Build/check report for BioC 3.22 - CHECK results for singleCellTK on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4886
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 nebbiolo2

To the developers/maintainers of the singleCellTK package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singleCellTK.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: singleCellTK

Version: 2.20.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings singleCellTK_2.20.1.tar.gz

StartedAt: 2026-01-20 04:11:16 -0500 (Tue, 20 Jan 2026)

EndedAt: 2026-01-20 04:28:10 -0500 (Tue, 20 Jan 2026)

EllapsedTime: 1013.9 seconds

RetCode: 1

Status: ERROR

CheckDir: singleCellTK.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings singleCellTK_2.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.20.1’
* 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 44.695  0.411  45.108
plotDoubletFinderResults 40.107  0.285  40.471
runDoubletFinder         37.826  0.086  37.914
runSeuratSCTransform     29.325  0.252  29.581
plotScDblFinderResults   27.606  0.719  28.369
runScDblFinder           17.642  0.466  18.061
plotBatchCorrCompare     12.894  0.190  13.266
importExampleData         9.762  0.400  10.600
plotDecontXResults        8.421  0.183   8.605
plotUMAP                  7.949  0.062   8.089
plotScdsHybridResults     7.826  0.113   8.018
runUMAP                   7.647  0.117   7.844
runDecontX                7.363  0.065   7.428
plotCxdsResults           7.350  0.014   7.445
plotDEGViolin             6.680  0.140   6.814
plotEmptyDropsResults     6.634  0.036   6.671
plotEmptyDropsScatter     6.533  0.020   6.553
detectCellOutlier         6.278  0.176   6.455
runEmptyDrops             6.248  0.012   6.260
plotBcdsResults           5.679  0.096   5.854
plotTSCANClusterDEG       5.150  0.006   5.158
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-qc.R:100:3'): Testing plotResults functions ────────────────────
  Error in `if (all(summ$value > 1)) {     summ$label <- paste0(summary, ": ", round(summ$value, 2)) } else {     summ$label <- paste0(summary, ": ", signif(summ$value, 2)) }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─singleCellTK::plotScdsHybridResults(...) at test-qc.R:100:3
   2.   └─singleCellTK::plotSCEViolinColData(...)
   3.     └─base::lapply(...)
   4.       └─singleCellTK (local) FUN(X[[i]], ...)
   5.         └─singleCellTK:::.ggViolin(...)
  
  [ FAIL 1 | WARN 48 | SKIP 0 | PASS 222 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 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/bbs-3.22-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘singleCellTK’ ...
** this is package ‘singleCellTK’ version ‘2.20.1’
** using staged installation
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (singleCellTK)

Tests output

singleCellTK.Rcheck/tests/spelling.Rout


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
  0.153   0.035   0.175

singleCellTK.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

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

Attaching package: 'MatrixGenerics'

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

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

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

Attaching package: 'generics'

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

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


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: SingleCellExperiment
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep


Attaching package: 'singleCellTK'

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

    plotPCA

> 
> test_check("singleCellTK")
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 0 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Found 2 batches
Using null model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Uploading data to Enrichr... Done.
  Querying HDSigDB_Human_2021... Done.
Parsing results... Done.
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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Saving _problems/test-qc-100.R
Performing log-normalization
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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
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Calculating feature variances of standardized and clipped values
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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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[----|----|----|----|----|----|----|----|----|----|
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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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Performing log-normalization
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[ FAIL 1 | WARN 48 | SKIP 0 | PASS 222 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-qc.R:100:3'): Testing plotResults functions ────────────────────
Error in `if (all(summ$value > 1)) {     summ$label <- paste0(summary, ": ", round(summ$value, 2)) } else {     summ$label <- paste0(summary, ": ", signif(summ$value, 2)) }`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. └─singleCellTK::plotScdsHybridResults(...) at test-qc.R:100:3
 2.   └─singleCellTK::plotSCEViolinColData(...)
 3.     └─base::lapply(...)
 4.       └─singleCellTK (local) FUN(X[[i]], ...)
 5.         └─singleCellTK:::.ggViolin(...)

[ FAIL 1 | WARN 48 | SKIP 0 | PASS 222 ]
Error:
! Test failures.
Execution halted

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

name	user	system	elapsed
MitoGenes	0.001	0.000	0.003
SEG	0.002	0.002	0.003
calcEffectSizes	0.177	0.003	0.182
combineSCE	0.701	0.003	0.705
computeZScore	0.218	0.014	0.235
convertSCEToSeurat	4.444	0.093	4.537
convertSeuratToSCE	0.332	0.011	0.344
dedupRowNames	0.054	0.000	0.054
detectCellOutlier	6.278	0.176	6.455
diffAbundanceFET	0.054	0.000	0.053
discreteColorPalette	0.006	0.000	0.005
distinctColors	0.002	0.000	0.002
downSampleCells	0.461	0.064	0.525
downSampleDepth	0.398	0.003	0.401
expData-ANY-character-method	0.124	0.001	0.125
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method	0.157	0.000	0.156
expData-set	0.146	0.001	0.146
expData	0.119	0.001	0.119
expDataNames-ANY-method	0.110	0.004	0.114
expDataNames	0.112	0.023	0.136
expDeleteDataTag	0.029	0.005	0.033
expSetDataTag	0.024	0.001	0.024
expTaggedData	0.025	0.000	0.024
exportSCE	0.020	0.001	0.022
exportSCEtoAnnData	0.089	0.010	0.100
exportSCEtoFlatFile	0.090	0.008	0.097
featureIndex	0.033	0.003	0.036
generateSimulatedData	0.077	0.009	0.085
getBiomarker	0.055	0.004	0.059
getDEGTopTable	0.625	0.027	0.652
getDiffAbundanceResults	0.046	0.000	0.045
getEnrichRResult	0.374	0.032	2.722
getFindMarkerTopTable	1.528	0.045	1.573
getMSigDBTable	0.002	0.001	0.004
getPathwayResultNames	0.020	0.003	0.023
getSampleSummaryStatsTable	0.194	0.000	0.194
getSoupX	0	0	0
getTSCANResults	0.905	0.011	0.916
getTopHVG	0.774	0.010	0.784
importAnnData	0.001	0.000	0.002
importBUStools	0.14	0.00	0.14
importCellRanger	0.687	0.009	0.696
importCellRangerV2Sample	0.133	0.000	0.132
importCellRangerV3Sample	0.255	0.003	0.258
importDropEst	1.168	0.007	1.175
importExampleData	9.762	0.400	10.600
importGeneSetsFromCollection	1.773	0.089	1.862
importGeneSetsFromGMT	0.06	0.00	0.06
importGeneSetsFromList	0.124	0.001	0.125
importGeneSetsFromMSigDB	44.695	0.411	45.108
importMitoGeneSet	0.054	0.003	0.057
importOptimus	0.001	0.001	0.002
importSEQC	0.150	0.019	0.169
importSTARsolo	0.166	0.011	0.177
iterateSimulations	0.192	0.021	0.213
listSampleSummaryStatsTables	0.266	0.029	0.296
mergeSCEColData	0.376	0.018	0.395
mouseBrainSubsetSCE	0.037	0.000	0.037
msigdb_table	0.001	0.000	0.001
plotBarcodeRankDropsResults	0.860	0.008	0.869
plotBarcodeRankScatter	0.835	0.013	0.848
plotBatchCorrCompare	12.894	0.190	13.266
plotBatchVariance	0.44	0.01	0.45
plotBcdsResults	5.679	0.096	5.854
plotBubble	0.746	0.004	0.750
plotClusterAbundance	1.296	0.028	1.324
plotCxdsResults	7.350	0.014	7.445
plotDEGHeatmap	2.027	0.009	2.036
plotDEGRegression	4.244	0.039	4.275
plotDEGViolin	6.680	0.140	6.814
plotDEGVolcano	0.914	0.030	0.945
plotDecontXResults	8.421	0.183	8.605
plotDimRed	0.263	0.005	0.268
plotDoubletFinderResults	40.107	0.285	40.471
plotEmptyDropsResults	6.634	0.036	6.671
plotEmptyDropsScatter	6.533	0.020	6.553
plotFindMarkerHeatmap	3.692	0.039	3.732
plotMASTThresholdGenes	1.219	0.014	1.234
plotPCA	0.357	0.000	0.358
plotPathway	0.679	0.003	0.682
plotRunPerCellQCResults	2.880	0.039	2.920
plotSCEBarAssayData	0.305	0.001	0.307
plotSCEBarColData	0.210	0.001	0.211
plotSCEBatchFeatureMean	0.368	0.001	0.368
plotSCEDensity	0.310	0.002	0.312
plotSCEDensityAssayData	0.308	0.002	0.311
plotSCEDensityColData	0.283	0.000	0.284
plotSCEDimReduceColData	0.706	0.002	0.708
plotSCEDimReduceFeatures	0.394	0.002	0.396
plotSCEHeatmap	0.391	0.002	0.394
plotSCEScatter	0.349	0.001	0.350
plotSCEViolin	0.397	0.001	0.398
plotSCEViolinAssayData	0.371	0.000	0.371
plotSCEViolinColData	0.347	0.000	0.346
plotScDblFinderResults	27.606	0.719	28.369
plotScanpyDotPlot	0.024	0.000	0.024
plotScanpyEmbedding	0.023	0.000	0.023
plotScanpyHVG	0.021	0.000	0.022
plotScanpyHeatmap	0.020	0.002	0.022
plotScanpyMarkerGenes	0.021	0.002	0.023
plotScanpyMarkerGenesDotPlot	0.022	0.000	0.022
plotScanpyMarkerGenesHeatmap	0.024	0.000	0.024
plotScanpyMarkerGenesMatrixPlot	0.023	0.000	0.023
plotScanpyMarkerGenesViolin	0.022	0.000	0.023
plotScanpyMatrixPlot	0.021	0.001	0.022
plotScanpyPCA	0.022	0.001	0.022
plotScanpyPCAGeneRanking	0.020	0.003	0.023
plotScanpyPCAVariance	0.021	0.001	0.023
plotScanpyViolin	0.023	0.000	0.022
plotScdsHybridResults	7.826	0.113	8.018
plotScrubletResults	0.023	0.001	0.024
plotSeuratElbow	0.021	0.001	0.022
plotSeuratHVG	0.022	0.000	0.022
plotSeuratJackStraw	0.022	0.000	0.021
plotSeuratReduction	0.022	0.000	0.022
plotSoupXResults	0	0	0
plotTSCANClusterDEG	5.150	0.006	5.158
plotTSCANClusterPseudo	1.475	0.006	1.481
plotTSCANDimReduceFeatures	1.392	0.004	1.396
plotTSCANPseudotimeGenes	1.707	0.002	1.708
plotTSCANPseudotimeHeatmap	1.385	0.003	1.388
plotTSCANResults	1.255	0.002	1.257
plotTSNE	0.385	0.001	0.386
plotTopHVG	0.682	0.004	0.686
plotUMAP	7.949	0.062	8.089
readSingleCellMatrix	0.006	0.000	0.005
reportCellQC	0.082	0.000	0.082
reportDropletQC	0.022	0.000	0.022
reportQCTool	0.082	0.000	0.082
retrieveSCEIndex	0.031	0.000	0.031
runBBKNN	0	0	0
runBarcodeRankDrops	0.224	0.000	0.225
runBcds	0.08	0.00	0.08
runCellQC	0.081	0.000	0.082
runClusterSummaryMetrics	0.371	0.001	0.372
runComBatSeq	0.440	0.004	0.444
runCxds	0.367	0.001	0.368
runCxdsBcdsHybrid	0.087	0.003	0.090
runDEAnalysis	0.379	0.000	0.379
runDecontX	7.363	0.065	7.428
runDimReduce	0.297	0.001	0.298
runDoubletFinder	37.826	0.086	37.914
runDropletQC	0.022	0.000	0.022
runEmptyDrops	6.248	0.012	6.260
runEnrichR	0.403	0.027	2.546
runFastMNN	1.680	0.008	1.688
runFeatureSelection	0.208	0.000	0.208
runFindMarker	1.408	0.013	1.422
runGSVA	0.836	0.027	0.864
runHarmony	0.038	0.001	0.038
runKMeans	0.170	0.001	0.171
runLimmaBC	0.077	0.000	0.076
runMNNCorrect	0.393	0.000	0.392
runModelGeneVar	0.289	0.008	0.296
runNormalization	2.436	0.085	2.521
runPerCellQC	0.32	0.00	0.32
runSCANORAMA	0.001	0.000	0.000
runSCMerge	0.003	0.001	0.004
runScDblFinder	17.642	0.466	18.061
runScanpyFindClusters	0.024	0.006	0.030
runScanpyFindHVG	0.021	0.000	0.022
runScanpyFindMarkers	0.020	0.001	0.021
runScanpyNormalizeData	0.094	0.000	0.094
runScanpyPCA	0.021	0.001	0.022
runScanpyScaleData	0.021	0.000	0.021
runScanpyTSNE	0.021	0.000	0.021
runScanpyUMAP	0.022	0.001	0.021
runScranSNN	0.274	0.003	0.277
runScrublet	0.021	0.001	0.022
runSeuratFindClusters	0.022	0.000	0.022
runSeuratFindHVG	0.447	0.000	0.446
runSeuratHeatmap	0.023	0.000	0.023
runSeuratICA	0.023	0.000	0.023
runSeuratJackStraw	0.023	0.001	0.023
runSeuratNormalizeData	0.022	0.000	0.021
runSeuratPCA	0.021	0.000	0.021
runSeuratSCTransform	29.325	0.252	29.581
runSeuratScaleData	0.022	0.000	0.022
runSeuratUMAP	0.022	0.000	0.022
runSingleR	0.037	0.000	0.036
runSoupX	0	0	0
runTSCAN	0.663	0.003	0.666
runTSCANClusterDEAnalysis	0.723	0.002	0.724
runTSCANDEG	0.722	0.000	0.722
runTSNE	0.728	0.014	0.741
runUMAP	7.647	0.117	7.844
runVAM	0.288	0.000	0.289
runZINBWaVE	0.004	0.001	0.004
sampleSummaryStats	0.15	0.00	0.15
scaterCPM	0.132	0.005	0.137
scaterPCA	0.427	0.001	0.428
scaterlogNormCounts	0.229	0.004	0.232
sce	0.021	0.000	0.021
sctkListGeneSetCollections	0.078	0.000	0.077
sctkPythonInstallConda	0.001	0.000	0.000
sctkPythonInstallVirtualEnv	0	0	0
selectSCTKConda	0.001	0.000	0.000
selectSCTKVirtualEnvironment	0	0	0
setRowNames	0.083	0.001	0.084
setSCTKDisplayRow	0.416	0.000	0.416
singleCellTK	0	0	0
subDiffEx	0.326	0.000	0.327
subsetSCECols	0.081	0.000	0.082
subsetSCERows	0.263	0.001	0.264
summarizeSCE	0.07	0.00	0.07
trimCounts	0.201	0.005	0.206