
setSCTKDisplayRow	0.391	0.004	0.395
singleCellTK	0	0	0
subDiffEx	0.401	0.004	0.406
subsetSCECols	0.101	0.000	0.102
subsetSCERows	0.314	0.000	0.315
summarizeSCE	0.083	0.000	0.082
trimCounts	0.243	0.004	0.248