Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-07 12:08 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2015/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.19.2  (landing page)
Joshua David Campbell
Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 Oct 2025)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: devel
git_last_commit: 238aed05
git_last_commit_date: 2025-09-26 08:22:06 -0400 (Fri, 26 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for singleCellTK on taishan

To the developers/maintainers of the singleCellTK package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singleCellTK.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: singleCellTK
Version: 2.19.2
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_2.19.2.tar.gz
StartedAt: 2025-10-07 12:13:44 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 12:34:24 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 1239.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: singleCellTK.Rcheck
Warnings: NA

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_2.19.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/singleCellTK.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.19.2’
* 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 ... ERROR
Running examples in ‘singleCellTK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runGSVA
> ### Title: Run GSVA analysis on a SingleCellExperiment object
> ### Aliases: runGSVA
> 
> ### ** 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 <- runGSVA(inSCE = sce, 
+                geneSetCollectionName = "GeneSetCollection", 
+                useAssay = "logcounts")
Tue Oct  7 12:27:01 2025 ... Running GSVA
ℹ GSVA version 2.3.3
ℹ Calculating GSVA ranks
ℹ kcdf='auto' (default)
ℹ GSVA dense (classical) algorithm
ℹ Row-wise ECDF estimation with Gaussian kernels
ℹ Calculating GSVA column ranks
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 't': ✖ No identifiers in the gene sets could be matched to the identifiers in
  the expression data.
Calls: runGSVA ... <Anonymous> -> signal_abort -> signalCondition -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
importGeneSetsFromMSigDB 51.512  0.789  52.402
plotDoubletFinderResults 45.465  2.136  47.854
runDoubletFinder         36.649  0.289  37.042
plotScDblFinderResults   34.831  0.619  35.802
importExampleData        15.789  1.509  23.006
plotBatchCorrCompare     15.004  0.180  15.545
plotScdsHybridResults    12.500  0.117  12.673
plotBcdsResults          11.264  0.379  11.025
plotDecontXResults       10.698  0.319  11.138
plotCxdsResults           8.749  0.669   9.563
plotDEGViolin             8.656  0.271   8.954
plotUMAP                  7.943  0.151   8.127
runDecontX                7.765  0.041   7.825
plotTSCANClusterDEG       7.230  0.044   7.298
plotDEGRegression         6.881  0.259   7.314
detectCellOutlier         6.237  0.020   6.279
plotEmptyDropsResults     5.889  0.093   6.001
plotFindMarkerHeatmap     5.668  0.180   5.861
plotEmptyDropsScatter     5.710  0.072   5.790
convertSCEToSeurat        5.632  0.092   5.752
runEmptyDrops             5.247  0.008   5.264
getEnrichRResult          0.441  0.212   9.673
runEnrichR                0.391  0.016  27.043
* 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:
    5. │   └─GSVA (local) .local(param, ...)
    6. │     ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
    7. │     └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
    8. │       └─GSVA (local) .local(param, ...)
    9. │         └─GSVA:::.filterAndMapGeneSets(...)
   10. │           └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
   11. │             └─cli::cli_abort(c(x = msg))
   12. │               └─rlang::abort(...)
   13. │                 └─rlang:::signal_abort(cnd, .file)
   14. │                   └─base::signalCondition(cnd)
   15. └─base (local) `<fn>`(`<rlng_rrr>`)
  
  [ FAIL 2 | WARN 22 | SKIP 0 | PASS 222 ]
  Error: Test failures
  Execution halted
* 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: 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/R/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘singleCellTK’ ...
** this is package ‘singleCellTK’ version ‘2.19.2’
** using staged installation
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (singleCellTK)

Tests output

singleCellTK.Rcheck/tests/spelling.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

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

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

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.184   0.034   0.204 

singleCellTK.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

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

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

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

Attaching package: 'MatrixGenerics'

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

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

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

Attaching package: 'generics'

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

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


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

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

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

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

Attaching package: 'Matrix'

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

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep


Attaching package: 'singleCellTK'

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

    plotPCA

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

  |                                                                            
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  |                                                                            
  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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:0.452573 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.320290 
[3]	train-logloss:0.237363 
[4]	train-logloss:0.182378 
[5]	train-logloss:0.144113 
[6]	train-logloss:0.117560 
[7]	train-logloss:0.098812 
[8]	train-logloss:0.084977 
[9]	train-logloss:0.075059 
[10]	train-logloss:0.067480 
[11]	train-logloss:0.061855 
[12]	train-logloss:0.057358 
[13]	train-logloss:0.053969 
[14]	train-logloss:0.050909 
[15]	train-logloss:0.047615 
[16]	train-logloss:0.045564 
[17]	train-logloss:0.043868 
[1]	train-logloss:0.453064 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321072 
[3]	train-logloss:0.238210 
[4]	train-logloss:0.183469 
[5]	train-logloss:0.145239 
[6]	train-logloss:0.118860 
[7]	train-logloss:0.100304 
[8]	train-logloss:0.086606 
[9]	train-logloss:0.076012 
[10]	train-logloss:0.068021 
[11]	train-logloss:0.062325 
[12]	train-logloss:0.057942 
[13]	train-logloss:0.054289 
[14]	train-logloss:0.051302 
[15]	train-logloss:0.048796 
[1]	train-logloss:0.453064 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321072 
[3]	train-logloss:0.238210 
[4]	train-logloss:0.183469 
[5]	train-logloss:0.145239 
[6]	train-logloss:0.118860 
[7]	train-logloss:0.100304 
[8]	train-logloss:0.086606 
[9]	train-logloss:0.076012 
[10]	train-logloss:0.068021 
[11]	train-logloss:0.062325 
[12]	train-logloss:0.057942 
[13]	train-logloss:0.054289 
[14]	train-logloss:0.051302 
[15]	train-logloss:0.048796 
[16]	train-logloss:0.046452 
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%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 22 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 22 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
385.049   7.799 427.707 

singleCellTK.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

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

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

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

Attaching package: 'MatrixGenerics'

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

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

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

Attaching package: 'generics'

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

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


Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

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

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

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

Attaching package: 'Matrix'

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

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep


Attaching package: 'singleCellTK'

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

    plotPCA

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

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

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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Uploading data to Enrichr... Done.
  Querying HDSigDB_Human_2021... Done.
Parsing results... Done.
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
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:0.452573 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.320290 
[3]	train-logloss:0.237363 
[4]	train-logloss:0.182378 
[5]	train-logloss:0.144113 
[6]	train-logloss:0.117560 
[7]	train-logloss:0.098812 
[8]	train-logloss:0.084977 
[9]	train-logloss:0.075059 
[10]	train-logloss:0.067480 
[11]	train-logloss:0.061855 
[12]	train-logloss:0.057358 
[13]	train-logloss:0.053969 
[14]	train-logloss:0.050909 
[15]	train-logloss:0.047615 
[16]	train-logloss:0.045564 
[17]	train-logloss:0.043868 
[1]	train-logloss:0.453064 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321072 
[3]	train-logloss:0.238210 
[4]	train-logloss:0.183469 
[5]	train-logloss:0.145239 
[6]	train-logloss:0.118860 
[7]	train-logloss:0.100304 
[8]	train-logloss:0.086606 
[9]	train-logloss:0.076012 
[10]	train-logloss:0.068021 
[11]	train-logloss:0.062325 
[12]	train-logloss:0.057942 
[13]	train-logloss:0.054289 
[14]	train-logloss:0.051302 
[15]	train-logloss:0.048796 
[1]	train-logloss:0.453064 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321072 
[3]	train-logloss:0.238210 
[4]	train-logloss:0.183469 
[5]	train-logloss:0.145239 
[6]	train-logloss:0.118860 
[7]	train-logloss:0.100304 
[8]	train-logloss:0.086606 
[9]	train-logloss:0.076012 
[10]	train-logloss:0.068021 
[11]	train-logloss:0.062325 
[12]	train-logloss:0.057942 
[13]	train-logloss:0.054289 
[14]	train-logloss:0.051302 
[15]	train-logloss:0.048796 
[16]	train-logloss:0.046452 
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%
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 2 | WARN 22 | SKIP 0 | PASS 222 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-misc.R:64:3'): Testing runGSVA ─────────────────────────────────
Error in `(function (cond) 
.Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c(x = "No identifiers in the gene sets could be matched to the identifiers in the expression data."), 
    trace = structure(list(call = list(runGSVA(inSCE = sce, geneSetCollectionName = "H", 
        useAssay = "logcounts"), t(GSVA::gsva(gsvaPar)), GSVA::gsva(gsvaPar), 
        GSVA::gsva(gsvaPar), .local(param, ...), gsvaScores(param = rankspar, 
            verbose = verbose, BPPARAM = BPPARAM), gsvaScores(param = rankspar, 
            verbose = verbose, BPPARAM = BPPARAM), .local(param, 
            ...), .filterAndMapGeneSets(param = param, filteredDataMatrix = filteredDataMatrix, 
            verbose = verbose), .mapGeneSetsToFeatures(geneSets, 
            rownames(filteredDataMatrix)), cli_abort(c(x = msg)), 
        rlang::abort(message, ..., call = call, use_cli_format = TRUE, 
            .frame = .frame)), parent = c(0L, 1L, 1L, 1L, 4L, 
    5L, 5L, 7L, 8L, 9L, 10L, 11L), visible = c(TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE), 
        namespace = c("singleCellTK", "base", "GSVA", "GSVA", 
        "GSVA", "GSVA", "GSVA", "GSVA", "GSVA", "GSVA", "cli", 
        "rlang"), scope = c("::", "::", "::", "::", "local", 
        "::", "::", "local", ":::", ":::", "::", "::"), error_frame = c(FALSE, 
        FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, 
        TRUE, FALSE, FALSE)), row.names = c(NA, -12L), version = 2L, class = c("rlang_trace", 
    "rlib_trace", "tbl", "data.frame")), parent = NULL, rlang = list(
        inherit = TRUE), call = .mapGeneSetsToFeatures(geneSets, 
        rownames(filteredDataMatrix)), use_cli_format = TRUE), class = c("rlang_error", 
"error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 't': ✖ No identifiers in the gene sets could be matched to the identifiers in
  the expression data.
Backtrace:
     ▆
  1. ├─singleCellTK::runGSVA(...) at test-misc.R:64:3
  2. │ ├─base::t(GSVA::gsva(gsvaPar))
  3. │ ├─GSVA::gsva(gsvaPar)
  4. │ └─GSVA::gsva(gsvaPar)
  5. │   └─GSVA (local) .local(param, ...)
  6. │     ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  7. │     └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  8. │       └─GSVA (local) .local(param, ...)
  9. │         └─GSVA:::.filterAndMapGeneSets(...)
 10. │           └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
 11. │             └─cli::cli_abort(c(x = msg))
 12. │               └─rlang::abort(...)
 13. │                 └─rlang:::signal_abort(cnd, .file)
 14. │                   └─base::signalCondition(cnd)
 15. └─base (local) `<fn>`(`<rlng_rrr>`)
── Error ('test-pathway.R:36:5'): Testing GSVA ─────────────────────────────────
Error in `(function (cond) 
.Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = c(x = "No identifiers in the gene sets could be matched to the identifiers in the expression data."), 
    trace = structure(list(call = list(runGSVA(sce, geneSetCollectionName = "GeneSetCollection", 
        useAssay = "logcounts"), t(GSVA::gsva(gsvaPar)), GSVA::gsva(gsvaPar), 
        GSVA::gsva(gsvaPar), .local(param, ...), gsvaScores(param = rankspar, 
            verbose = verbose, BPPARAM = BPPARAM), gsvaScores(param = rankspar, 
            verbose = verbose, BPPARAM = BPPARAM), .local(param, 
            ...), .filterAndMapGeneSets(param = param, filteredDataMatrix = filteredDataMatrix, 
            verbose = verbose), .mapGeneSetsToFeatures(geneSets, 
            rownames(filteredDataMatrix)), cli_abort(c(x = msg)), 
        rlang::abort(message, ..., call = call, use_cli_format = TRUE, 
            .frame = .frame)), parent = c(0L, 1L, 1L, 1L, 4L, 
    5L, 5L, 7L, 8L, 9L, 10L, 11L), visible = c(TRUE, TRUE, TRUE, 
    TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE), 
        namespace = c("singleCellTK", "base", "GSVA", "GSVA", 
        "GSVA", "GSVA", "GSVA", "GSVA", "GSVA", "GSVA", "cli", 
        "rlang"), scope = c("::", "::", "::", "::", "local", 
        "::", "::", "local", ":::", ":::", "::", "::"), error_frame = c(FALSE, 
        FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, 
        TRUE, FALSE, FALSE)), row.names = c(NA, -12L), version = 2L, class = c("rlang_trace", 
    "rlib_trace", "tbl", "data.frame")), parent = NULL, rlang = list(
        inherit = TRUE), call = .mapGeneSetsToFeatures(geneSets, 
        rownames(filteredDataMatrix)), use_cli_format = TRUE), class = c("rlang_error", 
"error", "condition")))`: error in evaluating the argument 'x' in selecting a method for function 't': ✖ No identifiers in the gene sets could be matched to the identifiers in
  the expression data.
Backtrace:
     ▆
  1. ├─singleCellTK::runGSVA(...) at test-pathway.R:36:5
  2. │ ├─base::t(GSVA::gsva(gsvaPar))
  3. │ ├─GSVA::gsva(gsvaPar)
  4. │ └─GSVA::gsva(gsvaPar)
  5. │   └─GSVA (local) .local(param, ...)
  6. │     ├─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  7. │     └─GSVA::gsvaScores(param = rankspar, verbose = verbose, BPPARAM = BPPARAM)
  8. │       └─GSVA (local) .local(param, ...)
  9. │         └─GSVA:::.filterAndMapGeneSets(...)
 10. │           └─GSVA:::.mapGeneSetsToFeatures(geneSets, rownames(filteredDataMatrix))
 11. │             └─cli::cli_abort(c(x = msg))
 12. │               └─rlang::abort(...)
 13. │                 └─rlang:::signal_abort(cnd, .file)
 14. │                   └─base::signalCondition(cnd)
 15. └─base (local) `<fn>`(`<rlng_rrr>`)

[ FAIL 2 | WARN 22 | SKIP 0 | PASS 222 ]
Error: Test failures
Execution halted

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0030.0000.003
SEG0.0020.0000.003
calcEffectSizes0.2830.0000.284
combineSCE1.0270.0081.039
computeZScore0.2670.0000.268
convertSCEToSeurat5.6320.0925.752
convertSeuratToSCE0.4760.0040.481
dedupRowNames0.0800.0000.082
detectCellOutlier6.2370.0206.279
diffAbundanceFET0.0630.0000.064
discreteColorPalette0.0080.0000.008
distinctColors0.0030.0000.003
downSampleCells0.7130.0670.783
downSampleDepth0.5870.0050.592
expData-ANY-character-method0.1680.0000.168
expData-set-ANY-character-CharacterOrNullOrMissing-logical-method0.2140.0030.218
expData-set0.2040.0000.204
expData0.1660.0040.170
expDataNames-ANY-method0.1560.0000.156
expDataNames0.1530.0030.158
expDeleteDataTag0.0390.0000.039
expSetDataTag0.0240.0040.028
expTaggedData0.0280.0000.028
exportSCE0.0250.0000.026
exportSCEtoAnnData0.0780.0000.079
exportSCEtoFlatFile0.0740.0040.079
featureIndex0.0390.0040.043
generateSimulatedData0.0610.0040.065
getBiomarker0.0700.0040.074
getDEGTopTable0.9830.0201.010
getDiffAbundanceResults0.0570.0000.058
getEnrichRResult0.4410.2129.673
getFindMarkerTopTable2.1230.7672.899
getMSigDBTable0.0040.0000.004
getPathwayResultNames0.0270.0000.028
getSampleSummaryStatsTable0.2420.0200.264
getSoupX0.0000.0000.001
getTSCANResults1.4470.1841.637
getTopHVG1.1310.1071.242
importAnnData0.0020.0000.002
importBUStools0.1890.0320.224
importCellRanger1.0730.0591.141
importCellRangerV2Sample0.2260.0010.228
importCellRangerV3Sample0.3880.0270.416
importDropEst0.2770.0160.295
importExampleData15.789 1.50923.006
importGeneSetsFromCollection2.1400.0922.237
importGeneSetsFromGMT0.0890.0040.093
importGeneSetsFromList0.1960.0000.196
importGeneSetsFromMSigDB51.512 0.78952.402
importMitoGeneSet0.0740.0000.075
importOptimus0.0020.0000.002
importSEQC0.2110.0120.226
importSTARsolo0.1960.0280.226
iterateSimulations0.2540.0160.271
listSampleSummaryStatsTables0.4280.0200.451
mergeSCEColData0.5040.0160.522
mouseBrainSubsetSCE0.0410.0000.040
msigdb_table0.0000.0010.002
plotBarcodeRankDropsResults1.2730.0251.302
plotBarcodeRankScatter1.2830.0001.287
plotBatchCorrCompare15.004 0.18015.545
plotBatchVariance0.6800.0040.685
plotBcdsResults11.264 0.37911.025
plotBubble1.2360.0841.324
plotClusterAbundance2.2950.1752.477
plotCxdsResults8.7490.6699.563
plotDEGHeatmap3.1500.0763.301
plotDEGRegression6.8810.2597.314
plotDEGViolin8.6560.2718.954
plotDEGVolcano1.2960.0401.338
plotDecontXResults10.698 0.31911.138
plotDimRed0.4860.0150.504
plotDoubletFinderResults45.465 2.13647.854
plotEmptyDropsResults5.8890.0936.001
plotEmptyDropsScatter5.7100.0725.790
plotFindMarkerHeatmap5.6680.1805.861
plotMASTThresholdGenes1.9100.0401.954
plotPCA0.5210.0120.535
plotPathway0.9540.0080.966
plotRunPerCellQCResults4.8220.1154.949
plotSCEBarAssayData0.5020.0310.535
plotSCEBarColData0.3340.0000.334
plotSCEBatchFeatureMean0.6090.0200.631
plotSCEDensity0.4850.0040.489
plotSCEDensityAssayData0.4870.0120.500
plotSCEDensityColData0.4440.0080.453
plotSCEDimReduceColData1.1860.0041.197
plotSCEDimReduceFeatures0.5800.0040.585
plotSCEHeatmap0.6160.0080.626
plotSCEScatter2.2400.1882.433
plotSCEViolin0.5490.0040.553
plotSCEViolinAssayData0.6140.0080.625
plotSCEViolinColData0.6240.0200.645
plotScDblFinderResults34.831 0.61935.802
plotScanpyDotPlot0.0220.0030.025
plotScanpyEmbedding0.0250.0000.025
plotScanpyHVG0.0220.0030.026
plotScanpyHeatmap0.0250.0000.026
plotScanpyMarkerGenes0.0270.0000.027
plotScanpyMarkerGenesDotPlot0.0290.0000.029
plotScanpyMarkerGenesHeatmap0.0270.0000.026
plotScanpyMarkerGenesMatrixPlot0.0260.0000.027
plotScanpyMarkerGenesViolin0.0280.0000.028
plotScanpyMatrixPlot0.0280.0000.028
plotScanpyPCA0.0240.0040.028
plotScanpyPCAGeneRanking0.0240.0000.024
plotScanpyPCAVariance0.0240.0000.025
plotScanpyViolin0.0250.0000.025
plotScdsHybridResults12.500 0.11712.673
plotScrubletResults0.0240.0000.024
plotSeuratElbow0.0230.0000.022
plotSeuratHVG0.0220.0000.023
plotSeuratJackStraw0.0230.0000.022
plotSeuratReduction0.0220.0000.023
plotSoupXResults000
plotTSCANClusterDEG7.2300.0447.298
plotTSCANClusterPseudo1.9460.0081.960
plotTSCANDimReduceFeatures2.0790.0282.114
plotTSCANPseudotimeGenes2.5020.0122.524
plotTSCANPseudotimeHeatmap1.9470.0001.953
plotTSCANResults1.9430.0211.970
plotTSNE0.5690.0080.579
plotTopHVG0.9030.0000.906
plotUMAP7.9430.1518.127
readSingleCellMatrix0.0070.0000.007
reportCellQC0.1080.0010.108
reportDropletQC0.0240.0000.025
reportQCTool0.1110.0000.111
retrieveSCEIndex0.0310.0040.034
runBBKNN000
runBarcodeRankDrops0.3170.0000.317
runBcds3.1660.0873.216
runCellQC0.1050.0000.106
runClusterSummaryMetrics0.5110.0040.515
runComBatSeq0.6430.0120.658
runCxds0.4140.0040.419
runCxdsBcdsHybrid2.7740.1052.466
runDEAnalysis0.6240.0200.646
runDecontX7.7650.0417.825
runDimReduce0.3800.0040.386
runDoubletFinder36.649 0.28937.042
runDropletQC0.0270.0000.028
runEmptyDrops5.2470.0085.264
runEnrichR 0.391 0.01627.043
runFastMNN2.4510.0082.487
runFeatureSelection0.3260.0000.327
runFindMarker2.0910.0162.113