Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-03 12:04 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 300/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
celda 1.25.0  (landing page)
Joshua Campbell
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 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 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


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: 2025-10-02 20:15:17 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 20:25:45 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 628.2 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 Patched (2025-09-10 r88807)
* 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: ‘MacOSX11.3.1.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        38.051  0.677  61.253
plotDimReduceGrid    22.327  0.273  22.749
findMarkersTree      16.879  0.302  17.293
plotDendro           16.703  0.276  17.037
plotMarkerHeatmap    16.261  0.315  16.690
recursiveSplitCell   15.155  0.263  15.507
decontX              12.331  0.160  12.560
recursiveSplitModule 10.415  0.214  10.704
plotDimReduceModule   7.064  0.111   7.219
plotDimReduceFeature  5.968  0.112   6.135
plotDimReduceCluster  5.702  0.120   5.871
sceCeldaCGGridSearch  0.313  0.014  49.278
* 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: ‘MacOSX11.3.1.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 Patched (2025-09-10 r88807) -- "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 
 73.312   1.510  86.891 

Example timings

celda.Rcheck/celda-Ex.timings

nameusersystemelapsed
appendCeldaList0.0050.0030.008
bestLogLikelihood0.1350.0060.142
celda0.0010.0010.001
celdaClusters0.0630.0110.074
celdaGridSearch000
celdaHeatmap0.6620.0490.715
celdaModel0.0850.0040.089
celdaModules0.0530.0030.056
celdaPerplexity-celdaList-method0.0130.0030.016
celdaPerplexity0.0020.0020.004
celdaProbabilityMap3.5290.0743.638
celdaTsne2.5680.0892.686
celdaUmap3.7640.0713.848
celda_C0.5000.0070.509
celda_CG4.5920.0904.710
celda_G3.2730.0393.331
celdatosce0.8280.0210.853
clusterProbability0.3980.0110.412
compareCountMatrix0.0090.0050.013
countChecksum-celdaList-method0.0020.0020.004
countChecksum0.0020.0030.005
decontX12.331 0.16012.560
distinctColors0.0010.0000.001
factorizeMatrix0.2840.0110.298
featureModuleLookup0.2110.0040.217
featureModuleTable0.2960.0040.302
findMarkersTree16.879 0.30217.293
geneSetEnrich38.051 0.67761.253
logLikelihood0.7070.0080.718
logLikelihoodHistory0.0470.0040.053
matrixNames0.0030.0050.008
moduleHeatmap4.7730.0764.873
normalizeCounts0.0020.0010.004
params0.0010.0020.003
perplexity0.5270.0170.545
plotCeldaViolin1.0470.0301.082
plotDendro16.703 0.27617.037
plotDimReduceCluster5.7020.1205.871
plotDimReduceFeature5.9680.1126.135
plotDimReduceGrid22.327 0.27322.749
plotDimReduceModule7.0640.1117.219
plotGridSearchPerplexity1.1000.0141.118
plotHeatmap0.1190.0030.122
plotMarkerHeatmap16.261 0.31516.690
plotRPC1.0990.0271.137
recodeClusterY0.2310.0040.236
recodeClusterZ0.2400.0040.246
recursiveSplitCell15.155 0.26315.507
recursiveSplitModule10.415 0.21410.704
reorderCelda1.2200.0221.247
reportceldaCG0.0010.0030.004
resList0.0530.0040.057
resamplePerplexity1.0460.0201.074
retrieveFeatureIndex0.0020.0030.005
runParams0.0630.0060.069
sampleLabel0.0640.0140.078
sceCeldaC0.3460.0090.360
sceCeldaCG3.7480.0713.843
sceCeldaCGGridSearch 0.313 0.01449.278
sceCeldaG0.8410.0160.861
selectBestModel0.1840.0060.190
selectFeatures0.2330.0060.240
simulateCells0.1940.0030.197
simulateContamination0.0110.0010.011
splitModule0.2140.0040.218
subsetCeldaList0.3760.0160.392
topRank0.0010.0020.004