Yichen Wang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/singleCellTK |
| git_branch: RELEASE_3_14 |
| git_last_commit: 91f98fc |
| git_last_commit_date: 2021-10-27 11:24:49 -0400 (Wed, 27 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:08:48 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1807/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| singleCellTK 2.4.0 (landing page) Yichen Wang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: singleCellTK |
| Version: 2.4.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.4.0.tar.gz |
| StartedAt: 2022-04-12 18:37:24 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 18:56:15 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1130.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: singleCellTK.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singleCellTK_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.4.0’
* 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 6.3Mb
sub-directories of 1Mb or more:
extdata 1.5Mb
shiny 2.8Mb
* 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
plotScDblFinderResults 32.604 0.538 33.176
importExampleData 27.459 2.170 31.255
plotDoubletFinderResults 27.785 0.144 27.949
runDoubletFinder 19.573 0.049 19.632
runScDblFinder 15.900 0.356 16.272
plotBatchCorrCompare 12.134 0.107 12.237
plotMarkerDiffExp 11.670 0.040 11.723
plotScdsHybridResults 11.305 0.124 11.436
plotBcdsResults 10.362 0.255 10.620
findMarkerTopTable 10.215 0.047 10.274
findMarkerDiffExp 9.982 0.090 10.079
plotDEGHeatmap 9.637 0.090 9.736
plotEmptyDropsResults 9.609 0.026 9.649
runDESeq2 9.588 0.042 9.642
plotEmptyDropsScatter 9.586 0.017 9.613
plotDecontXResults 9.441 0.064 9.517
runEmptyDrops 9.135 0.017 9.161
runDecontX 7.865 0.026 7.896
plotCxdsResults 7.726 0.051 7.773
plotDEGViolin 7.407 0.152 7.571
runMAST 7.226 0.042 7.272
detectCellOutlier 6.853 0.240 7.103
plotUMAP 6.427 0.046 6.476
importGeneSetsFromMSigDB 6.102 0.331 6.442
plotDEGRegression 6.062 0.042 6.113
seuratSCTransform 4.927 0.091 5.030
enrichRSCE 0.725 0.031 6.832
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.14-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.
singleCellTK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL singleCellTK ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)
singleCellTK.Rcheck/tests/spelling.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
0.331 0.081 0.386
singleCellTK.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
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[----|----|----|----|----|----|----|----|----|----|
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Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
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Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
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Estimating GSVA scores for 34 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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[18:53:28] 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.
[18:53:31] 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.
[18:54:08] 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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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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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
Error in x$.self$finalize() : attempt to apply non-function
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[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 126 ]
>
> proc.time()
user system elapsed
333.734 4.496 339.974
singleCellTK.Rcheck/singleCellTK-Ex.timings
| name | user | system | elapsed | |
| MitoGenes | 0.004 | 0.003 | 0.006 | |
| SEG | 0.003 | 0.004 | 0.007 | |
| calcEffectSizes | 0.230 | 0.004 | 0.235 | |
| combineSCE | 3.282 | 0.015 | 3.300 | |
| computeZScore | 0.524 | 0.027 | 0.552 | |
| convertSCEToSeurat | 4.631 | 0.156 | 4.791 | |
| convertSeuratToSCE | 1.065 | 0.098 | 1.164 | |
| dedupRowNames | 0.107 | 0.010 | 0.118 | |
| detectCellOutlier | 6.853 | 0.240 | 7.103 | |
| diffAbundanceFET | 0.071 | 0.001 | 0.072 | |
| discreteColorPalette | 0.010 | 0.001 | 0.010 | |
| distinctColors | 0.003 | 0.000 | 0.003 | |
| downSampleCells | 1.328 | 0.104 | 1.433 | |
| downSampleDepth | 1.121 | 0.026 | 1.147 | |
| enrichRSCE | 0.725 | 0.031 | 6.832 | |
| exportSCE | 0.002 | 0.004 | 0.005 | |
| exportSCEtoAnnData | 0.191 | 0.005 | 0.196 | |
| exportSCEtoFlatFile | 0.198 | 0.007 | 0.204 | |
| featureIndex | 0.053 | 0.004 | 0.057 | |
| findMarkerDiffExp | 9.982 | 0.090 | 10.079 | |
| findMarkerTopTable | 10.215 | 0.047 | 10.274 | |
| generateSimulatedData | 0.065 | 0.002 | 0.067 | |
| getBiomarker | 0.076 | 0.001 | 0.078 | |
| getDEGTopTable | 1.535 | 0.010 | 1.544 | |
| getMSigDBTable | 0.007 | 0.004 | 0.011 | |
| getTSNE | 0.678 | 0.012 | 0.692 | |
| getTopHVG | 0.567 | 0.007 | 0.575 | |
| getUMAP | 4.479 | 0.046 | 4.520 | |
| importAnnData | 0.001 | 0.000 | 0.002 | |
| importBUStools | 0.635 | 0.003 | 0.639 | |
| importCellRanger | 2.409 | 0.055 | 2.469 | |
| importCellRangerV2Sample | 0.676 | 0.004 | 0.680 | |
| importCellRangerV3Sample | 0.826 | 0.016 | 0.844 | |
| importDropEst | 0.843 | 0.004 | 0.848 | |
| importExampleData | 27.459 | 2.170 | 31.255 | |
| importGeneSetsFromCollection | 1.333 | 0.090 | 1.424 | |
| importGeneSetsFromGMT | 0.124 | 0.004 | 0.129 | |
| importGeneSetsFromList | 0.348 | 0.011 | 0.359 | |
| importGeneSetsFromMSigDB | 6.102 | 0.331 | 6.442 | |
| importMitoGeneSet | 0.112 | 0.006 | 0.118 | |
| importOptimus | 0.001 | 0.000 | 0.003 | |
| importSEQC | 0.611 | 0.005 | 0.617 | |
| importSTARsolo | 0.640 | 0.003 | 0.644 | |
| iterateSimulations | 0.774 | 0.006 | 0.779 | |
| mergeSCEColData | 1.058 | 0.015 | 1.074 | |
| mouseBrainSubsetSCE | 0.001 | 0.002 | 0.003 | |
| msigdb_table | 0.001 | 0.001 | 0.003 | |
| plotBarcodeRankDropsResults | 1.984 | 0.016 | 2.001 | |
| plotBarcodeRankScatter | 1.600 | 0.009 | 1.611 | |
| plotBatchCorrCompare | 12.134 | 0.107 | 12.237 | |
| plotBatchVariance | 0.502 | 0.033 | 0.536 | |
| plotBcdsResults | 10.362 | 0.255 | 10.620 | |
| plotClusterAbundance | 1.106 | 0.027 | 1.136 | |
| plotCxdsResults | 7.726 | 0.051 | 7.773 | |
| plotDEGHeatmap | 9.637 | 0.090 | 9.736 | |
| plotDEGRegression | 6.062 | 0.042 | 6.113 | |
| plotDEGViolin | 7.407 | 0.152 | 7.571 | |
| plotDecontXResults | 9.441 | 0.064 | 9.517 | |
| plotDimRed | 0.567 | 0.004 | 0.571 | |
| plotDoubletFinderResults | 27.785 | 0.144 | 27.949 | |
| plotEmptyDropsResults | 9.609 | 0.026 | 9.649 | |
| plotEmptyDropsScatter | 9.586 | 0.017 | 9.613 | |
| plotMASTThresholdGenes | 3.353 | 0.017 | 3.372 | |
| plotMarkerDiffExp | 11.670 | 0.040 | 11.723 | |
| plotPCA | 1.288 | 0.012 | 1.303 | |
| plotRunPerCellQCResults | 0.002 | 0.000 | 0.002 | |
| plotSCEBarAssayData | 0.213 | 0.001 | 0.215 | |
| plotSCEBarColData | 0.171 | 0.001 | 0.173 | |
| plotSCEBatchFeatureMean | 0.291 | 0.002 | 0.294 | |
| plotSCEDensity | 0.287 | 0.003 | 0.292 | |
| plotSCEDensityAssayData | 0.237 | 0.003 | 0.241 | |
| plotSCEDensityColData | 0.309 | 0.003 | 0.313 | |
| plotSCEDimReduceColData | 1.722 | 0.009 | 1.733 | |
| plotSCEDimReduceFeatures | 0.818 | 0.005 | 0.825 | |
| plotSCEHeatmap | 1.635 | 0.013 | 1.653 | |
| plotSCEScatter | 0.724 | 0.003 | 0.728 | |
| plotSCEViolin | 0.317 | 0.002 | 0.321 | |
| plotSCEViolinAssayData | 0.341 | 0.004 | 0.346 | |
| plotSCEViolinColData | 0.336 | 0.003 | 0.341 | |
| plotScDblFinderResults | 32.604 | 0.538 | 33.176 | |
| plotScdsHybridResults | 11.305 | 0.124 | 11.436 | |
| plotScrubletResults | 0.002 | 0.001 | 0.004 | |
| plotTSNE | 1.259 | 0.019 | 1.281 | |
| plotTopHVG | 0.870 | 0.009 | 0.881 | |
| plotUMAP | 6.427 | 0.046 | 6.476 | |
| readSingleCellMatrix | 0.007 | 0.001 | 0.008 | |
| reportCellQC | 0.458 | 0.003 | 0.461 | |
| reportDropletQC | 0.002 | 0.001 | 0.002 | |
| reportQCTool | 0.373 | 0.002 | 0.376 | |
| retrieveSCEIndex | 0.020 | 0.001 | 0.021 | |
| runANOVA | 2.280 | 0.006 | 2.289 | |
| runBBKNN | 0.000 | 0.001 | 0.001 | |
| runBarcodeRankDrops | 1.102 | 0.005 | 1.108 | |
| runBcds | 3.884 | 0.037 | 3.928 | |
| runCellQC | 0.449 | 0.002 | 0.451 | |
| runComBatSeq | 0.819 | 0.013 | 0.835 | |
| runCxds | 1.252 | 0.024 | 1.280 | |
| runCxdsBcdsHybrid | 4.192 | 0.033 | 4.233 | |
| runDEAnalysis | 2.126 | 0.028 | 2.154 | |
| runDESeq2 | 9.588 | 0.042 | 9.642 | |
| runDecontX | 7.865 | 0.026 | 7.896 | |
| runDimReduce | 2.218 | 0.028 | 2.258 | |
| runDoubletFinder | 19.573 | 0.049 | 19.632 | |
| runDropletQC | 0.001 | 0.000 | 0.003 | |
| runEmptyDrops | 9.135 | 0.017 | 9.161 | |
| runFastMNN | 3.084 | 0.024 | 3.112 | |
| runFeatureSelection | 0.393 | 0.004 | 0.399 | |
| runGSVA | 1.886 | 0.014 | 1.902 | |
| runKMeans | 1.302 | 0.008 | 1.310 | |
| runLimmaBC | 0.220 | 0.001 | 0.221 | |
| runLimmaDE | 1.890 | 0.006 | 1.898 | |
| runMAST | 7.226 | 0.042 | 7.272 | |
| runMNNCorrect | 1.211 | 0.005 | 1.217 | |
| runNormalization | 2.986 | 0.021 | 3.009 | |
| runPerCellQC | 0.732 | 0.003 | 0.735 | |
| runSCANORAMA | 0 | 0 | 0 | |
| runSCMerge | 0.002 | 0.000 | 0.002 | |
| runScDblFinder | 15.900 | 0.356 | 16.272 | |
| runScranSNN | 1.218 | 0.012 | 1.230 | |
| runScrublet | 0.002 | 0.001 | 0.003 | |
| runSingleR | 0.097 | 0.002 | 0.100 | |
| runVAM | 1.647 | 0.020 | 1.670 | |
| runWilcox | 1.868 | 0.011 | 1.882 | |
| runZINBWaVE | 0.002 | 0.001 | 0.002 | |
| sampleSummaryStats | 0.712 | 0.003 | 0.717 | |
| scaterCPM | 0.261 | 0.009 | 0.269 | |
| scaterPCA | 1.200 | 0.006 | 1.206 | |
| scaterlogNormCounts | 1.690 | 0.012 | 1.703 | |
| sce | 0.002 | 0.004 | 0.005 | |
| scranModelGeneVar | 0.478 | 0.011 | 0.490 | |
| sctkListGeneSetCollections | 0.387 | 0.009 | 0.397 | |
| sctkPythonInstallConda | 0 | 0 | 0 | |
| sctkPythonInstallVirtualEnv | 0.000 | 0.000 | 0.001 | |
| selectSCTKConda | 0.000 | 0.001 | 0.000 | |
| selectSCTKVirtualEnvironment | 0.000 | 0.001 | 0.001 | |
| setSCTKDisplayRow | 0.827 | 0.010 | 0.839 | |
| seuratComputeHeatmap | 0.003 | 0.001 | 0.004 | |
| seuratComputeJackStraw | 0.002 | 0.001 | 0.003 | |
| seuratElbowPlot | 0.002 | 0.001 | 0.003 | |
| seuratFindClusters | 0.002 | 0.001 | 0.003 | |
| seuratFindHVG | 0.003 | 0.001 | 0.004 | |
| seuratICA | 0.002 | 0.001 | 0.004 | |
| seuratJackStrawPlot | 0.003 | 0.001 | 0.004 | |
| seuratNormalizeData | 0.002 | 0.001 | 0.003 | |
| seuratPCA | 0.001 | 0.001 | 0.002 | |
| seuratPlotHVG | 0.002 | 0.001 | 0.002 | |
| seuratReductionPlot | 0.002 | 0.002 | 0.003 | |
| seuratRunUMAP | 0.002 | 0.002 | 0.004 | |
| seuratSCTransform | 4.927 | 0.091 | 5.030 | |
| seuratScaleData | 0.003 | 0.001 | 0.004 | |
| singleCellTK | 0.000 | 0.000 | 0.001 | |
| subDiffEx | 1.202 | 0.012 | 1.215 | |
| subsetSCECols | 0.500 | 0.006 | 0.506 | |
| subsetSCERows | 1.038 | 0.009 | 1.048 | |
| summarizeSCE | 0.126 | 0.003 | 0.128 | |
| trimCounts | 0.521 | 0.019 | 0.541 | |