Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 297/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
celda 1.25.0  (landing page)
Joshua Campbell
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/celda
git_branch: devel
git_last_commit: b623680
git_last_commit_date: 2025-04-15 11:46:22 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'scran' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for celda on lconway

To the developers/maintainers of the celda package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/celda.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.

raw results


Summary

Package: celda
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:celda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings celda_1.25.0.tar.gz
StartedAt: 2025-08-08 19:52:03 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 20:02:00 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 597.1 seconds
RetCode: 0
Status:   OK  
CheckDir: celda.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:celda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings celda_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/celda.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘celda/DESCRIPTION’ ... OK
* this is package ‘celda’ version ‘1.25.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 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 ‘celda’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 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 ... NOTE
.removeZeroVariance: no visible global function definition for
  ‘complete.cases’
.splitMetricIGpIGd: no visible global function definition for
  ‘model.matrix’
.splitMetricModF1: no visible global function definition for
  ‘model.matrix’
findMarkersTree: no visible global function definition for ‘Idents’
findMarkersTree: no visible global function definition for ‘RunUMAP’
findMarkersTree: no visible global function definition for ‘dendrapply’
plotDendro: no visible binding for global variable ‘xend’
plotDendro: no visible binding for global variable ‘y’
plotDendro: no visible binding for global variable ‘label’
plotMarkerHeatmap: no visible global function definition for ‘head’
plotMarkerHeatmap: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  Idents RunUMAP complete.cases dendrapply head label model.matrix
  setNames xend y
Consider adding
  importFrom("stats", "complete.cases", "dendrapply", "model.matrix",
             "setNames")
  importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bestLogLikelihood.Rd: SingleCellExperiment-class, altExp
  celdaClusters.Rd: SingleCellExperiment-class, altExp
  celdaGridSearch.Rd: SingleCellExperiment-class, assay, altExp,
    metadata
  celdaHeatmap.Rd: assay, altExp
  celdaModel.Rd: altExp
  celdaModules.Rd: SingleCellExperiment-class, altExp
  celdaProbabilityMap.Rd: assay, altExp
  celdaTsne.Rd: SingleCellExperiment-class, assay, altExp, reducedDim
  celdaUmap.Rd: assay, altExp, reducedDim
  celda_C.Rd: assay, altExp, SingleCellExperiment-class, metadata,
    colData
  celda_CG.Rd: assay, altExp, SingleCellExperiment-class, metadata,
    colData, rowData
  celda_G.Rd: assay, altExp, SingleCellExperiment-class, metadata,
    rowData
  celdatosce.Rd: SingleCellExperiment-class, assay, altExp, metadata,
    colData, rowData
  clusterProbability.Rd: SingleCellExperiment-class, assay, altExp
  decontX.Rd: SingleCellExperiment-class, Matrix
  decontXcounts.Rd: SingleCellExperiment-class, assay, assay<-
  factorizeMatrix.Rd: SingleCellExperiment-class, assay, altExp
  featureModuleLookup.Rd: SingleCellExperiment-class, altExp
  featureModuleTable.Rd: SingleCellExperiment-class, assay, altExp
  geneSetEnrich.Rd: SingleCellExperiment-class, assay, altExp
  logLikelihood.Rd: SingleCellExperiment-class, assay, altExp
  logLikelihoodHistory.Rd: SingleCellExperiment-class, altExp
  moduleHeatmap.Rd: SingleCellExperiment-class, assay, altExp
  perplexity.Rd: SingleCellExperiment-class, assay, altExp
  plotCeldaViolin.Rd: SingleCellExperiment-class, assay, altExp
  plotDecontXContamination.Rd: SingleCellExperiment-class
  plotDecontXMarkerExpression.Rd: SingleCellExperiment-class
  plotDecontXMarkerPercentage.Rd: SingleCellExperiment-class
  plotDimReduceCluster.Rd: SingleCellExperiment-class, altExp
  plotDimReduceFeature.Rd: SingleCellExperiment-class, assay, altExp,
    scale_colour_gradient2
  plotDimReduceGrid.Rd: SingleCellExperiment-class, assay, altExp,
    scale_colour_gradient2
  plotDimReduceModule.Rd: SingleCellExperiment-class, assay, altExp,
    scale_colour_gradient
  plotGridSearchPerplexity.Rd: SingleCellExperiment-class, altExp,
    geom_jitter
  plotRPC.Rd: SingleCellExperiment-class, altExp, geom_jitter
  recodeClusterY.Rd: SingleCellExperiment-class, rowData, altExp
  recodeClusterZ.Rd: SingleCellExperiment-class, colData, altExp
  recursiveSplitCell.Rd: SingleCellExperiment-class, assay, altExp,
    metadata
  recursiveSplitModule.Rd: SingleCellExperiment-class, assay, altExp,
    metadata
  reorderCelda.Rd: SingleCellExperiment-class, assay, altExp
  reportceldaCG.Rd: SingleCellExperiment-class, altExp, assay
  resList.Rd: SingleCellExperiment-class, altExp
  resamplePerplexity.Rd: SingleCellExperiment-class, assay, altExp
  retrieveFeatureIndex.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  runParams.Rd: SingleCellExperiment-class, altExp
  sampleLabel.Rd: SingleCellExperiment-class, altExp
  sceCeldaC.Rd: SingleCellExperiment-class
  sceCeldaCG.Rd: SingleCellExperiment-class
  sceCeldaCGGridSearch.Rd: SingleCellExperiment-class
  sceCeldaG.Rd: SingleCellExperiment-class
  selectBestModel.Rd: SingleCellExperiment-class, altExp, metadata
  selectFeatures.Rd: SingleCellExperiment-class, altExp, assay,
    metadata
  simulateCells.Rd: SingleCellExperiment-class, metadata, colData,
    rowData
  splitModule.Rd: SingleCellExperiment-class, assay, altExp, rowData
  subsetCeldaList.Rd: SingleCellExperiment-class, altExp, metadata
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
geneSetEnrich        36.899  0.555  53.748
plotDimReduceGrid    18.027  0.229  18.361
findMarkersTree      16.890  0.290  17.279
plotMarkerHeatmap    16.265  0.285  16.644
plotDendro           16.021  0.267  16.362
recursiveSplitCell   14.534  0.246  14.874
decontX               9.754  0.134   9.935
recursiveSplitModule  9.238  0.177   9.470
plotDimReduceModule   6.966  0.117   7.143
plotDimReduceFeature  5.574  0.088   5.700
plotDimReduceCluster  5.299  0.091   5.434
sceCeldaCGGridSearch  0.329  0.017  48.064
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/celda.Rcheck/00check.log’
for details.


Installation output

celda.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL celda
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘celda’ ...
** this is package ‘celda’ version ‘1.25.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c DecontX.cpp -o DecontX.o
DecontX.cpp:321:10: warning: variable 'x' set but not used [-Wunused-but-set-variable]
  double x;
         ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c cG_calcGibbsProbY.cpp -o cG_calcGibbsProbY.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c eigenMatMultInt.cpp -o eigenMatMultInt.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c matrixNorm.cpp -o matrixNorm.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c matrixSums.c -o matrixSums.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include     -fPIC  -falign-functions=64 -Wall -g -O2   -c matrixSumsSparse.cpp -o matrixSumsSparse.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppEigen/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c perplexity.c -o perplexity.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o celda.so DecontX.o RcppExports.o cG_calcGibbsProbY.o eigenMatMultInt.o matrixNorm.o matrixSums.o matrixSumsSparse.o perplexity.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-celda/00new/celda/libs
** R
** data
*** moving datasets to lazyload DB
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (celda)

Tests output

celda.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> Sys.unsetenv("R_TESTS")
> library(testthat)
> test_check("celda")
Loading required package: celda
Loading required package: SingleCellExperiment
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: Matrix

Attaching package: 'Matrix'

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

    expand


Attaching package: 'celda'

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

    params

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 101 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-decon.R:27:1', 'test-decon.R:48:1'

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 101 ]
> 
> proc.time()
   user  system elapsed 
 71.228   1.459  84.106 

Example timings

celda.Rcheck/celda-Ex.timings

nameusersystemelapsed
appendCeldaList0.0400.0040.043
bestLogLikelihood0.1170.0050.121
celda0.0010.0010.001
celdaClusters0.0550.0070.062
celdaGridSearch000
celdaHeatmap0.5690.0110.582
celdaModel0.0770.0030.081
celdaModules0.0540.0030.057
celdaPerplexity-celdaList-method0.0020.0020.004
celdaPerplexity0.0030.0020.004
celdaProbabilityMap3.4850.0933.597
celdaTsne2.4440.0722.530
celdaUmap3.6210.0733.708
celda_C0.4880.0070.499
celda_CG4.6940.0884.807
celda_G3.2730.0343.324
celdatosce0.8580.0210.883
clusterProbability0.4150.0100.427
compareCountMatrix0.0070.0040.011
countChecksum-celdaList-method0.0020.0030.005
countChecksum0.0030.0020.004
decontX9.7540.1349.935
distinctColors000
factorizeMatrix0.2430.0100.255
featureModuleLookup0.1950.0030.200
featureModuleTable0.2960.0060.303
findMarkersTree16.890 0.29017.279
geneSetEnrich36.899 0.55553.748
logLikelihood0.6740.0130.689
logLikelihoodHistory0.0570.0040.063
matrixNames0.0020.0030.006
moduleHeatmap4.7850.0734.880
normalizeCounts0.0030.0010.004
params0.0020.0030.004
perplexity0.5580.0190.578
plotCeldaViolin0.7910.0200.814
plotDendro16.021 0.26716.362
plotDimReduceCluster5.2990.0915.434
plotDimReduceFeature5.5740.0885.700
plotDimReduceGrid18.027 0.22918.361
plotDimReduceModule6.9660.1177.143
plotGridSearchPerplexity0.8500.0150.872
plotHeatmap0.1250.0030.130
plotMarkerHeatmap16.265 0.28516.644
plotRPC0.7210.0180.744
recodeClusterY0.2350.0040.242
recodeClusterZ0.2230.0030.227
recursiveSplitCell14.534 0.24614.874
recursiveSplitModule9.2380.1779.470
reorderCelda1.3010.0231.327
reportceldaCG0.0010.0020.004
resList0.0550.0040.060
resamplePerplexity0.7030.0100.716
retrieveFeatureIndex0.0020.0020.004
runParams0.0540.0050.058
sampleLabel0.0530.0110.064
sceCeldaC0.3340.0070.341
sceCeldaCG3.8040.0783.901
sceCeldaCGGridSearch 0.329 0.01748.064
sceCeldaG0.9170.0140.941
selectBestModel0.1830.0050.189
selectFeatures0.2370.0080.245
simulateCells0.2220.0100.232
simulateContamination0.0110.0000.011
splitModule0.2070.0050.216
subsetCeldaList0.3260.0070.334
topRank0.0020.0020.004