Multiple platform 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	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4814
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4603
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4547
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4553
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: 2.19.1

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_2.19.1.tar.gz

StartedAt: 2025-09-22 04:23:53 -0400 (Mon, 22 Sep 2025)

EndedAt: 2025-09-22 04:37:56 -0400 (Mon, 22 Sep 2025)

EllapsedTime: 842.7 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_2.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘2.19.1’
* 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 ... ERROR
Running examples in ‘singleCellTK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotPathway
> ### Title: Generate violin plots for pathway analysis results
> ### Aliases: plotPathway
> 
> ### ** Examples
> 
> data("scExample", package = "singleCellTK")
> sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
> sce <- scaterlogNormCounts(sce, assayName = "logcounts")
> gs1 <- rownames(sce)[seq(10)]
> gs2 <- rownames(sce)[seq(11,20)]
> gs <- list("geneset1" = gs1, "geneset2" = gs2)
> sce <- importGeneSetsFromList(inSCE = sce, geneSetList = gs,
+                               by = "rownames")
> sce <- runVAM(inSCE = sce, geneSetCollectionName = "GeneSetCollection",
+               useAssay = "logcounts")
Mon Sep 22 04:31:54 2025 ... Running VAM
gene.weights not specified, defaulting all weights to 1
Computing VAM distances for 2 gene sets, 195 cells and 200 genes.
Min set size: 10, median size: 10
> plotPathway(sce, "VAM_GeneSetCollection_CDF", "geneset1")
Error in S7::prop(x, "meta")[[i]] : subscript out of bounds
Calls: plotPathway -> plotSCEViolin -> [[ -> [[.ggplot2::gg
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
importGeneSetsFromMSigDB 47.412  0.674  48.087
plotDoubletFinderResults 41.255  0.346  41.683
plotBatchCorrCompare     13.384  0.145  13.710
importExampleData        12.254  0.558  13.269
plotBcdsResults          10.697  0.193   9.134
plotDecontXResults        8.550  0.068   8.619
plotCxdsResults           7.525  0.095   7.700
detectCellOutlier         6.854  0.202   7.057
plotEmptyDropsResults     6.619  0.016   6.634
plotEmptyDropsScatter     6.538  0.007   6.546
plotDEGViolin             5.571  0.051   5.597
* 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:
   3.     ├─plotlist[[1]]
   4.     └─ggplot2 (local) `[[.ggplot2::gg`(plotlist, 1)
  ── Error ('test-pathway.R:39:5'): Testing GSVA ─────────────────────────────────
  <subscriptOutOfBoundsError/error/condition>
  Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─singleCellTK::plotPathway(...) at test-pathway.R:39:5
   2.   └─singleCellTK::plotSCEViolin(...)
   3.     ├─plotlist[[1]]
   4.     └─ggplot2 (local) `[[.ggplot2::gg`(plotlist, 1)
  
  [ FAIL 2 | WARN 22 | SKIP 0 | PASS 223 ]
  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: 2 ERRORs, 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 ‘2.19.1’
** using staged installation
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (singleCellTK)

Tests output

singleCellTK.Rcheck/tests/spelling.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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 
  0.132   0.040   0.161

singleCellTK.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
[1]	train-logloss:0.452540 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.320237 
[3]	train-logloss:0.237326 
[4]	train-logloss:0.182355 
[5]	train-logloss:0.144099 
[6]	train-logloss:0.117553 
[7]	train-logloss:0.098814 
[8]	train-logloss:0.084978 
[9]	train-logloss:0.075063 
[10]	train-logloss:0.067483 
[11]	train-logloss:0.061861 
[12]	train-logloss:0.057362 
[13]	train-logloss:0.053725 
[14]	train-logloss:0.050620 
[15]	train-logloss:0.047937 
[16]	train-logloss:0.045355 
[17]	train-logloss:0.043608 
[18]	train-logloss:0.042678 
[1]	train-logloss:0.452932 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.320861 
[3]	train-logloss:0.238138 
[4]	train-logloss:0.183327 
[5]	train-logloss:0.145234 
[6]	train-logloss:0.118471 
[7]	train-logloss:0.099668 
[8]	train-logloss:0.085972 
[9]	train-logloss:0.076338 
[10]	train-logloss:0.068629 
[11]	train-logloss:0.062967 
[12]	train-logloss:0.057971 
[13]	train-logloss:0.053386 
[14]	train-logloss:0.050623 
[1]	train-logloss:0.453030 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321019 
[3]	train-logloss:0.238344 
[4]	train-logloss:0.183572 
[5]	train-logloss:0.145515 
[6]	train-logloss:0.118784 
[7]	train-logloss:0.100283 
[8]	train-logloss:0.086178 
[9]	train-logloss:0.076766 
[10]	train-logloss:0.069198 
[11]	train-logloss:0.063614 
[12]	train-logloss:0.059085 
[13]	train-logloss:0.055346 
[14]	train-logloss:0.052474 
[15]	train-logloss:0.049706 
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%
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...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

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

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

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

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

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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 2 | WARN 22 | SKIP 0 | PASS 223 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pathway.R:29:5'): Testing VAM ──────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─singleCellTK::plotPathway(...) at test-pathway.R:29:5
 2.   └─singleCellTK::plotSCEViolin(...)
 3.     ├─plotlist[[1]]
 4.     └─ggplot2 (local) `[[.ggplot2::gg`(plotlist, 1)
── Error ('test-pathway.R:39:5'): Testing GSVA ─────────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─singleCellTK::plotPathway(...) at test-pathway.R:39:5
 2.   └─singleCellTK::plotSCEViolin(...)
 3.     ├─plotlist[[1]]
 4.     └─ggplot2 (local) `[[.ggplot2::gg`(plotlist, 1)

[ FAIL 2 | WARN 22 | SKIP 0 | PASS 223 ]
Error: Test failures
Execution halted

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

name	user	system	elapsed
MitoGenes	0.002	0.001	0.002
SEG	0.002	0.000	0.003
calcEffectSizes	0.184	0.009	0.194
combineSCE	0.705	0.006	0.712
computeZScore	0.229	0.006	0.235
convertSCEToSeurat	4.368	0.101	4.468
convertSeuratToSCE	0.350	0.018	0.368
dedupRowNames	0.056	0.003	0.059
detectCellOutlier	6.854	0.202	7.057
diffAbundanceFET	0.062	0.000	0.062
discreteColorPalette	0.006	0.001	0.006
distinctColors	0.003	0.000	0.003
downSampleCells	0.504	0.066	0.571
downSampleDepth	0.423	0.001	0.424
expData-ANY-character-method	0.126	0.000	0.126
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method	0.166	0.000	0.167
expData-set	0.157	0.012	0.168
expData	0.130	0.009	0.140
expDataNames-ANY-method	0.115	0.011	0.126
expDataNames	0.110	0.008	0.119
expDeleteDataTag	0.032	0.000	0.033
expSetDataTag	0.024	0.000	0.023
expTaggedData	0.022	0.002	0.024
exportSCE	0.017	0.004	0.022
exportSCEtoAnnData	0.089	0.010	0.098
exportSCEtoFlatFile	0.090	0.008	0.098
featureIndex	0.035	0.000	0.035
generateSimulatedData	0.049	0.005	0.053
getBiomarker	0.058	0.001	0.059
getDEGTopTable	0.670	0.055	0.725
getDiffAbundanceResults	0.047	0.000	0.047
getEnrichRResult	0.449	0.022	3.290
getFindMarkerTopTable	1.653	0.027	1.680
getMSigDBTable	0.003	0.001	0.004
getPathwayResultNames	0.023	0.001	0.025
getSampleSummaryStatsTable	0.197	0.001	0.198
getSoupX	0	0	0
getTSCANResults	1.076	0.013	1.089
getTopHVG	0.832	0.012	0.844
importAnnData	0.002	0.000	0.001
importBUStools	0.144	0.001	0.145
importCellRanger	0.696	0.013	0.710
importCellRangerV2Sample	0.141	0.001	0.142
importCellRangerV3Sample	0.272	0.002	0.274
importDropEst	0.200	0.001	0.201
importExampleData	12.254	0.558	13.269
importGeneSetsFromCollection	2.042	0.026	2.068
importGeneSetsFromGMT	0.066	0.002	0.068
importGeneSetsFromList	0.136	0.001	0.138
importGeneSetsFromMSigDB	47.412	0.674	48.087
importMitoGeneSet	0.053	0.002	0.055
importOptimus	0.001	0.001	0.001
importSEQC	0.149	0.008	0.157
importSTARsolo	0.153	0.011	0.164
iterateSimulations	0.177	0.014	0.191
listSampleSummaryStatsTables	0.322	0.018	0.340
mergeSCEColData	0.321	0.004	0.325
mouseBrainSubsetSCE	0.034	0.001	0.035
msigdb_table	0.001	0.001	0.001
plotBarcodeRankDropsResults	0.892	0.009	0.902
plotBarcodeRankScatter	0.841	0.000	0.840
plotBatchCorrCompare	13.384	0.145	13.710
plotBatchVariance	0.428	0.000	0.428
plotBcdsResults	10.697	0.193	9.134
plotBubble	0.801	0.002	0.802
plotClusterAbundance	1.398	0.001	1.400
plotCxdsResults	7.525	0.095	7.700
plotDEGHeatmap	2.013	0.006	2.020
plotDEGRegression	4.345	0.018	4.337
plotDEGViolin	5.571	0.051	5.597
plotDEGVolcano	0.896	0.001	0.898
plotDecontXResults	8.550	0.068	8.619
plotDimRed	0.326	0.000	0.326
plotDoubletFinderResults	41.255	0.346	41.683
plotEmptyDropsResults	6.619	0.016	6.634
plotEmptyDropsScatter	6.538	0.007	6.546
plotFindMarkerHeatmap	3.688	0.005	3.693
plotMASTThresholdGenes	1.251	0.005	1.256
plotPCA	0.352	0.001	0.353