Multiple platform build/check report for BioC 3.22 - CHECK results for COTAN on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4844
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4631
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4576
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (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*

CHECK results for COTAN on lconway

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

Version: 2.9.6

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.9.6.tar.gz

StartedAt: 2025-10-01 20:31:17 -0400 (Wed, 01 Oct 2025)

EndedAt: 2025-10-01 20:53:47 -0400 (Wed, 01 Oct 2025)

EllapsedTime: 1350.6 seconds

RetCode: 0

Status: OK

CheckDir: COTAN.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.9.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/COTAN.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 ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.9.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ‘COTAN’ can be installed ... OK
* 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 whether 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
UniformClusters         118.489  2.583 120.425
CalculatingCOEX          56.351  1.071  57.688
HandlingClusterizations  43.967  1.095  44.779
HeatmapPlots             35.376  0.839  36.430
ParametersEstimations    23.475  0.716  24.326
GenesStatistics          11.430  0.343  11.654
COTAN_ObjectCreation     10.777  0.273  11.251
RawDataCleaning           5.178  0.301   5.318
Conversions               5.186  0.112   5.322
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘outputTestDatasetCreation.R’
  Running ‘spelling.R’
  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: OK

Installation output

COTAN.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘COTAN’ ...
** this is package ‘COTAN’ version ‘2.9.6’
** using staged installation
** R
** data
** 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 (COTAN)

Tests output

COTAN.Rcheck/tests/outputTestDatasetCreation.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.

> 
> # Creates the files to be reloaded by the tests for comparisons
> 
> outputTestDatasetCreation <-
+   function(testsDir = file.path("tests", "testthat")) {
+   utils::data("test.dataset", package = "COTAN")
+   options(parallelly.fork.enable = TRUE)
+   setLoggingLevel(3L)
+ 
+   obj <- COTAN(raw = test.dataset)
+   obj <- initializeMetaDataset(objCOTAN = obj, GEO = " ",
+                                sequencingMethod = "artificial",
+                                sampleCondition = "test")
+ 
+   obj <- proceedToCoex(objCOTAN = obj, cores = 6L, saveObj = FALSE)
+ 
+   if (FALSE) {
+     saveRDS(obj, file = file.path(testsDir,"test.COTAN.RDS"))
+   }
+ 
+   cells.names.test <- getCells(objCOTAN = obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+   genes.names.test <- getGenes(objCOTAN = obj)[c(1L:10L, 291L:310L, 591L: 600L)]
+   saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS"))
+   saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS"))
+ 
+   pcaRaw <- runPCA(x = getRawData(objCOTAN = obj), rank = 10L,
+                    BSPARAM = IrlbaParam(), get.rotation = FALSE)[["x"]]
+ 
+   pca.raw.test <- pcaRaw[genes.names.test, ]
+   saveRDS(pca.raw.test, file.path(testsDir, "pca.raw.test.RDS"))
+ 
+   dispersion.test <- getDispersion(objCOTAN = obj)[genes.names.test]
+   saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+ 
+   raw.norm.test <-
+     getNuNormData(objCOTAN = obj)[genes.names.test, cells.names.test]
+   saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+ 
+   coex.test <-
+     getGenesCoex(objCOTAN = obj, genes = genes.names.test, zeroDiagonal = FALSE)
+   saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+ 
+   lambda.test <- getLambda(objCOTAN = obj)[genes.names.test]
+   saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+ 
+   GDI.test <- calculateGDI(objCOTAN = obj)
+   GDI.test <- GDI.test[genes.names.test, ]
+   saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+ 
+   nu.test <- getNu(objCOTAN = obj)[cells.names.test]
+   saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+ 
+   pvalues.test <- calculatePValue(objCOTAN = obj,
+                                   geneSubsetCol = genes.names.test,
+                                   geneSubsetRow = genes.names.test)
+   saveRDS(pvalues.test, file.path(testsDir, "pvalues.test.RDS"))
+ 
+   groupMarkers <- list(G1 = c("g-000010", "g-000020", "g-000030"),
+                        G2 = c("g-000300", "g-000330", "g-000660"),
+                        G3 = c("g-000510", "g-000530", "g-000550",
+                               "g-000570", "g-000590"))
+ 
+   gcsData <- genesCoexSpace(objCOTAN = obj,
+                             primaryMarkers = unlist(groupMarkers),
+                             numGenesPerMarker = 11L)
+ 
+   genes.coex.space.test <- gcsData[["GCS"]]
+   saveRDS(genes.coex.space.test,
+           file.path(testsDir, "genes.coex.space.test.RDS"))
+ 
+   genesClustersData <-
+     establishGenesClusters(objCOTAN = obj,
+                            groupMarkers = groupMarkers,
+                            numGenesPerMarker = 11L,
+                            kCuts = 6L, distance = "cosine",
+                            hclustMethod = "ward.D2")
+ 
+   pca.genes.clusters.test <- genesClustersData[["pca_clusters"]]
+   saveRDS(pca.genes.clusters.test,
+           file.path(testsDir, "pca.genes.clusters.test.RDS"))
+ 
+   # Make it a less strict check as it is only for testing
+   checker <- new("AdvancedGDIUniformityCheck")
+   checker <- shiftCheckerThresholds(checker, 0.1)
+ 
+   initialResolution <- 0.8
+   splitData <- cellsUniformClustering(objCOTAN = obj,
+                                       checker = checker,
+                                       initialResolution = initialResolution,
+                                       useCoexEigen = TRUE,
+                                       dataMethod = "LL",
+                                       numReducedComp = 50L,
+                                       cores = 6L, optimizeForSpeed = TRUE,
+                                       deviceStr = "cuda", saveObj = FALSE)
+ 
+   split.clusters.test <- splitData[["clusters"]]
+   saveRDS(split.clusters.test, file.path(testsDir, "split.clusters.test.RDS"))
+ 
+   obj <- addClusterization(objCOTAN = obj,
+                            clName = "split",
+                            clusters = splitData[["clusters"]],
+                            coexDF = splitData[["coex"]])
+ 
+   coex.clusters.test <- splitData[["coex"]][genes.names.test, ]
+   saveRDS(coex.clusters.test, file.path(testsDir, "coex.clusters.test.RDS"))
+ 
+   pvalDF <- pValueFromDEA(splitData[["coex"]],
+                           getNumCells(objCOTAN = obj),
+                           adjustmentMethod = "none")
+ 
+   pvalues.clusters.test <- pvalDF[genes.names.test, ]
+   saveRDS(pvalues.clusters.test,
+           file.path(testsDir, "pvalues.clusters.test.RDS"))
+ 
+   mergedData <- mergeUniformCellsClusters(objCOTAN = obj,
+                                           clusters = splitData[["clusters"]],
+                                           checkers = checker,
+                                           cores = 6L,
+                                           distance = "cosine",
+                                           hclustMethod = "ward.D2",
+                                           saveObj = FALSE)
+ 
+   merge.clusters.test <- mergedData[["clusters"]]
+   saveRDS(merge.clusters.test, file.path(testsDir, "merge.clusters.test.RDS"))
+ 
+   obj <- addClusterization(objCOTAN = obj,
+                            clName = "merge",
+                            clusters = mergedData[["clusters"]],
+                            coexDF = mergedData[["coex"]])
+ }
> 
> proc.time()
   user  system elapsed 
  0.249   0.084   0.326

COTAN.Rcheck/tests/spelling.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.

> if (requireNamespace("spelling", quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.204   0.089   0.295

COTAN.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.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> library(zeallot)
> test_check("COTAN")
Setting new log level to 4
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.97673106193542
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.71598505973816
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000780105590820312
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00885200500488281
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.911616802215576
Total calculations elapsed time: 3.63723397254944
Calculate genes' COEX (legacy): DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 5 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 4 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 5.46026515960693
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 7 cells batches
Total calculations elapsed time: 0.934621810913086
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75595238095238 | median:  1.07156808035714 | mean:  1.07156808035714
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.74872207641602
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03734183779544 | max: 4.61112297272667 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.858587980270386
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0295487661210321 | median:  0.016072261901129 | mean:  0.016072261901129
`nu` mean: 1.69786080481514
Marginal errors | max: 1.95799528047999 | median 1.32268477389029 | mean: 1.33563364783916
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.90498805046082
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0585450475968788 | max: 3.52739274166646 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.934489011764526
Estimate `nu`: DONE
`nu` change (abs) | max: 0.417150556912302 | median:  0.240156504520849 | mean:  0.240156504520849
`nu` mean: 0.823005947608547
Marginal errors | max: 0.837672524335753 | median 0.704691669139061 | mean: 0.646575831699996
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.72700214385986
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.328845855849147 | max: 4.03031691940854 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.836984157562256
Estimate `nu`: DONE
`nu` change (abs) | max: 0.164439840041 | median:  0.0957105992188852 | mean:  0.0957105992188852
`nu` mean: 1.06872924082212
Marginal errors | max: 0.260109847946692 | median 0.21392791155499 | mean: 0.197565106613055
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.74676704406738
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.229469002841045 | max: 3.87206403670079 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.918884992599487
Estimate `nu`: DONE
`nu` change (abs) | max: 0.05539667181205 | median:  0.0321044921874999 | mean:  0.0321044921874999
`nu` mean: 0.97670782037545
Marginal errors | max: 0.095347789718808 | median 0.0796003827042702 | mean: 0.0725509735761708
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.74267196655273
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.263830434255107 | max: 3.92953043775907 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.876075029373169
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0196209299693411 | median:  0.0114037947200925 | mean:  0.0114037947200925
`nu` mean: 1.00821713524925
Marginal errors | max: 0.0329495161656741 | median 0.0273479725376307 | mean: 0.0250296751521313
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.80235600471497
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251734659898778 | max: 3.9096133246649 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.874081134796143
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0069104540740097 | median:  0.0040109538496062 | mean:  0.0040109538496062
`nu` mean: 0.997100499775596
Marginal errors | max: 0.0116950057438405 | median 0.00972280144874116 | mean: 0.00889105008777609
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.87716507911682
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.256009779031907 | max: 3.91667271750655 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.917715072631836
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00251004753849005 | median:  0.00146484374999994 | mean:  0.00146484374999994
`nu` mean: 1.00104520378849
Marginal errors | max: 0.00430755646112857 | median 0.00358203399504298 | mean: 0.00327684342604062
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.74530291557312
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.254429717857093 | max: 3.91406908073254 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.884257078170776
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00104629156456748 | median:  0.000592910406456731 | mean:  0.000592910406456731
`nu` mean: 0.999546618841889
Marginal errors | max: 0.00162038706091039 | median 0.00134441676098973 | mean: 0.00123030512553246
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.76735901832581
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255022049769696 | max: 3.91504587939868 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.904188871383667
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000418450901304768 | median:  0.000244140625000028 | mean:  0.000244140625000028
`nu` mean: 1.0001743102763
Marginal errors | max: 0.00071569233034019 | median 0.000597297218559056 | mean: 0.000545906995079548
Total calculations elapsed time: 48.2291288375854
Estimate `dispersion`/`nu`: DONE
Estimate `dispersion`/`nu`: START
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.84101605415344
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.89360022544861
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.00101780891418457
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00388312339782715
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.965687036514282
Total calculations elapsed time: 3.8641881942749
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.79687905311584
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000684022903442383
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00275397300720215
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.929429054260254
Total calculations elapsed time: 3.72974610328674
Calculate cells' COEX (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00935912132263184
Calculate `GDI`: DONE
Total calculations elapsed time: 2.80477499961853
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00253605842590332
Calculate `GDI`: DONE
Total calculations elapsed time: 2.8041980266571
Calculate GDI dataframe: DONE
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Selected 5 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 5 genes using HVG_Seurat selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer data
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Running genes' selection: START
Given 5 genes as input
Running genes' selection: DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.89517688751221
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.82352495193481
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Selected 8 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.85762691497803
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 8 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 2.84660887718201
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.69726586341858
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.72933292388916
Elaborating Reduced dimensionality Data Matrix - DONE
Initializing `COTAN` meta-data
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.7446391582489
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.92989706993103
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 1.735699617106 | median 1.3799744133366 | mean: 1.32181397451301
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.88553309440613
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0655494303592343 | max: 3.54400580804152 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.912134885787964
Estimate `nu`: DONE
`nu` change (abs) | max: 0.402649984216273 | median:  0.231868788425666 | mean:  0.231868788425666
`nu` mean: 0.829218804209393
Marginal errors | max: 0.803248939260364 | median 0.677504196374578 | mean: 0.619386446933353
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.91327500343323
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.326019058449519 | max: 4.02612397202046 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.911023855209351
Estimate `nu`: DONE
`nu` change (abs) | max: 0.158004893526231 | median:  0.0919692884670312 | mean:  0.0919692884670312
`nu` mean: 1.0660356050592
Marginal errors | max: 0.250677002875358 | median 0.206241644985115 | mean: 0.190402167377958
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.84072518348694
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.230397316576369 | max: 3.87365659194104 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.921861886978149
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0532774732102337 | median:  0.0308837890624999 | mean:  0.0308837890624999
`nu` mean: 0.977606315852266
Marginal errors | max: 0.0916920322976189 | median 0.0765360853958157 | mean: 0.069767303009408
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.85801291465759
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.263457616228195 | max: 3.928924407347 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.918872117996216
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0187878665732679 | median:  0.0109155550210726 | mean:  0.0109155550210726
`nu` mean: 1.0078723115522
Marginal errors | max: 0.0315207323253404 | median 0.0261635598193228 | mean: 0.0239435763640454
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.81414890289307
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251890641847532 | max: 3.90987172241566 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.880725860595703
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00649137083358098 | median:  0.00376680890457393 | mean:  0.00376680890457393
`nu` mean: 0.997275438070993
Marginal errors | max: 0.0109748802265024 | median 0.00912386940474885 | mean: 0.00834350038184297
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.86817216873169
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255902752363649 | max: 3.91649655995187 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.925863027572632
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00230094227000666 | median:  0.00132529141000018 | mean:  0.00132529141000018
`nu` mean: 1.00097565086001
Marginal errors | max: 0.00376864912836616 | median 0.00313421412286008 | mean: 0.00286709489297508
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.80098509788513
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.254520292119112 | max: 3.91421850264948 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.932003021240234
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837013154366462 | median:  0.000488281250000028 | mean:  0.000488281250000028
`nu` mean: 0.999651268095634
Marginal errors | max: 0.0014405532051498 | median 0.00119489364392944 | mean: 0.00109355439757195
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.86500406265259
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255046800817985 | max: 3.91508667609651 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.958537101745605
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000418448154490214 | median:  0.000244140624999917 | mean:  0.000244140624999917
`nu` mean: 1.00017430752949
Marginal errors | max: 0.000715683388516908 | median 0.000597284734240588 | mean: 0.000545899916522963
Total calculations elapsed time: 49.7668080329895
Estimate `dispersion`/`nu`: DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.78126287460327
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000805139541625977
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00223588943481445
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.941602945327759
Total calculations elapsed time: 3.72590684890747
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.72999501228333
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.000818967819213867
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00218415260314941
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.910744905471802
Total calculations elapsed time: 3.64374303817749
Calculate cells' COEX (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00380706787109375
Calculate `GDI`: DONE
Total calculations elapsed time: 2.6374340057373
Calculate GDI dataframe: DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.325
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 7.4030339717865
Calculate genes' partial COEX: DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 7.4335150718689
Calculate cells' partial COEX: DONE
Asked to drop 2 genes and 0 cells
Asked to drop 0 genes and 4 cells
Asked to drop 2 genes and 2 cells

Attaching package: 'rlang'

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

    is_false, is_null, is_true

Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating YN..NY..NN..t().. done
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.58032703399658
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
calculating NN.. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.79326486587524
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000766992568969727
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00143623352050781
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.00251698493958
Total calculations elapsed time: 3.7979850769043
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.84058213233948
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000782966613769531
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00206804275512695
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.959282875061035
Total calculations elapsed time: 3.80271601676941
Calculate genes' COEX (legacy): DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.1
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 7.3786449432373
Calculate genes' partial COEX: DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.4
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 7.52274918556213
Calculate genes' partial COEX: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating NY..YN..NN..t().. done
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.75527715682983
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.895462989807129
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.255290533439036 | median 0.0807313765005375 | mean: 0.101968565509113
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.78350901603699
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.950520992279053
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741771 | median 0.00111713187082163 | mean: 0.00132007186543017
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.62900805473328
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.916563987731934
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.68182247684001e-07 | mean: 5.57649710817287e-06
Total calculations elapsed time: 22.4882569313049
Estimate `dispersion`/`nu`: DONE
calculating NN.. done
calculating NN.. done
calculating YN..NY..YY..t().. done
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.84947419166565
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000969886779785156
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00214409828186035
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.895526885986328
Total calculations elapsed time: 3.74811506271362
Calculate cells' COEX (legacy): DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 7.32868194580078
Calculate cells' partial COEX: DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 7.51332497596741
Calculate cells' partial COEX: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.69946599006653
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.935839891433716
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.255290533439036 | median 0.0807313765005375 | mean: 0.101968565509113
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.841059923172
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.90410304069519
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741771 | median 0.00111713187082163 | mean: 0.00132007186543017
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.81186604499817
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.919545888900757
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.68182247684001e-07 | mean: 5.57649710817287e-06
Total calculations elapsed time: 22.6697249412537
Estimate `dispersion`/`nu`: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.77680015563965
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000787973403930664
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00200891494750977
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.939677000045776
Total calculations elapsed time: 3.71927404403687
Calculate genes' COEX (legacy): DONE
Calculating S: START
Calculating S: DONE
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.7019031047821
Calculating G: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values genome wide on columns and genome wide on rows
Total calculations elapsed time: 0.00301194190979004
calculating PValues: DONE
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.70100092887878
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 6.70229291915894
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00358700752258301
Calculate `GDI`: DONE
Total calculations elapsed time: 2.90191388130188
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.34056901931763
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00230789184570312
Calculate `GDI`: DONE
Total calculations elapsed time: 9.2224178314209
Calculate GDI dataframe: DONE
Calculate `GDI`: START
Calculating S: START
Calculating S: DONE
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00507402420043945
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00373601913452148
Calculate `GDI`: DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.965887069702148
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.3013391494751
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.19524383544922
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.47927713394165
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.010779857635498
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.045051097869873
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.883711099624634
Total calculations elapsed time: 4.41881918907166
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.32198405265808
Dataset analysis elapsed time: 9.48311495780945
COTAN dataset analysis: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.918379068374634
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.09389114379883
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.00097703933716
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.42483186721802
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0103890895843506
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0415849685668945
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.920424938201904
Total calculations elapsed time: 4.39723086357117
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.27906894683838
Dataset analysis elapsed time: 9.19842505455017
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.0246520042419434
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0322530269622803
Calculate `GDI`: DONE
Total calculations elapsed time: 2.85516405105591
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.953752040863037
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.15238285064697
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.03974604606628
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.58864188194275
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00981712341308594
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0467460155487061
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.984843015670776
Total calculations elapsed time: 4.63004803657532
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.52715587615967
Dataset analysis elapsed time: 9.52065396308899
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.0167088508605957
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0353901386260986
Calculate `GDI`: DONE
Total calculations elapsed time: 2.74848604202271
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.940786123275757
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.12589311599731
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.04076886177063
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.38321614265442
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00654196739196777
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.047860860824585
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.864367008209229
Total calculations elapsed time: 4.3019859790802
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.20818305015564
Dataset analysis elapsed time: 9.18973803520203
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.00747799873352051
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0308599472045898
Calculate `GDI`: DONE
Total calculations elapsed time: 2.79885792732239
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 1160 cells
COTAN dataset analysis: START
Asked to drop 31 genes and 0 cells
Genes/cells selection done: dropped [31] genes and [0] cells
Working on [569] genes and [40] cells
Dataset cleaning elapsed time: 0.912739992141724
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 6 iterations
Total calculations elapsed time: 1.82645797729492
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.212044752677142 | max: 85.4528331044021 | % negative: 62.2144112478032
Model parameter estimation elapsed time: 2.72286605834961
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.911922931671143
Dataset analysis elapsed time: 4.54752898216248
COTAN dataset analysis: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.73038291931152
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00790596008300781
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00670719146728516
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.93300986289978
Total calculations elapsed time: 3.6780059337616
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.71995687484741
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00942015647888184
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00781583786010742
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.904924154281616
Total calculations elapsed time: 3.64211702346802
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.78381204605103
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0070960521697998
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00760579109191895
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.968735218048096
Total calculations elapsed time: 3.76724910736084
Calculate genes' COEX (legacy): DONE
Hangling COTAN object with condition: test
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.00784397125244141
calculating PValues: DONE
Handling genes type: G2
Handling genes type: G3
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Clean plots: START
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Total calculations elapsed time: 2.17422890663147
Clean plots: DONE
Dataset cleaning elapsed time: 4.6906259059906
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 3.62602090835571
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 4.59284400939941
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.59667897224426
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00656700134277344
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0461549758911133
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.00415682792664
Total calculations elapsed time: 4.65355777740479
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.64621806144714
Dataset analysis elapsed time: 14.9296879768372
COTAN dataset analysis: DONE
Saving elaborated data locally at: /tmp/RtmpbRJSe6/test.cotan.RDS
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 3.13967609405518
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 41850

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5751
Number of communities: 2
Elapsed time: 0 seconds
Number of clusters is too small. Reclustering at resolution higher than: 0.8
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 41850

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3786
Number of communities: 7
Elapsed time: 0 seconds
2 singletons identified. 5 final clusters.
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 4.57287788391113
Creating new clusterization: DONE
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 3.2804319858551
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 29356

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5763
Number of communities: 2
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Total calculations elapsed time: 4.34874820709229
Creating new clusterization: DONE
Creating PDF UMAP in file:  /tmp/RtmpbRJSe6/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
20:49:27 UMAP embedding parameters a = 0.9922 b = 1.112
20:49:27 Read 1200 rows and found 65 numeric columns
20:49:27 Using Annoy for neighbor search, n_neighbors = 30
20:49:27 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:49:27 Writing NN index file to temp file /tmp/RtmpbRJSe6/file102a43425ad0
20:49:27 Searching Annoy index using 1 thread, search_k = 3000
20:49:27 Annoy recall = 100%
20:49:28 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:49:30 Initializing from normalized Laplacian + noise (using RSpectra)
20:49:30 Commencing optimization for 500 epochs, with 48472 positive edges
20:49:30 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:49:33 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 6.5804557800293
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
20:49:33 UMAP embedding parameters a = 0.9922 b = 1.112
20:49:33 Read 1200 rows and found 65 numeric columns
20:49:33 Using Annoy for neighbor search, n_neighbors = 30
20:49:33 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:49:34 Writing NN index file to temp file /tmp/RtmpbRJSe6/file102a44585d9a
20:49:34 Searching Annoy index using 1 thread, search_k = 3000
20:49:34 Annoy recall = 100%
20:49:35 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:49:37 Initializing from normalized Laplacian + noise (using RSpectra)
20:49:37 Commencing optimization for 500 epochs, with 48472 positive edges
20:49:37 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:49:40 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 6.39137387275696
UMAP plot: DONE
* checking uniformity of cluster '0' of 2 clusters
Asked to drop 0 genes and 587 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [613] cells
Dataset cleaning elapsed time: 1.00179004669189
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.20538187026978
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0334270578203965 | max: 8.68674670630126 | % negative: 4.16666666666667
Model parameter estimation elapsed time: 3.22453093528748
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.42941904067993
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00703310966491699
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0376279354095459
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.945756912231445
Total calculations elapsed time: 4.41983699798584
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.38331508636475
Dataset analysis elapsed time: 9.60963606834412
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0000' with 613 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0294609069824219
Calculate `GDI`: DONE
Total calculations elapsed time: 2.98780298233032
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0495870113372803
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 613, is uniform
Cluster 01_0000's shift to uniformity: -0.0159698218976119
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0333333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38103017810239, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0233333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42514299918547, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.4503882472624, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.5015551958585, isUniform = TRUE, clusterSize = 613
cluster 01_0000 is uniform

* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 613 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [587] cells
Dataset cleaning elapsed time: 1.01191306114197
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.20980310440063
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7
Model parameter estimation elapsed time: 3.27087783813477
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.35366106033325
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0151479244232178
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0510749816894531
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02057909965515
Total calculations elapsed time: 4.44046306610107
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.36747813224792
Dataset analysis elapsed time: 9.65026903152466
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 587 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0369100570678711
Calculate `GDI`: DONE
Total calculations elapsed time: 2.92169380187988
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0425429344177246
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 587, is uniform
Cluster 01_0001's shift to uniformity: -0.00930197949808731
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0433333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38769802050191, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42646635133469, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.46799318315158, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52850104542575, isUniform = TRUE, clusterSize = 587
cluster 01_0001 is uniform


Found 2 uniform and  0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0000, 01_0001
Differential Expression Analysis - START
* DEA on cluster '1' with 613 cells
* DEA on cluster '2' with 587 cells

Total calculations elapsed time: 0.0687680244445801
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 52.5600180625916
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Asked to drop 0 genes and 613 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [587] cells
Dataset cleaning elapsed time: 1.00165009498596
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.21506500244141
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7
Model parameter estimation elapsed time: 3.27120900154114
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.39677786827087
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.010775089263916
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0373730659484863
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.01115989685059
Total calculations elapsed time: 4.45608592033386
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.46859097480774
Dataset analysis elapsed time: 9.74145007133484
COTAN dataset analysis: DONE
Checking uniformity for the cluster 'Cluster_2' with 587 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0326130390167236
Calculate `GDI`: DONE
Total calculations elapsed time: 3.0276620388031
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0413098335266113
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_2, with size 587, is uniform
Cluster Cluster_2's shift to uniformity: -0.00930197949808731
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0433333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38769802050191, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42646635133469, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.46799318315158, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52850104542575, isUniform = TRUE, clusterSize = 587
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 611 cells
* DEA on cluster '2' with 539 cells

Total calculations elapsed time: 0.0636110305786133
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  2, 2  ->  1, -1  ->  -1
Applied reordering to clusterization is:
1  ->  1, 2  ->  2, -1  ->  -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0329029560089111
Calculate `GDI`: DONE
Total calculations elapsed time: 3.14037394523621
Calculate GDI dataframe: DONE
Included 186 genes with GDI below 1.3
Selected 600 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 6.18846297264099
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Total calculations elapsed time: 7.22472310066223
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file:  /tmp/RtmpbRJSe6/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
20:50:39 UMAP embedding parameters a = 0.9922 b = 1.112
20:50:39 Read 1200 rows and found 40 numeric columns
20:50:39 Using Annoy for neighbor search, n_neighbors = 30
20:50:39 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:50:39 Writing NN index file to temp file /tmp/RtmpbRJSe6/file102a413c97355
20:50:39 Searching Annoy index using 1 thread, search_k = 3000
20:50:40 Annoy recall = 100%
20:50:41 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:50:43 Initializing from normalized Laplacian + noise (using RSpectra)
20:50:43 Commencing optimization for 500 epochs, with 42644 positive edges
20:50:43 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:50:45 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 6.27273201942444
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
20:50:46 UMAP embedding parameters a = 0.9922 b = 1.112
20:50:46 Read 1200 rows and found 40 numeric columns
20:50:46 Using Annoy for neighbor search, n_neighbors = 30
20:50:46 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:50:46 Writing NN index file to temp file /tmp/RtmpbRJSe6/file102a46f2159
20:50:46 Searching Annoy index using 1 thread, search_k = 3000
20:50:46 Annoy recall = 100%
20:50:47 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:50:49 Initializing from normalized Laplacian + noise (using RSpectra)
20:50:49 Commencing optimization for 500 epochs, with 42644 positive edges
20:50:49 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:50:52 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 6.12348890304565
UMAP plot: DONE
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 600 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Dataset cleaning elapsed time: 0.981181859970093
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.11117386817932
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0387079873074399 | max: 19.3963889884382 | % negative: 6.5
Model parameter estimation elapsed time: 3.13440203666687
COTAN genes' COEX estimation: START
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.28917479515076
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00789403915405273
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0315139293670654
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.953521013259888
Total calculations elapsed time: 4.28210377693176
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.26299905776978
Dataset analysis elapsed time: 9.37858295440674
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0352818965911865
Calculate `GDI`: DONE
Total calculations elapsed time: 2.98088502883911
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0435309410095215
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 600, is uniform
Cluster 01_0001's shift to uniformity: -0.0123041937718968
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3846958062281, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42417208332107, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00666666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45335006989431, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 4, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.51519118633036, isUniform = TRUE, clusterSize = 600
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 600 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Dataset cleaning elapsed time: 0.989734172821045
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.13757801055908
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0329292435898063 | max: 10.0824885336881 | % negative: 3.66666666666667
Model parameter estimation elapsed time: 3.14168691635132
COTAN genes' COEX estimation: START
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.37118792533875
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00934815406799316
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0380818843841553
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.07479906082153
Total calculations elapsed time: 4.49341702461243
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.58023595809937
Dataset analysis elapsed time: 9.71165704727173
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.03438401222229
Calculate `GDI`: DONE
Total calculations elapsed time: 3.10022521018982
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0467848777770996
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 600, is uniform
Cluster 01_0002's shift to uniformity: -0.0203364702469133
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37666352975309, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42307834225193, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43781655605474, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50180130506577, isUniform = TRUE, clusterSize = 600
cluster 01_0002 is uniform


Found 2 uniform and  0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002
Differential Expression Analysis - START
* DEA on cluster '1' with 600 cells
* DEA on cluster '2' with 600 cells

Total calculations elapsed time: 0.0536701679229736
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 54.6241419315338
Creating cells' uniform clustering: DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'

Total calculations elapsed time: 1.98236012458801
Log Fold Change Analysis - DONE
Total calculations elapsed time: 1.9941520690918
findClustersMarkers - DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'

Total calculations elapsed time: 1.99573802947998
Log Fold Change Analysis - DONE
Total calculations elapsed time: 2.00515985488892
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1' with 613 cells
* DEA on cluster '2' with 587 cells

Total calculations elapsed time: 0.0610029697418213
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'

Total calculations elapsed time: 2.08944296836853
Log Fold Change Analysis - DONE
Total calculations elapsed time: 2.15874600410461
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 587 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [613] cells
Dataset cleaning elapsed time: 1.03684997558594
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.17062997817993
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0334270578203965 | max: 8.68674670630126 | % negative: 4.16666666666667
Model parameter estimation elapsed time: 3.13453912734985
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.40654802322388
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0123348236083984
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.045119047164917
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02413105964661
Total calculations elapsed time: 4.4881329536438
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.51452803611755
Dataset analysis elapsed time: 9.68591713905334
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0324649810791016
Calculate `GDI`: DONE
Total calculations elapsed time: 3.31593608856201
Calculate GDI dataframe: DONE
[1] "Tested cluster: 2"
Asked to drop 0 genes and 613 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [587] cells
Dataset cleaning elapsed time: 1.09660720825195
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.29222106933594
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7
Model parameter estimation elapsed time: 3.37800288200378
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.54857015609741
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00678682327270508
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0390000343322754
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02277398109436
Total calculations elapsed time: 4.61713099479675
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.70766806602478
Dataset analysis elapsed time: 10.1822781562805
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0330808162689209
Calculate `GDI`: DONE
Total calculations elapsed time: 2.82075500488281
Calculate GDI dataframe: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.23102211952209
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.898874998092651
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.4255039691925
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.39898300170898
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 1.1534411907196
Dataset analysis elapsed time: 5.45129919052124
COTAN dataset analysis: DONE
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
PC_ 1 
Positive:  g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 
	   g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 
	   g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 
Negative:  g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 
	   g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 
	   g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 
PC_ 2 
Positive:  g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 
	   g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 
	   g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 
Negative:  g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 
	   g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 
	   g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 
PC_ 3 
Positive:  g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 
	   g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 
	   g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 
Negative:  g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 
	   g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 
	   g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 
PC_ 4 
Positive:  g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 
	   g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 
	   g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 
Negative:  g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 
	   g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 
	   g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 
PC_ 5 
Positive:  g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 
	   g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 
	   g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 
Negative:  g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 
	   g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 
	   g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55940

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5920
Number of communities: 4
Elapsed time: 0 seconds
Clusterizations found: RNA_snn_res.0.8, seurat_clusters
Conditions found: orig.ident
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 1.12063002586365
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.15420293807983
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.07765793800354
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.931056022644043
Dataset analysis elapsed time: 5.12934398651123
COTAN dataset analysis: DONE
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.934680938720703
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.23109006881714
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.2491569519043
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.49437308311462
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00680303573608398
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0477950572967529
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.964651823043823
Total calculations elapsed time: 4.51362299919128
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.47792410850525
Dataset analysis elapsed time: 9.66176199913025
COTAN dataset analysis: DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00664186477661133
calculating PValues: DONE
Number of selected secondary markers: 6
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00890016555786133
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Total calculations elapsed time: 1.05763912200928
Calculating gene co-expression space - DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00795817375183105
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0101649761199951
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Total calculations elapsed time: 1.04924201965332
Calculating gene co-expression space - DONE
Establishing gene clusters - START
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00741004943847656
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00957608222961426
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Total calculations elapsed time: 1.02707099914551
Calculating gene co-expression space - DONE
Total calculations elapsed time: 1.11022114753723
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.95952296257019
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.26459503173828
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.29308199882507
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.937519073486328
Dataset analysis elapsed time: 5.19012403488159
COTAN dataset analysis: DONE
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells

Total calculations elapsed time: 0.0567271709442139
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'

Total calculations elapsed time: 2.02989912033081
Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.09087489420394
Handling cluster '2' with mean UDE 0.906669027574328
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 3 genes
In group G3 there are 5 detected over 5 genes
Merging cells' uniform clustering: START
The merge algorithm will use 2 passes
Start merging nearest clusters - the main threshold is: 1.297
Start merging nearest clusters: iteration 1
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells

Total calculations elapsed time: 0.0611410140991211
Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1", "2")
*1_2-merge
Asked to drop no genes or cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 1.04129886627197
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.33070802688599
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 4.03676104545593
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 6.08635091781616
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0604679584503174
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0790560245513916
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.991198062896729
Total calculations elapsed time: 7.2170729637146
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 8.02659010887146
Dataset analysis elapsed time: 13.1046500205994
COTAN dataset analysis: DONE
Checking uniformity for the cluster '1_2-merge' with 1200 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0246798992156982
Calculate `GDI`: DONE
Total calculations elapsed time: 2.66179299354553
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0309960842132568
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 1200, is not uniform
Cluster 1_2-merge's shift to uniformity: 0.273171158219277
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.696666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017115821928, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.665, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61241976619328, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.411666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64049230721132, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 247, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66511539543561, isUniform = FALSE, clusterSize = 1200
Clusters 1 and 2 cannot be merged
Finished the first batch - no merges were executed
Loop calculations elapsed time: 20.872495174408
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells

Total calculations elapsed time: 0.0599570274353027
Differential Expression Analysis - DONE
Updating check results for the 1 already tested pairs to align to new checker
0 new clusters pairs to be tested for merging:

No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.297 out of 1 checks
Start merging nearest clusters - the main threshold is: 1.397
Start merging nearest clusters: iteration 3
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells

Total calculations elapsed time: 0.06227707862854
Differential Expression Analysis - DONE
Updating check results for the 1 already tested pairs to align to new checker
0 new clusters pairs to be tested for merging:

No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.397 out of 1 checks
The final merged clusterization contains [2] different clusters: 1, 2
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells

Total calculations elapsed time: 0.0607430934906006
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 23.2002780437469
Merging cells' uniform clustering: DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'

Total calculations elapsed time: 1.98167896270752
Log Fold Change Analysis - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 592 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [608] cells
Dataset cleaning elapsed time: 1.03250980377197
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.1896960735321
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0337582853418583 | max: 10.9273420652533 | % negative: 4.33333333333333
Model parameter estimation elapsed time: 3.16275501251221
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.33502793312073
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0072021484375
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0402958393096924
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.973531007766724
Total calculations elapsed time: 4.35605692863464
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.31098413467407
Dataset analysis elapsed time: 9.50624895095825
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0350379943847656
Calculate `GDI`: DONE
Total calculations elapsed time: 4.70502591133118
Calculate GDI dataframe: DONE
[1] "Tested cluster: 2"
Asked to drop 0 genes and 608 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [592] cells
Dataset cleaning elapsed time: 2.24610495567322
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.45337200164795
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0390500444479481 | max: 19.2061656068405 | % negative: 7.33333333333333
Model parameter estimation elapsed time: 3.53221201896667
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.39127993583679
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0104398727416992
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0328640937805176
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02528095245361
Total calculations elapsed time: 4.45986485481262
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.43907499313354
Dataset analysis elapsed time: 11.2173919677734
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0350308418273926
Calculate `GDI`: DONE
Total calculations elapsed time: 3.04785394668579
Calculate GDI dataframe: DONE
Dispersion bisection: straddling used 2 iterations
Dispersion bisection: used 8 iterations
Dispersion bisection: straddling used 1 iterations
Dispersion bisection: used 9 iterations
Dispersion Newton-Raphson: used up to 4 iterations
Dispersion Newton-Raphson: used up to 4 iterations
parallel dispersion bisection: straddling used up to 2 iterations
Parallel dispersion bisection: used up to 9 iterations
Parallel dispersion Newton-Raphson: used up to 4 iterations
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ]
> 
> proc.time()
   user  system elapsed 
664.002  10.133 684.437

Example timings

COTAN.Rcheck/COTAN-Ex.timings

name	user	system	elapsed
COTAN_Legacy	0.002	0.001	0.003
COTAN_ObjectCreation	10.777	0.273	11.251
CalculatingCOEX	56.351	1.071	57.688
ClustersList	0.007	0.002	0.009
Conversions	5.186	0.112	5.322
GenesStatistics	11.430	0.343	11.654
HandleMetaData	0.090	0.007	0.098
HandlingClusterizations	43.967	1.095	44.779
HandlingConditions	0.120	0.008	0.127
HeatmapPlots	35.376	0.839	36.430
Installing_torch	0.001	0.001	0.001
LoggingFunctions	0.003	0.001	0.004
ParametersEstimations	23.475	0.716	24.326
RawDataCleaning	5.178	0.301	5.318
RawDataGetters	0.106	0.008	0.116
UniformClusters	118.489	2.583	120.425
getColorsVector	0.002	0.016	0.001