Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-26 11:06:50 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for singleCellTK on nebbiolo1


To the developers/maintainers of the singleCellTK package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1802/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singleCellTK 2.5.1  (landing page)
Yichen Wang
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/singleCellTK
git_branch: master
git_last_commit: cdbe999
git_last_commit_date: 2021-11-21 00:55:04 -0500 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: singleCellTK
Version: 2.5.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings singleCellTK_2.5.1.tar.gz
StartedAt: 2022-01-25 21:04:36 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 21:15:33 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 657.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: singleCellTK.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings singleCellTK_2.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/singleCellTK.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.5.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    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 R 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'AnnotationDbi' 'RColorBrewer'
  All declared Imports should be used.
* 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plotDoubletFinderResults 24.521  0.139  24.653
plotScDblFinderResults   22.033  0.493  22.454
runDoubletFinder         17.893  0.064  17.959
runScDblFinder           16.442  0.328  16.706
importExampleData        14.108  1.800  16.579
plotBatchCorrCompare     11.341  1.327  12.646
plotScdsHybridResults     8.738  0.064   7.921
plotBcdsResults           7.727  0.170   6.973
plotDecontXResults        7.342  0.087   7.430
plotEmptyDropsScatter     6.607  0.023   6.630
plotEmptyDropsResults     6.545  0.024   6.569
runEmptyDrops             6.302  0.000   6.302
plotCxdsResults           6.091  0.068   6.153
plotUMAP                  5.669  0.127   5.787
runDecontX                5.703  0.003   5.708
detectCellOutlier         5.380  0.092   5.472
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-batchCorrection.R:20:3): Testing BBKNN ────────────────────────
  "BBKNN" %in% reducedDimNames(sceBatches) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-batchCorrection.R:45:3): Testing SCANORAMA ────────────────────
  "SCANORAMA" %in% assayNames(sceBatches) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 17 | SKIP 0 | PASS 126 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.


Installation output

singleCellTK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL singleCellTK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘singleCellTK’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (singleCellTK)

Tests output

singleCellTK.Rcheck/tests/spelling.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> if (requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.203   0.034   0.220 

singleCellTK.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

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

Attaching package: 'Matrix'

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

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels

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

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  |======================================================================| 100%
[21:14:06] WARNING: amalgamation/../src/learner.cc:1115: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[21:14:07] WARNING: amalgamation/../src/learner.cc:1115: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
[21:14:30] WARNING: amalgamation/../src/learner.cc:1115: Starting in XGBoost 1.3.0, the default evaluation metric used with the objective 'binary:logistic' was changed from 'error' to 'logloss'. Explicitly set eval_metric if you'd like to restore the old behavior.
Performing log-normalization
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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

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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 2 | WARN 17 | SKIP 0 | PASS 126 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-batchCorrection.R:20:3): Testing BBKNN ────────────────────────
"BBKNN" %in% reducedDimNames(sceBatches) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure (test-batchCorrection.R:45:3): Testing SCANORAMA ────────────────────
"SCANORAMA" %in% assayNames(sceBatches) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 2 | WARN 17 | SKIP 0 | PASS 126 ]
Error: Test failures
Execution halted

Example timings

singleCellTK.Rcheck/singleCellTK-Ex.timings

nameusersystemelapsed
MitoGenes0.0000.0030.002
SEG0.0030.0000.002
calcEffectSizes0.1280.0000.128
combineSCE1.4780.0241.501
computeZScore0.2800.0200.301
convertSCEToSeurat2.1530.0802.233
convertSeuratToSCE0.3560.0040.359
dedupRowNames0.0330.0000.034
detectCellOutlier5.3800.0925.472
diffAbundanceFET0.0260.0000.026
discreteColorPalette0.0060.0000.006
distinctColors0.0020.0000.002
downSampleCells0.4670.0120.479
downSampleDepth0.370.000.37
enrichRSCE0.3030.0071.384
exportSCE0.0010.0000.002
exportSCEtoAnnData0.0870.0120.098
exportSCEtoFlatFile0.0810.0160.098
featureIndex0.0170.0000.016
findMarkerDiffExp1.2580.0441.303
findMarkerTopTable1.0090.0201.029
generateSimulatedData0.0230.0000.022
getBiomarker0.0200.0000.021
getDEGTopTable0.6060.0000.607
getMSigDBTable0.0010.0040.005
getTSNE0.1490.0000.149
getTopHVG0.2340.0120.247
getUMAP4.1670.0484.207
importAnnData0.0010.0000.001
importBUStools0.2110.0040.215
importCellRanger0.9490.0200.971
importCellRangerV2Sample0.2000.0070.207
importCellRangerV3Sample0.3180.0000.318
importDropEst0.3090.0000.310
importExampleData14.108 1.80016.579
importGeneSetsFromCollection0.7090.0600.768
importGeneSetsFromGMT0.0490.0000.050
importGeneSetsFromList0.0830.0240.106
importGeneSetsFromMSigDB3.3810.2643.646
importMitoGeneSet0.0350.0040.038
importOptimus0.0000.0010.002
importSEQC0.2220.0260.248
importSTARsolo0.3050.0400.345
iterateSimulations0.1030.0000.103
mergeSCEColData0.4390.0040.443
mouseBrainSubsetSCE0.0010.0000.001
msigdb_table0.0000.0010.001
plotBarcodeRankDropsResults0.9170.0100.927
plotBarcodeRankScatter0.6900.0240.714
plotBatchCorrCompare11.341 1.32712.646
plotBatchVariance0.2740.0640.338
plotBcdsResults7.7270.1706.973
plotClusterAbundance0.6280.0040.631
plotCxdsResults6.0910.0686.153
plotDEGHeatmap4.5250.0164.541
plotDEGRegression3.1190.0203.132
plotDEGViolin4.0610.0554.103
plotDecontXResults7.3420.0877.430
plotDimRed0.1310.0000.130
plotDoubletFinderResults24.521 0.13924.653
plotEmptyDropsResults6.5450.0246.569
plotEmptyDropsScatter6.6070.0236.630
plotMASTThresholdGenes1.2400.0241.265
plotMarkerDiffExp4.4280.0124.439
plotPCA0.2390.0000.238
plotRunPerCellQCResults0.0000.0020.002
plotSCEBarAssayData0.0980.0010.100
plotSCEBarColData0.0820.0000.082
plotSCEBatchFeatureMean0.2150.0040.219
plotSCEDensity0.1730.0000.173
plotSCEDensityAssayData0.1210.0000.120
plotSCEDensityColData0.1640.0000.165
plotSCEDimReduceColData0.4840.0000.484
plotSCEDimReduceFeatures0.2020.0040.205
plotSCEHeatmap0.6910.0000.692
plotSCEScatter0.1930.0000.194
plotSCEViolin0.1720.0000.172
plotSCEViolinAssayData0.1840.0000.185
plotSCEViolinColData0.1820.0000.182
plotScDblFinderResults22.033 0.49322.454
plotScdsHybridResults8.7380.0647.921
plotScrubletResults0.0020.0000.002
plotTSNE0.2510.0000.251
plotTopHVG0.470.000.47
plotUMAP5.6690.1275.787
readSingleCellMatrix0.0040.0000.004
reportCellQC0.1470.0040.151
reportDropletQC0.0010.0000.001
reportQCTool0.1520.0000.153
retrieveSCEIndex0.0110.0000.011
runANOVA0.8100.0040.814
runBBKNN000
runBarcodeRankDrops0.5990.0000.599
runBcds2.4480.0131.494
runCellQC0.1500.0070.158
runComBatSeq0.4050.0150.420
runCxds0.4790.0040.484
runCxdsBcdsHybrid2.4180.0451.578
runDEAnalysis0.7750.0000.775
runDESeq22.9280.0112.940
runDecontX5.7030.0035.708
runDimReduce0.9000.0000.901
runDoubletFinder17.893 0.06417.959
runDropletQC0.0020.0000.002
runEmptyDrops6.3020.0006.302
runFastMNN1.4970.0161.513
runFeatureSelection0.1720.0000.172
runGSVA0.6390.0320.670
runKMeans0.0920.0000.093
runLimmaBC0.0740.0000.074
runLimmaDE0.6880.0040.692
runMAST3.2030.0043.178
runMNNCorrect0.5010.0000.502
runNormalization0.5370.0200.557
runPerCellQC0.40.00.4
runSCANORAMA000
runSCMerge0.0020.0000.001
runScDblFinder16.442 0.32816.706
runScranSNN0.090.000.09
runScrublet0.0010.0000.002
runSingleR0.030.000.03
runVAM0.5130.0240.536
runWilcox0.6810.0120.693
runZINBWaVE0.0010.0000.001
sampleSummaryStats0.2950.0000.295
scaterCPM0.1290.0000.128
scaterPCA0.4720.0040.476
scaterlogNormCounts0.2960.0160.311
sce0.0010.0000.002
scranModelGeneVar0.2120.0040.216
sctkListGeneSetCollections0.1750.0110.185
sctkPythonInstallConda000
sctkPythonInstallVirtualEnv000
selectSCTKConda000
selectSCTKVirtualEnvironment0.0000.0000.001
setSCTKDisplayRow0.3620.0080.371
seuratComputeHeatmap0.0020.0000.002
seuratComputeJackStraw0.0020.0000.002
seuratElbowPlot0.0010.0000.001
seuratFindClusters0.0010.0000.001
seuratFindHVG0.0020.0000.001
seuratICA0.0020.0000.001
seuratJackStrawPlot0.0020.0000.002
seuratNormalizeData0.0000.0010.002
seuratPCA0.0000.0010.002
seuratPlotHVG0.0010.0000.002
seuratReductionPlot0.0010.0000.002
seuratRunUMAP0.0010.0000.001
seuratSCTransform2.5240.0722.596
seuratScaleData0.0020.0000.001
singleCellTK0.0000.0000.001
subDiffEx0.1930.0000.193
subsetSCECols0.1610.0000.162
subsetSCERows0.3830.0000.383
summarizeSCE0.0370.0000.037
trimCounts0.2680.0110.279