Yichen Wang
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/singleCellTK |
| git_branch: RELEASE_3_17 |
| git_last_commit: 277e675 |
| git_last_commit_date: 2023-04-25 11:01:21 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:47 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1934/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singleCellTK 2.10.0 (landing page) Yichen Wang
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 2.10.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings singleCellTK_2.10.0.tar.gz |
| StartedAt: 2023-10-16 01:09:46 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 01:23:47 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 841.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: singleCellTK.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings singleCellTK_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/singleCellTK.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.10.0’
* 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 5.5Mb
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 loading without being on the library search path ... OK
* checking 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 ... 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 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
plotScDblFinderResults 27.770 0.580 28.347
plotDoubletFinderResults 26.815 0.392 27.204
runScDblFinder 20.192 0.712 20.904
importExampleData 17.779 2.392 20.788
runDoubletFinder 18.344 0.028 18.372
plotBatchCorrCompare 14.406 0.644 15.044
plotBcdsResults 12.569 0.352 11.940
plotScdsHybridResults 10.456 0.108 9.672
plotDecontXResults 9.330 0.192 9.523
plotCxdsResults 7.474 0.223 7.695
plotEmptyDropsResults 6.768 0.040 6.808
plotEmptyDropsScatter 6.705 0.079 6.784
runDecontX 6.363 0.084 6.446
runEmptyDrops 6.309 0.004 6.312
plotUMAP 5.973 0.152 6.121
runUMAP 5.806 0.284 6.089
detectCellOutlier 5.497 0.184 5.681
plotTSCANClusterDEG 5.026 0.032 5.058
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘singleCellTK.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.
singleCellTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL singleCellTK ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘singleCellTK’ ... ** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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
0.161 0.024 0.175
singleCellTK.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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, aperm, 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 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: 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
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
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
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
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Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
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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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[----|----|----|----|----|----|----|----|----|----|
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Estimating GSVA scores for 34 gene sets.
Estimating ECDFs with Gaussian kernels
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Error in fitdistr(mahalanobis.sq.null[nonzero.values], "gamma", lower = 0.01) :
optimization failed
Estimating GSVA scores for 2 gene sets.
Estimating ECDFs with Gaussian kernels
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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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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 390
Number of edges: 9590
Running Louvain algorithm...
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[----|----|----|----|----|----|----|----|----|----|
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Maximum modularity in 10 random starts: 0.8042
Number of communities: 6
Elapsed time: 0 seconds
Using method 'umap'
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[ FAIL 0 | WARN 20 | SKIP 0 | PASS 220 ]
[ FAIL 0 | WARN 20 | SKIP 0 | PASS 220 ]
>
> proc.time()
user system elapsed
238.112 8.657 248.050
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| MitoGenes | 0.003 | 0.000 | 0.003 | |
| SEG | 0.003 | 0.000 | 0.003 | |
| calcEffectSizes | 0.148 | 0.036 | 0.184 | |
| combineSCE | 1.528 | 0.043 | 1.573 | |
| computeZScore | 0.281 | 0.020 | 0.301 | |
| convertSCEToSeurat | 3.189 | 0.255 | 3.445 | |
| convertSeuratToSCE | 0.427 | 0.003 | 0.431 | |
| dedupRowNames | 0.064 | 0.000 | 0.064 | |
| detectCellOutlier | 5.497 | 0.184 | 5.681 | |
| diffAbundanceFET | 0.048 | 0.000 | 0.048 | |
| discreteColorPalette | 0.006 | 0.000 | 0.006 | |
| distinctColors | 0.000 | 0.002 | 0.002 | |
| downSampleCells | 0.631 | 0.041 | 0.672 | |
| downSampleDepth | 0.491 | 0.012 | 0.503 | |
| expData-ANY-character-method | 0.279 | 0.011 | 0.290 | |
| expData-set-ANY-character-CharacterOrNullOrMissing-logical-method | 0.348 | 0.001 | 0.347 | |
| expData-set | 0.364 | 0.000 | 0.364 | |
| expData | 0.295 | 0.000 | 0.294 | |
| expDataNames-ANY-method | 0.319 | 0.011 | 0.330 | |
| expDataNames | 0.288 | 0.000 | 0.288 | |
| expDeleteDataTag | 0.032 | 0.004 | 0.036 | |
| expSetDataTag | 0.026 | 0.000 | 0.026 | |
| expTaggedData | 0.026 | 0.000 | 0.027 | |
| exportSCE | 0.020 | 0.003 | 0.024 | |
| exportSCEtoAnnData | 0.097 | 0.001 | 0.097 | |
| exportSCEtoFlatFile | 0.091 | 0.004 | 0.095 | |
| featureIndex | 0.036 | 0.000 | 0.037 | |
| generateSimulatedData | 0.041 | 0.003 | 0.045 | |
| getBiomarker | 0.050 | 0.001 | 0.050 | |
| getDEGTopTable | 0.819 | 0.024 | 0.842 | |
| getDiffAbundanceResults | 0.038 | 0.000 | 0.038 | |
| getEnrichRResult | 0.779 | 0.063 | 2.996 | |
| getFindMarkerTopTable | 3.425 | 0.236 | 3.661 | |
| getMSigDBTable | 0.004 | 0.000 | 0.005 | |
| getPathwayResultNames | 0.018 | 0.008 | 0.026 | |
| getSampleSummaryStatsTable | 0.362 | 0.016 | 0.378 | |
| getSoupX | 0.000 | 0.000 | 0.001 | |
| getTSCANResults | 1.789 | 0.132 | 1.922 | |
| getTopHVG | 0.834 | 0.040 | 0.875 | |
| importAnnData | 0.002 | 0.000 | 0.001 | |
| importBUStools | 0.294 | 0.008 | 0.302 | |
| importCellRanger | 1.161 | 0.060 | 1.223 | |
| importCellRangerV2Sample | 0.249 | 0.004 | 0.253 | |
| importCellRangerV3Sample | 0.415 | 0.028 | 0.444 | |
| importDropEst | 0.371 | 0.004 | 0.376 | |
| importExampleData | 17.779 | 2.392 | 20.788 | |
| importGeneSetsFromCollection | 0.782 | 0.040 | 0.822 | |
| importGeneSetsFromGMT | 0.078 | 0.000 | 0.077 | |
| importGeneSetsFromList | 0.140 | 0.008 | 0.148 | |
| importGeneSetsFromMSigDB | 2.581 | 0.260 | 2.841 | |
| importMitoGeneSet | 0.054 | 0.004 | 0.058 | |
| importOptimus | 0.002 | 0.000 | 0.002 | |
| importSEQC | 0.441 | 0.092 | 0.534 | |
| importSTARsolo | 0.280 | 0.036 | 0.316 | |
| iterateSimulations | 0.373 | 0.020 | 0.392 | |
| listSampleSummaryStatsTables | 0.490 | 0.008 | 0.498 | |
| mergeSCEColData | 0.543 | 0.020 | 0.563 | |
| mouseBrainSubsetSCE | 0.021 | 0.008 | 0.029 | |
| msigdb_table | 0.001 | 0.000 | 0.002 | |
| plotBarcodeRankDropsResults | 1.022 | 0.064 | 1.085 | |
| plotBarcodeRankScatter | 0.755 | 0.044 | 0.799 | |
| plotBatchCorrCompare | 14.406 | 0.644 | 15.044 | |
| plotBatchVariance | 0.379 | 0.023 | 0.402 | |
| plotBcdsResults | 12.569 | 0.352 | 11.940 | |
| plotClusterAbundance | 1.273 | 0.024 | 1.296 | |
| plotCxdsResults | 7.474 | 0.223 | 7.695 | |
| plotDEGHeatmap | 3.199 | 0.071 | 3.270 | |
| plotDEGRegression | 4.107 | 0.052 | 4.152 | |
| plotDEGViolin | 4.838 | 0.128 | 4.959 | |
| plotDEGVolcano | 1.153 | 0.032 | 1.185 | |
| plotDecontXResults | 9.330 | 0.192 | 9.523 | |
| plotDimRed | 0.266 | 0.007 | 0.273 | |
| plotDoubletFinderResults | 26.815 | 0.392 | 27.204 | |
| plotEmptyDropsResults | 6.768 | 0.040 | 6.808 | |
| plotEmptyDropsScatter | 6.705 | 0.079 | 6.784 | |
| plotFindMarkerHeatmap | 4.555 | 0.032 | 4.587 | |
| plotMASTThresholdGenes | 1.489 | 0.008 | 1.497 | |
| plotPCA | 0.501 | 0.000 | 0.501 | |
| plotPathway | 0.824 | 0.000 | 0.824 | |
| plotRunPerCellQCResults | 2.084 | 0.008 | 2.090 | |
| plotSCEBarAssayData | 0.176 | 0.000 | 0.176 | |
| plotSCEBarColData | 0.128 | 0.000 | 0.128 | |
| plotSCEBatchFeatureMean | 0.216 | 0.000 | 0.216 | |
| plotSCEDensity | 0.201 | 0.004 | 0.205 | |
| plotSCEDensityAssayData | 0.157 | 0.004 | 0.161 | |
| plotSCEDensityColData | 0.195 | 0.004 | 0.199 | |
| plotSCEDimReduceColData | 0.896 | 0.000 | 0.896 | |
| plotSCEDimReduceFeatures | 0.351 | 0.000 | 0.351 | |
| plotSCEHeatmap | 0.787 | 0.000 | 0.787 | |
| plotSCEScatter | 0.342 | 0.012 | 0.354 | |
| plotSCEViolin | 0.218 | 0.008 | 0.226 | |
| plotSCEViolinAssayData | 0.241 | 0.000 | 0.241 | |
| plotSCEViolinColData | 0.227 | 0.004 | 0.231 | |
| plotScDblFinderResults | 27.770 | 0.580 | 28.347 | |
| plotScanpyDotPlot | 0.027 | 0.000 | 0.026 | |
| plotScanpyEmbedding | 0.026 | 0.000 | 0.026 | |
| plotScanpyHVG | 0.026 | 0.000 | 0.025 | |
| plotScanpyHeatmap | 0.025 | 0.000 | 0.025 | |
| plotScanpyMarkerGenes | 0.026 | 0.000 | 0.026 | |
| plotScanpyMarkerGenesDotPlot | 0.026 | 0.000 | 0.026 | |
| plotScanpyMarkerGenesHeatmap | 0.027 | 0.000 | 0.027 | |
| plotScanpyMarkerGenesMatrixPlot | 0.027 | 0.000 | 0.027 | |
| plotScanpyMarkerGenesViolin | 0.028 | 0.000 | 0.027 | |
| plotScanpyMatrixPlot | 0.026 | 0.000 | 0.027 | |
| plotScanpyPCA | 0.025 | 0.000 | 0.025 | |
| plotScanpyPCAGeneRanking | 0.023 | 0.003 | 0.026 | |
| plotScanpyPCAVariance | 0.024 | 0.004 | 0.028 | |
| plotScanpyViolin | 0.028 | 0.000 | 0.028 | |
| plotScdsHybridResults | 10.456 | 0.108 | 9.672 | |
| plotScrubletResults | 0.024 | 0.000 | 0.025 | |
| plotSeuratElbow | 0.024 | 0.000 | 0.023 | |
| plotSeuratHVG | 0.023 | 0.000 | 0.024 | |
| plotSeuratJackStraw | 0.021 | 0.003 | 0.023 | |
| plotSeuratReduction | 0.024 | 0.000 | 0.024 | |
| plotSoupXResults | 0.001 | 0.000 | 0.000 | |
| plotTSCANClusterDEG | 5.026 | 0.032 | 5.058 | |
| plotTSCANClusterPseudo | 2.028 | 0.044 | 2.071 | |
| plotTSCANDimReduceFeatures | 1.973 | 0.012 | 1.984 | |
| plotTSCANPseudotimeGenes | 1.905 | 0.012 | 1.917 | |
| plotTSCANPseudotimeHeatmap | 2.029 | 0.028 | 2.058 | |
| plotTSCANResults | 1.914 | 0.012 | 1.925 | |
| plotTSNE | 0.454 | 0.000 | 0.454 | |
| plotTopHVG | 0.379 | 0.004 | 0.383 | |
| plotUMAP | 5.973 | 0.152 | 6.121 | |
| readSingleCellMatrix | 0.001 | 0.004 | 0.005 | |
| reportCellQC | 0.17 | 0.00 | 0.17 | |
| reportDropletQC | 0.026 | 0.000 | 0.026 | |
| reportQCTool | 0.17 | 0.00 | 0.17 | |
| retrieveSCEIndex | 0.029 | 0.000 | 0.029 | |
| runBBKNN | 0 | 0 | 0 | |
| runBarcodeRankDrops | 0.405 | 0.004 | 0.409 | |
| runBcds | 2.357 | 0.016 | 1.466 | |
| runCellQC | 0.192 | 0.000 | 0.192 | |
| runComBatSeq | 0.431 | 0.004 | 0.435 | |
| runCxds | 0.516 | 0.004 | 0.519 | |
| runCxdsBcdsHybrid | 2.440 | 0.020 | 1.533 | |
| runDEAnalysis | 0.677 | 0.008 | 0.686 | |
| runDecontX | 6.363 | 0.084 | 6.446 | |
| runDimReduce | 0.460 | 0.004 | 0.464 | |
| runDoubletFinder | 18.344 | 0.028 | 18.372 | |
| runDropletQC | 0.024 | 0.000 | 0.024 | |
| runEmptyDrops | 6.309 | 0.004 | 6.312 | |
| runEnrichR | 0.709 | 0.020 | 2.569 | |
| runFastMNN | 1.777 | 0.576 | 2.353 | |
| runFeatureSelection | 0.210 | 0.028 | 0.238 | |
| runFindMarker | 3.286 | 0.460 | 3.746 | |
| runGSVA | 0.652 | 0.192 | 0.844 | |
| runHarmony | 0.039 | 0.004 | 0.043 | |
| runKMeans | 0.441 | 0.068 | 0.509 | |
| runLimmaBC | 0.074 | 0.000 | 0.074 | |
| runMNNCorrect | 0.502 | 0.024 | 0.526 | |
| runModelGeneVar | 0.436 | 0.036 | 0.472 | |
| runNormalization | 0.556 | 0.040 | 0.596 | |
| runPerCellQC | 0.559 | 0.088 | 0.647 | |
| runSCANORAMA | 0.001 | 0.000 | 0.000 | |
| runSCMerge | 0.005 | 0.000 | 0.005 | |
| runScDblFinder | 20.192 | 0.712 | 20.904 | |
| runScanpyFindClusters | 0.022 | 0.003 | 0.025 | |
| runScanpyFindHVG | 0.024 | 0.000 | 0.024 | |
| runScanpyFindMarkers | 0.024 | 0.000 | 0.024 | |
| runScanpyNormalizeData | 0.185 | 0.020 | 0.206 | |
| runScanpyPCA | 0.021 | 0.004 | 0.025 | |
| runScanpyScaleData | 0.023 | 0.000 | 0.023 | |
| runScanpyTSNE | 0.023 | 0.000 | 0.023 | |
| runScanpyUMAP | 0.023 | 0.000 | 0.023 | |
| runScranSNN | 0.659 | 0.064 | 0.722 | |
| runScrublet | 0.025 | 0.000 | 0.024 | |
| runSeuratFindClusters | 0.019 | 0.004 | 0.023 | |
| runSeuratFindHVG | 0.639 | 0.084 | 0.723 | |
| runSeuratHeatmap | 0.024 | 0.000 | 0.023 | |
| runSeuratICA | 0.019 | 0.004 | 0.023 | |
| runSeuratJackStraw | 0.023 | 0.000 | 0.023 | |
| runSeuratNormalizeData | 0.023 | 0.000 | 0.023 | |
| runSeuratPCA | 0.022 | 0.000 | 0.023 | |
| runSeuratSCTransform | 2.805 | 0.348 | 3.154 | |
| runSeuratScaleData | 0.024 | 0.000 | 0.025 | |
| runSeuratUMAP | 0.016 | 0.007 | 0.023 | |
| runSingleR | 0.036 | 0.000 | 0.036 | |
| runSoupX | 0.001 | 0.000 | 0.000 | |
| runTSCAN | 1.528 | 0.032 | 1.561 | |
| runTSCANClusterDEAnalysis | 1.513 | 0.020 | 1.534 | |
| runTSCANDEG | 1.373 | 0.020 | 1.393 | |
| runTSNE | 0.839 | 0.000 | 0.839 | |
| runUMAP | 5.806 | 0.284 | 6.089 | |
| runVAM | 0.512 | 0.008 | 0.519 | |
| runZINBWaVE | 0.004 | 0.000 | 0.005 | |
| sampleSummaryStats | 0.265 | 0.008 | 0.273 | |
| scaterCPM | 0.133 | 0.008 | 0.141 | |
| scaterPCA | 0.425 | 0.008 | 0.433 | |
| scaterlogNormCounts | 0.238 | 0.020 | 0.258 | |
| sce | 0.023 | 0.000 | 0.024 | |
| sctkListGeneSetCollections | 0.075 | 0.004 | 0.080 | |
| sctkPythonInstallConda | 0 | 0 | 0 | |
| sctkPythonInstallVirtualEnv | 0.000 | 0.000 | 0.001 | |
| selectSCTKConda | 0 | 0 | 0 | |
| selectSCTKVirtualEnvironment | 0 | 0 | 0 | |
| setRowNames | 0.086 | 0.002 | 0.089 | |
| setSCTKDisplayRow | 0.395 | 0.008 | 0.403 | |
| singleCellTK | 0 | 0 | 0 | |
| subDiffEx | 0.476 | 0.016 | 0.493 | |
| subsetSCECols | 0.164 | 0.000 | 0.164 | |
| subsetSCERows | 0.381 | 0.000 | 0.381 | |
| summarizeSCE | 0.053 | 0.004 | 0.057 | |
| trimCounts | 0.228 | 0.004 | 0.231 | |