| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-20 11:32 -0400 (Wed, 20 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 2081/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singleCellTK 2.22.0 (landing page) Joshua David Campbell
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| See other builds for singleCellTK in R Universe. | ||||||||||||||
|
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. |
| Package: singleCellTK |
| Version: 2.22.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings singleCellTK_2.22.0.tar.gz |
| StartedAt: 2026-05-20 05:06:09 -0400 (Wed, 20 May 2026) |
| EndedAt: 2026-05-20 05:23:52 -0400 (Wed, 20 May 2026) |
| EllapsedTime: 1062.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: singleCellTK.Rcheck |
| Warnings: 3 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings singleCellTK_2.22.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/singleCellTK.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-20 09:06:10 UTC
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.22.0’
* 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 5.6Mb
sub-directories of 1Mb or more:
R 1.0Mb
shiny 2.3Mb
* 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 ... WARNING
Missing or unexported object: 'harmony::HarmonyMatrix'
* 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 ... WARNING
Missing link(s) in Rd file 'runHarmony.Rd':
‘[harmony]{HarmonyMatrix}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
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 ... WARNING
Found the following significant warnings:
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'pairwiseWilcox' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'sumCountsAcrossCells' is deprecated.
Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Warning in fitTrendVar(fm, fv, ...) : 'fitTrendVar' is deprecated.
Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runDoubletFinder 35.591 0.874 37.944
plotDoubletFinderResults 34.382 0.612 34.995
plotScDblFinderResults 30.836 0.979 28.735
runSeuratSCTransform 30.382 0.462 30.847
runScDblFinder 17.603 0.809 15.383
importExampleData 10.614 1.219 72.002
plotBatchCorrCompare 10.929 0.609 11.541
plotScdsHybridResults 9.301 0.526 9.223
plotBcdsResults 8.104 0.472 7.957
plotDecontXResults 7.807 0.283 8.091
plotCxdsResults 6.741 0.250 6.992
runUMAP 6.965 0.013 6.979
runDecontX 6.699 0.246 6.948
plotEmptyDropsResults 6.666 0.065 6.731
plotUMAP 6.309 0.397 6.708
plotEmptyDropsScatter 6.645 0.043 6.688
runEmptyDrops 6.317 0.016 6.333
detectCellOutlier 6.191 0.132 6.327
convertSCEToSeurat 4.926 0.304 5.231
plotDEGViolin 4.983 0.098 5.075
plotTSCANClusterDEG 4.881 0.195 5.076
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.
singleCellTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL singleCellTK ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘singleCellTK’ ... ** this is package ‘singleCellTK’ version ‘2.22.0’ ** 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)
singleCellTK.Rcheck/tests/spelling.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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
0.145 0.049 0.181
singleCellTK.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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| | 0%
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|======================================================================| 100%
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
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| | 0%
|
|======================================================================| 100%
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Uploading data to Enrichr... Done.
Querying HDSigDB_Human_2021... Done.
Parsing results... Done.
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene means
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
[05:21:35] WARNING: src/learner.cc:782:
Parameters: { "nthreads" } are not used.
[05:21:36] WARNING: src/learner.cc:782:
Parameters: { "nthreads" } are not used.
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 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...
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.8351
Number of communities: 7
Elapsed time: 0 seconds
Using method 'umap'
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 84 | SKIP 0 | PASS 225 ]
[ FAIL 0 | WARN 84 | SKIP 0 | PASS 225 ]
>
> proc.time()
user system elapsed
289.972 10.488 300.021
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| MitoGenes | 0.001 | 0.001 | 0.003 | |
| SEG | 0.002 | 0.001 | 0.003 | |
| calcEffectSizes | 0.153 | 0.002 | 0.155 | |
| combineSCE | 0.753 | 0.093 | 0.847 | |
| computeZScore | 0.292 | 0.013 | 0.305 | |
| convertSCEToSeurat | 4.926 | 0.304 | 5.231 | |
| convertSeuratToSCE | 0.32 | 0.00 | 0.32 | |
| dedupRowNames | 0.059 | 0.001 | 0.061 | |
| detectCellOutlier | 6.191 | 0.132 | 6.327 | |
| diffAbundanceFET | 0.054 | 0.003 | 0.058 | |
| discreteColorPalette | 0.006 | 0.000 | 0.006 | |
| distinctColors | 0.003 | 0.000 | 0.002 | |
| downSampleCells | 0.524 | 0.036 | 0.560 | |
| downSampleDepth | 0.466 | 0.011 | 0.478 | |
| expData-ANY-character-method | 0.136 | 0.000 | 0.136 | |
| expData-set-ANY-character-CharacterOrNullOrMissing-logical-method | 0.174 | 0.003 | 0.177 | |
| expData-set | 0.163 | 0.007 | 0.170 | |
| expData | 0.126 | 0.002 | 0.129 | |
| expDataNames-ANY-method | 0.118 | 0.003 | 0.122 | |
| expDataNames | 0.115 | 0.000 | 0.114 | |
| expDeleteDataTag | 0.031 | 0.001 | 0.033 | |
| expSetDataTag | 0.023 | 0.001 | 0.023 | |
| expTaggedData | 0.024 | 0.001 | 0.024 | |
| exportSCE | 0.021 | 0.000 | 0.021 | |
| exportSCEtoAnnData | 0.092 | 0.005 | 0.097 | |
| exportSCEtoFlatFile | 0.087 | 0.009 | 0.095 | |
| featureIndex | 0.036 | 0.000 | 0.035 | |
| generateSimulatedData | 0.049 | 0.000 | 0.050 | |
| getBiomarker | 0.058 | 0.001 | 0.059 | |
| getDEGTopTable | 0.688 | 0.078 | 0.767 | |
| getDiffAbundanceResults | 0.048 | 0.002 | 0.049 | |
| getEnrichRResult | 0.614 | 0.054 | 3.094 | |
| getFindMarkerTopTable | 1.653 | 0.097 | 1.750 | |
| getMSigDBTable | 0.002 | 0.002 | 0.005 | |
| getPathwayResultNames | 0.021 | 0.001 | 0.022 | |
| getSampleSummaryStatsTable | 0.273 | 0.026 | 0.299 | |
| getSoupX | 0 | 0 | 0 | |
| getTSCANResults | 1.162 | 0.111 | 1.273 | |
| getTopHVG | 0.728 | 0.052 | 0.780 | |
| importAnnData | 0.002 | 0.000 | 0.002 | |
| importBUStools | 0.153 | 0.002 | 0.155 | |
| importCellRanger | 0.822 | 0.092 | 0.916 | |
| importCellRangerV2Sample | 0.145 | 0.001 | 0.146 | |
| importCellRangerV3Sample | 0.298 | 0.013 | 0.311 | |
| importDropEst | 0.194 | 0.004 | 0.199 | |
| importExampleData | 10.614 | 1.219 | 72.002 | |
| importGeneSetsFromCollection | 0.071 | 0.001 | 0.072 | |
| importGeneSetsFromGMT | 0.056 | 0.003 | 0.059 | |
| importGeneSetsFromList | 0.112 | 0.002 | 0.114 | |
| importGeneSetsFromMSigDB | 2.094 | 0.175 | 2.269 | |
| importMitoGeneSet | 0.049 | 0.002 | 0.051 | |
| importOptimus | 0.001 | 0.000 | 0.001 | |
| importSEQC | 0.104 | 0.001 | 0.106 | |
| importSTARsolo | 0.129 | 0.002 | 0.131 | |
| iterateSimulations | 0.154 | 0.006 | 0.159 | |
| listSampleSummaryStatsTables | 0.267 | 0.003 | 0.269 | |
| mergeSCEColData | 0.309 | 0.004 | 0.313 | |
| mouseBrainSubsetSCE | 0.033 | 0.001 | 0.034 | |
| msigdb_table | 0.000 | 0.001 | 0.001 | |
| plotBarcodeRankDropsResults | 0.809 | 0.025 | 0.834 | |
| plotBarcodeRankScatter | 0.764 | 0.030 | 0.794 | |
| plotBatchCorrCompare | 10.929 | 0.609 | 11.541 | |
| plotBatchVariance | 0.411 | 0.095 | 0.508 | |
| plotBcdsResults | 8.104 | 0.472 | 7.957 | |
| plotBubble | 0.772 | 0.007 | 0.779 | |
| plotClusterAbundance | 1.281 | 0.020 | 1.301 | |
| plotCxdsResults | 6.741 | 0.250 | 6.992 | |
| plotDEGHeatmap | 2.018 | 0.104 | 2.121 | |
| plotDEGRegression | 4.107 | 0.040 | 4.140 | |
| plotDEGViolin | 4.983 | 0.098 | 5.075 | |
| plotDEGVolcano | 0.881 | 0.012 | 0.893 | |
| plotDecontXResults | 7.807 | 0.283 | 8.091 | |
| plotDimRed | 0.253 | 0.007 | 0.260 | |
| plotDoubletFinderResults | 34.382 | 0.612 | 34.995 | |
| plotEmptyDropsResults | 6.666 | 0.065 | 6.731 | |
| plotEmptyDropsScatter | 6.645 | 0.043 | 6.688 | |
| plotFindMarkerHeatmap | 3.719 | 0.106 | 3.825 | |
| plotMASTThresholdGenes | 1.202 | 0.010 | 1.213 | |
| plotPCA | 0.371 | 0.001 | 0.372 | |
| plotPathway | 0.644 | 0.005 | 0.649 | |
| plotRunPerCellQCResults | 2.891 | 0.032 | 2.923 | |
| plotSCEBarAssayData | 0.261 | 0.001 | 0.261 | |
| plotSCEBarColData | 0.218 | 0.002 | 0.220 | |
| plotSCEBatchFeatureMean | 0.377 | 0.001 | 0.379 | |
| plotSCEDensity | 0.303 | 0.000 | 0.304 | |
| plotSCEDensityAssayData | 0.281 | 0.001 | 0.281 | |
| plotSCEDensityColData | 0.286 | 0.002 | 0.288 | |
| plotSCEDimReduceColData | 0.749 | 0.024 | 0.773 | |
| plotSCEDimReduceFeatures | 0.372 | 0.001 | 0.374 | |
| plotSCEHeatmap | 0.453 | 0.010 | 0.463 | |
| plotSCEScatter | 0.352 | 0.003 | 0.355 | |
| plotSCEViolin | 0.361 | 0.002 | 0.363 | |
| plotSCEViolinAssayData | 0.378 | 0.002 | 0.380 | |
| plotSCEViolinColData | 0.388 | 0.000 | 0.389 | |
| plotScDblFinderResults | 30.836 | 0.979 | 28.735 | |
| plotScanpyDotPlot | 0.021 | 0.002 | 0.022 | |
| plotScanpyEmbedding | 0.022 | 0.000 | 0.022 | |
| plotScanpyHVG | 0.022 | 0.000 | 0.022 | |
| plotScanpyHeatmap | 0.022 | 0.000 | 0.022 | |
| plotScanpyMarkerGenes | 0.022 | 0.000 | 0.022 | |
| plotScanpyMarkerGenesDotPlot | 0.023 | 0.000 | 0.022 | |
| plotScanpyMarkerGenesHeatmap | 0.021 | 0.001 | 0.022 | |
| plotScanpyMarkerGenesMatrixPlot | 0.022 | 0.000 | 0.022 | |
| plotScanpyMarkerGenesViolin | 0.022 | 0.001 | 0.022 | |
| plotScanpyMatrixPlot | 0.021 | 0.001 | 0.022 | |
| plotScanpyPCA | 0.022 | 0.000 | 0.022 | |
| plotScanpyPCAGeneRanking | 0.021 | 0.000 | 0.022 | |
| plotScanpyPCAVariance | 0.021 | 0.001 | 0.022 | |
| plotScanpyViolin | 0.021 | 0.001 | 0.022 | |
| plotScdsHybridResults | 9.301 | 0.526 | 9.223 | |
| plotScrubletResults | 0.021 | 0.001 | 0.022 | |
| plotSeuratElbow | 0.020 | 0.001 | 0.021 | |
| plotSeuratHVG | 0.019 | 0.002 | 0.022 | |
| plotSeuratJackStraw | 0.021 | 0.001 | 0.021 | |
| plotSeuratReduction | 0.022 | 0.000 | 0.022 | |
| plotSoupXResults | 0.001 | 0.000 | 0.000 | |
| plotTSCANClusterDEG | 4.881 | 0.195 | 5.076 | |
| plotTSCANClusterPseudo | 1.379 | 0.068 | 1.448 | |
| plotTSCANDimReduceFeatures | 1.352 | 0.027 | 1.379 | |
| plotTSCANPseudotimeGenes | 1.654 | 0.093 | 1.748 | |
| plotTSCANPseudotimeHeatmap | 1.303 | 0.076 | 1.379 | |
| plotTSCANResults | 1.216 | 0.063 | 1.280 | |
| plotTSNE | 0.397 | 0.002 | 0.399 | |
| plotTopHVG | 0.612 | 0.008 | 0.621 | |
| plotUMAP | 6.309 | 0.397 | 6.708 | |
| readSingleCellMatrix | 0.004 | 0.001 | 0.005 | |
| reportCellQC | 0.079 | 0.002 | 0.081 | |
| reportDropletQC | 0.019 | 0.003 | 0.022 | |
| reportQCTool | 0.078 | 0.001 | 0.079 | |
| retrieveSCEIndex | 0.027 | 0.002 | 0.029 | |
| runBBKNN | 0 | 0 | 0 | |
| runBarcodeRankDrops | 0.226 | 0.019 | 0.244 | |
| runBcds | 1.545 | 0.094 | 1.029 | |
| runCellQC | 0.081 | 0.002 | 0.082 | |
| runClusterSummaryMetrics | 0.389 | 0.006 | 0.396 | |
| runComBatSeq | 0.479 | 0.015 | 0.494 | |
| runCxds | 0.321 | 0.002 | 0.323 | |
| runCxdsBcdsHybrid | 1.489 | 0.042 | 0.968 | |
| runDEAnalysis | 0.370 | 0.005 | 0.375 | |
| runDecontX | 6.699 | 0.246 | 6.948 | |
| runDimReduce | 0.284 | 0.003 | 0.287 | |
| runDoubletFinder | 35.591 | 0.874 | 37.944 | |
| runDropletQC | 0.022 | 0.002 | 0.024 | |
| runEmptyDrops | 6.317 | 0.016 | 6.333 | |
| runEnrichR | 0.529 | 0.086 | 2.624 | |
| runFastMNN | 1.745 | 0.164 | 1.909 | |
| runFeatureSelection | 0.228 | 0.018 | 0.246 | |
| runFindMarker | 1.619 | 0.190 | 1.809 | |
| runGSVA | 0.751 | 0.058 | 0.809 | |
| runHarmony | 0.043 | 0.004 | 0.046 | |
| runKMeans | 0.234 | 0.033 | 0.267 | |
| runLimmaBC | 0.092 | 0.001 | 0.093 | |
| runMNNCorrect | 0.410 | 0.022 | 0.432 | |
| runModelGeneVar | 0.293 | 0.037 | 0.329 | |
| runNormalization | 2.402 | 0.346 | 2.749 | |
| runPerCellQC | 0.391 | 0.007 | 0.398 | |
| runSCANORAMA | 0.000 | 0.001 | 0.000 | |
| runSCMerge | 0.003 | 0.001 | 0.005 | |
| runScDblFinder | 17.603 | 0.809 | 15.383 | |
| runScanpyFindClusters | 0.023 | 0.001 | 0.024 | |
| runScanpyFindHVG | 0.022 | 0.001 | 0.023 | |
| runScanpyFindMarkers | 0.023 | 0.000 | 0.023 | |
| runScanpyNormalizeData | 0.103 | 0.001 | 0.105 | |
| runScanpyPCA | 0.021 | 0.001 | 0.022 | |
| runScanpyScaleData | 0.023 | 0.000 | 0.023 | |
| runScanpyTSNE | 0.023 | 0.000 | 0.023 | |
| runScanpyUMAP | 0.023 | 0.000 | 0.023 | |
| runScranSNN | 0.298 | 0.004 | 0.302 | |
| runScrublet | 0.025 | 0.000 | 0.025 | |
| runSeuratFindClusters | 0.023 | 0.000 | 0.023 | |
| runSeuratFindHVG | 0.482 | 0.002 | 0.484 | |
| runSeuratHeatmap | 0.023 | 0.000 | 0.023 | |
| runSeuratICA | 0.023 | 0.001 | 0.024 | |
| runSeuratJackStraw | 0.022 | 0.001 | 0.023 | |
| runSeuratNormalizeData | 0.023 | 0.000 | 0.024 | |
| runSeuratPCA | 0.022 | 0.002 | 0.024 | |
| runSeuratSCTransform | 30.382 | 0.462 | 30.847 | |
| runSeuratScaleData | 0.024 | 0.001 | 0.025 | |
| runSeuratUMAP | 0.022 | 0.001 | 0.022 | |
| runSingleR | 0.042 | 0.000 | 0.043 | |
| runSoupX | 0.000 | 0.001 | 0.000 | |
| runTSCAN | 0.673 | 0.006 | 0.680 | |
| runTSCANClusterDEAnalysis | 0.839 | 0.030 | 0.870 | |
| runTSCANDEG | 0.736 | 0.003 | 0.740 | |
| runTSNE | 0.733 | 0.002 | 0.736 | |
| runUMAP | 6.965 | 0.013 | 6.979 | |
| runVAM | 0.305 | 0.002 | 0.307 | |
| runZINBWaVE | 0.005 | 0.000 | 0.005 | |
| sampleSummaryStats | 0.165 | 0.003 | 0.169 | |
| scaterCPM | 0.153 | 0.005 | 0.158 | |
| scaterPCA | 0.459 | 0.003 | 0.462 | |
| scaterlogNormCounts | 0.245 | 0.004 | 0.249 | |
| sce | 0.023 | 0.000 | 0.024 | |
| sctkListGeneSetCollections | 0.088 | 0.000 | 0.087 | |
| sctkPythonInstallConda | 0.001 | 0.000 | 0.000 | |
| sctkPythonInstallVirtualEnv | 0 | 0 | 0 | |
| selectSCTKConda | 0.000 | 0.001 | 0.000 | |
| selectSCTKVirtualEnvironment | 0.000 | 0.001 | 0.001 | |
| setRowNames | 0.090 | 0.001 | 0.091 | |
| setSCTKDisplayRow | 0.459 | 0.002 | 0.461 | |
| singleCellTK | 0 | 0 | 0 | |
| subDiffEx | 0.329 | 0.005 | 0.335 | |
| subsetSCECols | 0.086 | 0.001 | 0.087 | |
| subsetSCERows | 0.222 | 0.004 | 0.226 | |
| summarizeSCE | 0.069 | 0.000 | 0.070 | |
| trimCounts | 0.222 | 0.002 | 0.224 | |