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"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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: 2.9.7

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_2.9.7.tar.gz

StartedAt: 2025-10-24 20:25:52 -0400 (Fri, 24 Oct 2025)

EndedAt: 2025-10-24 20:47:18 -0400 (Fri, 24 Oct 2025)

EllapsedTime: 1286.5 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_2.9.7.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 ‘2.9.7’
* 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         66.259  1.890  67.478
CalculatingCOEX         52.342  1.003  53.609
HandlingClusterizations 41.629  1.129  42.403
HeatmapPlots            30.788  0.813  31.768
ParametersEstimations   21.042  0.626  21.778
GenesStatistics         10.605  0.291  10.801
COTAN_ObjectCreation    10.225  0.261  10.550
* 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 ‘2.9.7’
** 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(131L:140L, 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-000138"),
+                        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 <- 1.3
+   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 = file.path(testsDir, "split.clusters.test.RDS"))
+ 
+   test.dataset.clusters1 <- split.clusters.test
+   save(test.dataset.clusters1, compress = TRUE,
+        file = file.path("data", "test.dataset.clusters1.rda"))
+ 
+   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,
+                                           batchSize = 1L,
+                                           cores = 6L,
+                                           distance = "cosine",
+                                           hclustMethod = "ward.D2",
+                                           saveObj = FALSE)
+ 
+   merge.clusters.test <- mergedData[["clusters"]]
+   saveRDS(merge.clusters.test,
+           file = file.path(testsDir, "merge.clusters.test.RDS"))
+ 
+   test.dataset.clusters2 <- merge.clusters.test
+   save(test.dataset.clusters2, compress = TRUE,
+        file = file.path("data", "test.dataset.clusters2.rda"))
+ 
+   obj <- addClusterization(objCOTAN = obj,
+                            clName = "merge",
+                            clusters = mergedData[["clusters"]],
+                            coexDF = mergedData[["coex"]])
+ }
> 
> proc.time()
   user  system elapsed 
   0.26    0.08    0.34

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 
  0.195   0.079   0.266

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: 1.73777008056641
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: 2.52756714820862
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000799894332885742
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00653290748596191
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.816416025161743
Total calculations elapsed time: 3.35131597518921
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: 5.1073260307312
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: 0.854619026184082
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: 1.73574686050415
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: 0.860028982162476
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: 1.62912702560425
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: 0.884139060974121
Estimate `nu`: DONE
`nu` change (abs) | max: 0.417150556912302 | median:  0.240156504520849 | mean:  0.240156504520849
`nu` mean: 0.823005947608547
Marginal errors | max: 0.837672524335755 | median 0.704691669139065 | mean: 0.646575831699997
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: 1.78265714645386
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: 0.814770936965942
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: 0.197565106613054
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: 1.67721605300903
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: 0.842437982559204
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: 1.72083020210266
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: 0.945459127426147
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: 0.0250296751521303
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: 1.65368700027466
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: 0.859621047973633
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: 0.00889105008777591
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: 1.65755796432495
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: 0.833333969116211
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: 0.00327684342604027
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: 1.70484519004822
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: 0.833373069763184
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: 0.00123030512553282
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: 1.68715500831604
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: 0.917603969573975
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: 0.000545906995079193
Total calculations elapsed time: 46.2333159446716
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: 1.78932309150696
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: 2.78555202484131
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000992059707641602
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.004241943359375
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.01151704788208
Total calculations elapsed time: 3.80230307579041
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: 2.74624705314636
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.00108480453491211
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00282120704650879
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.93295693397522
Total calculations elapsed time: 3.683109998703
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: 0.012610912322998
Calculate `GDI`: DONE
Total calculations elapsed time: 2.74312400817871
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: 0.00264382362365723
Calculate `GDI`: DONE
Total calculations elapsed time: 2.67895102500916
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: 1.75107598304749
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: 1.71787881851196
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: 1.81061816215515
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: 2.74329209327698
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: 2.61999702453613
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: 2.63455700874329
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: 1.77372217178345
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: 0.865051031112671
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 1.37997441333659 | 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: 1.75214290618896
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: 0.859400033950806
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 0.677504196374571 | mean: 0.619386446933351
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: 1.70917105674744
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: 0.886107921600342
Estimate `nu`: DONE
`nu` change (abs) | max: 0.158004893526231 | median:  0.0919692884670312 | mean:  0.0919692884670312
`nu` mean: 1.0660356050592
Marginal errors | max: 0.25067700287536 | 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: 1.66659688949585
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: 0.861815214157104
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 0.0765360853958175 | mean: 0.0697673030094085
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: 1.75096201896667
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: 0.933398008346558
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: 0.0239435763640456
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: 1.75672197341919
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: 0.864421129226685
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: 1.80801200866699
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: 0.880632162094116
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 0.00313421412286186 | mean: 0.00286709489297632
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: 1.73821997642517
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: 0.878063201904297
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: 0.0010935543975723
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: 1.83861994743347
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: 0.913622140884399
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 0.0005972847342397 | mean: 0.00054589991652243
Total calculations elapsed time: 47.3446660041809
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: 2.62118792533875
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000518083572387695
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00130891799926758
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.808408975601196
Total calculations elapsed time: 3.4314239025116
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: 2.46016502380371
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.000543117523193359
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00191092491149902
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.868448972702026
Total calculations elapsed time: 3.33106803894043
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: 0.0022578239440918
Calculate `GDI`: DONE
Total calculations elapsed time: 2.54582095146179
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: 6.94216799736023
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: 7.06064891815186
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: 3.49451088905334
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: 2.69270706176758
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000975847244262695
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00132203102111816
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.897622108459473
Total calculations elapsed time: 3.59262704849243
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: 2.79856491088867
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000627994537353516
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00142002105712891
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.925475120544434
Total calculations elapsed time: 3.72608804702759
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: 7.27470803260803
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: 7.1113429069519
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: 3.69074416160583
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: 0.884661912918091
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: 3.49098801612854
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: 0.922996997833252
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964
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: 3.49549102783203
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: 0.846100807189941
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06
Total calculations elapsed time: 21.306853055954
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: 2.59700798988342
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000697135925292969
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00155782699584961
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.897253036499023
Total calculations elapsed time: 3.49651598930359
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: 7.09593820571899
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: 7.16272878646851
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: 3.6011848449707
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: 0.957115173339844
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: 3.6655809879303
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: 0.889125108718872
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964
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: 3.529137134552
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: 0.843463897705078
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06
Total calculations elapsed time: 21.604896068573
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: 2.72210001945496
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000519037246704102
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00223898887634277
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.852712869644165
Total calculations elapsed time: 3.57757091522217
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: 6.32406306266785
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: 0.0029749870300293
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: 6.31828093528748
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: 6.31991481781006
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: 0.00227189064025879
Calculate `GDI`: DONE
Total calculations elapsed time: 2.78281593322754
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: 6.58160996437073
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00273704528808594
Calculate `GDI`: DONE
Total calculations elapsed time: 9.2568941116333
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: 0.00418496131896973
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00332999229431152
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 [1000] cells
Dataset cleaning elapsed time: 0.910113096237183
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.18402814865112
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.04463601112366
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: 3.09016704559326
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0113990306854248
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0557148456573486
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.86829400062561
Total calculations elapsed time: 4.02557492256165
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.88428282737732
Dataset analysis elapsed time: 8.83903193473816
COTAN dataset analysis: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.816861152648926
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.97025990486145
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.81007790565491
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: 3.07360315322876
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00860190391540527
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0567259788513184
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.938239097595215
Total calculations elapsed time: 4.0771701335907
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.00241994857788
Dataset analysis elapsed time: 8.62935900688171
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: 0.0287199020385742
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: 0.0352861881256104
Calculate `GDI`: DONE
Total calculations elapsed time: 2.80878305435181
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.917104005813599
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.94211292266846
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.8106210231781
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: 3.15902996063232
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00653910636901855
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0637779235839844
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.942996025085449
Total calculations elapsed time: 4.17234301567078
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.08246898651123
Dataset analysis elapsed time: 8.81019401550293
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: 0.0176258087158203
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: 0.02994704246521
Calculate `GDI`: DONE
Total calculations elapsed time: 2.74427318572998
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.872386932373047
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.11283016204834
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.98698902130127
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: 3.40283298492432
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00731301307678223
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0544049739837646
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.950576066970825
Total calculations elapsed time: 4.41512703895569
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.29864096641541
Dataset analysis elapsed time: 9.15801692008972
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: 0.00632095336914062
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: 0.0298271179199219
Calculate `GDI`: DONE
Total calculations elapsed time: 2.8042368888855
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 960 cells
COTAN dataset analysis: START
Asked to drop 83 genes and 0 cells
Genes/cells selection done: dropped [83] genes and [0] cells
Working on [517] genes and [40] cells
Dataset cleaning elapsed time: 0.937685012817383
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.80789709091187
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.267567793681876 | max: 101.923257389521 | % negative: 52.6112185686654
Model parameter estimation elapsed time: 2.6763129234314
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.873213052749634
Dataset analysis elapsed time: 4.48721098899841
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: 2.66910004615784
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00450706481933594
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00955486297607422
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.904415130615234
Total calculations elapsed time: 3.58757710456848
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: 2.75682902336121
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: 0.0127980709075928
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.865787982940674
Total calculations elapsed time: 3.64198207855225
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: 2.70973682403564
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00688505172729492
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0108261108398438
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.887158870697021
Total calculations elapsed time: 3.6146068572998
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: 0.00595211982727051
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 [1000] cells
Clean plots: START
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Total calculations elapsed time: 2.00848197937012
Clean plots: DONE
Dataset cleaning elapsed time: 4.35571503639221
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.08416485786438
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.01190900802612
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: 3.32432198524475
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00917506217956543
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0591528415679932
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.958477020263672
Total calculations elapsed time: 4.35112690925598
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.29367685317993
Dataset analysis elapsed time: 12.6613008975983
COTAN dataset analysis: DONE
Saving elaborated data locally at: /tmp/RtmpQ4102t/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: 2.87568593025208
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: 1000
Number of edges: 44886

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.4008
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 3.89372181892395
Creating new clusterization: DONE
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1000 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: 2.93520903587341
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: 1000
Number of edges: 36652

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3743
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 3.86877012252808
Creating new clusterization: DONE
Creating PDF UMAP in file:  /tmp/RtmpQ4102t/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
20:42:12 UMAP embedding parameters a = 0.9922 b = 1.112
20:42:12 Read 1000 rows and found 65 numeric columns
20:42:12 Using Annoy for neighbor search, n_neighbors = 30
20:42:12 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:42:12 Writing NN index file to temp file /tmp/RtmpQ4102t/filef9d978f642b2
20:42:12 Searching Annoy index using 1 thread, search_k = 3000
20:42:12 Annoy recall = 100%
20:42:13 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:42:15 Initializing from normalized Laplacian + noise (using RSpectra)
20:42:15 Commencing optimization for 500 epochs, with 39044 positive edges
20:42:15 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:42:18 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 6.05858492851257
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
20:42:18 UMAP embedding parameters a = 0.9922 b = 1.112
20:42:18 Read 1000 rows and found 65 numeric columns
20:42:18 Using Annoy for neighbor search, n_neighbors = 30
20:42:18 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:42:18 Writing NN index file to temp file /tmp/RtmpQ4102t/filef9d91ba65953
20:42:18 Searching Annoy index using 1 thread, search_k = 3000
20:42:18 Annoy recall = 100%
20:42:19 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:42:21 Initializing from normalized Laplacian + noise (using RSpectra)
20:42:21 Commencing optimization for 500 epochs, with 39044 positive edges
20:42:21 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:42:24 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.73444795608521
UMAP plot: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 687 cells
COTAN dataset analysis: START
Asked to drop 43 genes and 0 cells
Genes/cells selection done: dropped [43] genes and [0] cells
Working on [557] genes and [313] cells
Dataset cleaning elapsed time: 0.989712953567505
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 11 iterations
Total calculations elapsed time: 1.98322582244873
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.126565269702225 | max: 788.372048308528 | % negative: 38.5996409335727
Model parameter estimation elapsed time: 2.90321111679077
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: 2.98815298080444
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00674986839294434
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.030102014541626
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.00092697143555
Total calculations elapsed time: 4.02593183517456
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.96677494049072
Dataset analysis elapsed time: 8.859699010849
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0000' with 313 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: 0.0260381698608398
Calculate `GDI`: DONE
Total calculations elapsed time: 2.91756081581116
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0377449989318848
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 313, is uniform
Cluster 01_0000's shift to uniformity: -0.0175178017151378
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0412926391382406, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37948219828486, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0323159784560144, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.43089123341117, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00179533213644524, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.44383613651629, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 1, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.47612588512221, isUniform = TRUE, clusterSize = 313
cluster 01_0000 is uniform

* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 743 cells
COTAN dataset analysis: START
Asked to drop 51 genes and 0 cells
Genes/cells selection done: dropped [51] genes and [0] cells
Working on [549] genes and [257] cells
Dataset cleaning elapsed time: 0.930289030075073
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 1.91470885276794
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.86210703849792
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: 3.00929999351501
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00513005256652832
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.025954008102417
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.985120058059692
Total calculations elapsed time: 4.02550411224365
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.99807095527649
Dataset analysis elapsed time: 8.79046702384949
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 257 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: 0.0270900726318359
Calculate `GDI`: DONE
Total calculations elapsed time: 2.98531293869019
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0447399616241455
Clean plots: DONE
GDI plot
Removed 1 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 257, is uniform
Cluster 01_0001's shift to uniformity: -0.0466523594845973
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00910746812386157, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3503476405154, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00728597449908925, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37278730407692, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.3866416314687, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.45240567481124, isUniform = TRUE, clusterSize = 257
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 758 cells
COTAN dataset analysis: START
Asked to drop 77 genes and 0 cells
Genes/cells selection done: dropped [77] genes and [0] cells
Working on [523] genes and [242] cells
Dataset cleaning elapsed time: 0.942609071731567
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.92549300193787
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.166254045792573 | max: 224.924342782861 | % negative: 42.6386233269598
Model parameter estimation elapsed time: 2.95000696182251
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: 2.95947790145874
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00495100021362305
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0254800319671631
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.987396955490112
Total calculations elapsed time: 3.97730588912964
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.96058201789856
Dataset analysis elapsed time: 8.85319805145264
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0002' with 242 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: 0.0253820419311523
Calculate `GDI`: DONE
Total calculations elapsed time: 2.92719006538391
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0396828651428223
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 242, is uniform
Cluster 01_0002's shift to uniformity: -0.047352793630024
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00764818355640535, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.34964720636998, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00764818355640535, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37472946305404, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38771313919655, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.43097703442028, isUniform = TRUE, clusterSize = 242
cluster 01_0002 is uniform

* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 812 cells
COTAN dataset analysis: START
Asked to drop 79 genes and 0 cells
Genes/cells selection done: dropped [79] genes and [0] cells
Working on [521] genes and [188] cells
Dataset cleaning elapsed time: 0.960453987121582
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: 1.95072484016418
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818729 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 2.89796113967896
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: 3.10711193084717
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00496697425842285
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0199379920959473
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.982679128646851
Total calculations elapsed time: 4.11469602584839
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.09298491477966
Dataset analysis elapsed time: 8.9514000415802
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0003' with 188 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: 0.0236489772796631
Calculate `GDI`: DONE
Total calculations elapsed time: 3.01738405227661
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0454180240631104
Clean plots: DONE
GDI plot
Removed 4 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 188, is uniform
Cluster 01_0003's shift to uniformity: -0.0672912272436446
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.32970877275636, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041519, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633951, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40148843025229, isUniform = TRUE, clusterSize = 188
cluster 01_0003 is uniform


Found 4 uniform and  0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003
Differential Expression Analysis - START
* DEA on cluster '1' with 313 cells
* DEA on cluster '2' with 257 cells
* DEA on cluster '3' with 242 cells
* DEA on cluster '4' with 188 cells

Total calculations elapsed time: 0.0360610485076904
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  3, 2  ->  1, 3  ->  2, 4  ->  4
Total calculations elapsed time: 80.50319480896
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2, 3  ->  3, 4  ->  4
Asked to drop 0 genes and 812 cells
COTAN dataset analysis: START
Asked to drop 79 genes and 0 cells
Genes/cells selection done: dropped [79] genes and [0] cells
Working on [521] genes and [188] cells
Dataset cleaning elapsed time: 0.931602954864502
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: 1.98529386520386
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818729 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 2.9568350315094
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: 2.9580659866333
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00560712814331055
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0203540325164795
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.972082853317261
Total calculations elapsed time: 3.95611000061035
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.89511489868164
Dataset analysis elapsed time: 8.78355288505554
COTAN dataset analysis: DONE
Checking uniformity for the cluster 'Cluster_4' with 188 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: 0.0257670879364014
Calculate `GDI`: DONE
Total calculations elapsed time: 3.02267098426819
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0550541877746582
Clean plots: DONE
GDI plot
Removed 4 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_4, with size 188, is uniform
Cluster Cluster_4's shift to uniformity: -0.0672912272436446
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.32970877275636, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041519, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633951, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40148843025229, isUniform = TRUE, clusterSize = 188
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 280 cells
* DEA on cluster '4' with 171 cells

Total calculations elapsed time: 0.0354058742523193
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  4, 2  ->  3, 3  ->  2, 4  ->  1, -1  ->  -1
Applied reordering to clusterization is:
1  ->  1, 2  ->  2, 3  ->  3, 4  ->  4, -1  ->  -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1000 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
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 600 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 3.64471483230591
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: 1000
Number of edges: 67288

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3650
Number of communities: 5
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 4.56799697875977
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file:  /tmp/RtmpQ4102t/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
20:43:49 UMAP embedding parameters a = 0.9922 b = 1.112
20:43:49 Read 1000 rows and found 40 numeric columns
20:43:49 Using Annoy for neighbor search, n_neighbors = 30
20:43:49 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:43:49 Writing NN index file to temp file /tmp/RtmpQ4102t/filef9d96125c39b
20:43:49 Searching Annoy index using 1 thread, search_k = 3000
20:43:49 Annoy recall = 100%
20:43:50 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:43:52 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
20:43:52 Using 'irlba' for PCA
20:43:52 PCA: 2 components explained 36.15% variance
20:43:52 Scaling init to sdev = 1
20:43:52 Commencing optimization for 500 epochs, with 41630 positive edges
20:43:52 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:43:54 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.74784302711487
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
20:43:55 UMAP embedding parameters a = 0.9922 b = 1.112
20:43:55 Read 1000 rows and found 40 numeric columns
20:43:55 Using Annoy for neighbor search, n_neighbors = 30
20:43:55 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:43:55 Writing NN index file to temp file /tmp/RtmpQ4102t/filef9d94337933d
20:43:55 Searching Annoy index using 1 thread, search_k = 3000
20:43:55 Annoy recall = 100%
20:43:56 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
20:43:58 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
20:43:58 Using 'irlba' for PCA
20:43:58 PCA: 2 components explained 36.15% variance
20:43:58 Scaling init to sdev = 1
20:43:58 Commencing optimization for 500 epochs, with 41630 positive edges
20:43:58 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
20:44:01 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.86072993278503
UMAP plot: DONE
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 500 cells
COTAN dataset analysis: START
Asked to drop 38 genes and 0 cells
Genes/cells selection done: dropped [38] genes and [0] cells
Working on [562] genes and [500] cells
Dataset cleaning elapsed time: 0.995109081268311
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.00656390190125
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.108871643378045 | max: 295.971778839086 | % negative: 35.0533807829181
Model parameter estimation elapsed time: 3.04675388336182
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: 3.10627198219299
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0072479248046875
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0380458831787109
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.984017133712769
Total calculations elapsed time: 4.13558292388916
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.14718699455261
Dataset analysis elapsed time: 9.18904995918274
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 500 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: 0.0261750221252441
Calculate `GDI`: DONE
Total calculations elapsed time: 2.90662503242493
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0478739738464355
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 500, is uniform
Cluster 01_0001's shift to uniformity: -0.0417301990665568
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0124555160142349, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35526980093344, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00889679715302491, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.38536328181506, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.40346106115488, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42565794715045, isUniform = TRUE, clusterSize = 500
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 500 cells
COTAN dataset analysis: START
Asked to drop 44 genes and 0 cells
Genes/cells selection done: dropped [44] genes and [0] cells
Working on [556] genes and [500] cells
Dataset cleaning elapsed time: 0.95747184753418
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.01587200164795
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0636486786621688 | max: 141.389145035675 | % negative: 36.1510791366906
Model parameter estimation elapsed time: 3.00615310668945
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: 3.06803798675537
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00729703903198242
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0326919555664062
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.919697046279907
Total calculations elapsed time: 4.02772402763367
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.98795294761658
Dataset analysis elapsed time: 8.95157790184021
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0002' with 500 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: 0.0283961296081543
Calculate `GDI`: DONE
Total calculations elapsed time: 3.05525183677673
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0519990921020508
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 500, is uniform
Cluster 01_0002's shift to uniformity: -0.0413872276843441
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00719424460431655, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35561277231566, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00359712230215827, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37204026755188, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38757136821583, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40876953414106, isUniform = TRUE, clusterSize = 500
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 500 cells
* DEA on cluster '2' with 500 cells

Total calculations elapsed time: 0.031980037689209
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 49.9216148853302
Creating cells' uniform clustering: DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'

Total calculations elapsed time: 3.69664406776428
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.70978403091431
findClustersMarkers - DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'

Total calculations elapsed time: 3.69040107727051
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.7020001411438
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells

Total calculations elapsed time: 0.0329749584197998
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'

Total calculations elapsed time: 3.73809385299683
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.78073787689209
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 743 cells
COTAN dataset analysis: START
Asked to drop 51 genes and 0 cells
Genes/cells selection done: dropped [51] genes and [0] cells
Working on [549] genes and [257] cells
Dataset cleaning elapsed time: 0.911190032958984
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 1.8747570514679
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.81376600265503
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: 3.06652998924255
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00740504264831543
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0290298461914062
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.998481035232544
Total calculations elapsed time: 4.10144591331482
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.07599401473999
Dataset analysis elapsed time: 8.800950050354
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: 0.026547908782959
Calculate `GDI`: DONE
Total calculations elapsed time: 2.91964888572693
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 [1000] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.2494900226593
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.98750901222229
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.14842987060547
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.99748778343201
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.919861078262329
Dataset analysis elapsed time: 4.90485787391663
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-000397, g-000525, g-000460, g-000458, g-000535, g-000217, g-000194, g-000497, g-000432, g-000383 
	   g-000318, g-000486, g-000464, g-000588, g-000549, g-000368, g-000252, g-000151, g-000209, g-000538 
	   g-000325, g-000514, g-000524, g-000244, g-000320, g-000201, g-000499, g-000309, g-000290, g-000483 
Negative:  g-000415, g-000506, g-000496, g-000579, g-000572, g-000421, g-000455, g-000328, g-000178, g-000567 
	   g-000405, g-000296, g-000387, g-000501, g-000493, g-000481, g-000343, g-000528, g-000551, g-000414 
	   g-000367, g-000594, g-000159, g-000517, g-000574, g-000229, g-000222, g-000533, g-000243, g-000306 
PC_ 2 
Positive:  g-000141, g-000093, g-000089, g-000033, g-000123, g-000557, g-000330, g-000156, g-000142, g-000095 
	   g-000061, g-000235, g-000032, g-000186, g-000056, g-000259, g-000027, g-000041, g-000333, g-000386 
	   g-000009, g-000395, g-000048, g-000116, g-000340, g-000418, g-000035, g-000332, g-000086, g-000040 
Negative:  g-000088, g-000158, g-000255, g-000115, g-000054, g-000472, g-000554, g-000391, g-000253, g-000226 
	   g-000051, g-000147, g-000541, g-000077, g-000224, g-000194, g-000290, g-000293, g-000313, g-000118 
	   g-000121, g-000220, g-000467, g-000500, g-000341, g-000039, g-000091, g-000249, g-000426, g-000288 
PC_ 3 
Positive:  g-000126, g-000083, g-000086, g-000117, g-000130, g-000010, g-000498, g-000333, g-000047, g-000179 
	   g-000340, g-000035, g-000531, g-000140, g-000527, g-000049, g-000316, g-000031, g-000014, g-000073 
	   g-000218, g-000445, g-000129, g-000175, g-000105, g-000581, g-000404, g-000025, g-000266, g-000354 
Negative:  g-000096, g-000575, g-000370, g-000337, g-000319, g-000364, g-000308, g-000293, g-000147, g-000307 
	   g-000038, g-000492, g-000541, g-000185, g-000008, g-000482, g-000562, g-000097, g-000222, g-000084 
	   g-000141, g-000377, g-000224, g-000223, g-000136, g-000434, g-000277, g-000426, g-000139, g-000093 
PC_ 4 
Positive:  g-000006, g-000043, g-000462, g-000279, g-000180, g-000576, g-000087, g-000584, g-000498, g-000333 
	   g-000189, g-000088, g-000451, g-000059, g-000135, g-000281, g-000106, g-000429, g-000316, g-000578 
	   g-000303, g-000031, g-000581, g-000026, g-000122, g-000561, g-000546, g-000164, g-000353, g-000300 
Negative:  g-000072, g-000012, g-000129, g-000052, g-000097, g-000262, g-000080, g-000056, g-000025, g-000092 
	   g-000354, g-000334, g-000423, g-000228, g-000002, g-000010, g-000086, g-000147, g-000185, g-000172 
	   g-000124, g-000009, g-000077, g-000476, g-000126, g-000145, g-000065, g-000268, g-000152, g-000348 
PC_ 5 
Positive:  g-000051, g-000150, g-000088, g-000476, g-000344, g-000116, g-000428, g-000012, g-000523, g-000394 
	   g-000101, g-000127, g-000069, g-000214, g-000049, g-000357, g-000075, g-000081, g-000576, g-000342 
	   g-000439, g-000018, g-000070, g-000079, g-000015, g-000550, g-000600, g-000247, g-000218, g-000331 
Negative:  g-000105, g-000037, g-000110, g-000054, g-000090, g-000389, g-000022, g-000578, g-000289, g-000147 
	   g-000547, g-000011, g-000477, g-000433, g-000200, g-000348, g-000404, g-000003, g-000250, g-000109 
	   g-000402, g-000241, g-000595, g-000341, g-000560, g-000385, g-000413, g-000352, g-000573, g-000265 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1000
Number of edges: 68112

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5999
Number of communities: 3
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 [1000] cells
Dataset cleaning elapsed time: 1.00573301315308
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.20369601249695
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.18790197372437
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.969011068344116
Dataset analysis elapsed time: 5.16264605522156
COTAN dataset analysis: DONE
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.98935604095459
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.20331907272339
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.19008803367615
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: 3.40974712371826
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00763297080993652
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0627388954162598
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.04578614234924
Total calculations elapsed time: 4.5259051322937
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.55715298652649
Dataset analysis elapsed time: 9.73659706115723
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: 0.0163319110870361
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: 0.00965213775634766
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Total calculations elapsed time: 1.12820291519165
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: 0.00739789009094238
calculating PValues: DONE
Number of selected secondary markers: 98
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00776195526123047
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 0.996926069259644
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: 0.0066688060760498
calculating PValues: DONE
Number of selected secondary markers: 98
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00808501243591309
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 1.08391618728638
Calculating gene co-expression space - DONE
Total calculations elapsed time: 1.1601779460907
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 [1000] cells
Dataset cleaning elapsed time: 0.985046148300171
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.31350684165955
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.34575486183167
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 1.03660607337952
Dataset analysis elapsed time: 5.36740708351135
COTAN dataset analysis: DONE
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells

Total calculations elapsed time: 0.0386800765991211
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'

Total calculations elapsed time: 4.08581805229187
Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.10997640736885
Handling cluster '2' with mean UDE 1.00770245700749
Handling cluster '3' with mean UDE 0.95940682189354
Handling cluster '4' with mean UDE 0.907328369455933
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 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells

Total calculations elapsed time: 0.0469260215759277
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 0 genes and 501 cells
COTAN dataset analysis: START
Asked to drop 16 genes and 0 cells
Genes/cells selection done: dropped [16] genes and [0] cells
Working on [584] genes and [499] cells
Dataset cleaning elapsed time: 0.92243218421936
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 2.01795291900635
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.96072387695312
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: 3.14740586280823
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00854921340942383
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0400838851928711
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.991143941879272
Total calculations elapsed time: 4.18718290328979
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.15853810310364
Dataset analysis elapsed time: 9.04169416427612
COTAN dataset analysis: DONE
Checking uniformity for the cluster '1_2-merge' with 499 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: 0.0274388790130615
Calculate `GDI`: DONE
Total calculations elapsed time: 2.7997100353241
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0429909229278564
Clean plots: DONE
GDI plot
Removed 1 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 499, is not uniform
Cluster 1_2-merge's shift to uniformity: 0.0566581136434088
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.178082191780822, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35365811364341, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.148972602739726, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37149326865972, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00513698630136986, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38256306292788, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 3, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42111642638126, isUniform = FALSE, clusterSize = 499
Clusters 1 and 2 cannot be merged
Finished the first batch - no merges were executed
Loop calculations elapsed time: 16.9581348896027
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells

Total calculations elapsed time: 0.0413429737091064
Differential Expression Analysis - DONE
Updating check results for the 1 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("3", "4")
*3_4-merge
Asked to drop 0 genes and 499 cells
COTAN dataset analysis: START
Asked to drop 37 genes and 0 cells
Genes/cells selection done: dropped [37] genes and [0] cells
Working on [563] genes and [501] cells
Dataset cleaning elapsed time: 1.03427791595459
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 11 iterations
Total calculations elapsed time: 2.06323313713074
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.107568326617881 | max: 698.639334552754 | % negative: 32.1492007104796
Model parameter estimation elapsed time: 3.06499218940735
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: 3.35318613052368
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00824594497680664
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0413320064544678
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.04869294166565
Total calculations elapsed time: 4.45145702362061
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.50415396690369
Dataset analysis elapsed time: 9.60342407226562
COTAN dataset analysis: DONE
Checking uniformity for the cluster '3_4-merge' with 501 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: 0.0270791053771973
Calculate `GDI`: DONE
Total calculations elapsed time: 2.96357202529907
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0471999645233154
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 501, is not uniform
Cluster 3_4-merge's shift to uniformity: 0.0813107504723087
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.259325044404973, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37831075047231, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.216696269982238, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41473792188165, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0301953818827709, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43341610223239, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 17, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.46173948790286, isUniform = FALSE, clusterSize = 501
Clusters 3 and 4 cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.297 out of 2 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 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells

Total calculations elapsed time: 0.0339629650115967
Differential Expression Analysis - DONE
Updating check results for the 2 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("2", "4")
*2_4-merge
Asked to drop 0 genes and 570 cells
COTAN dataset analysis: START
Asked to drop 9 genes and 0 cells
Genes/cells selection done: dropped [9] genes and [0] cells
Working on [591] genes and [430] cells
Dataset cleaning elapsed time: 0.954828977584839
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.95215082168579
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0739592351622374 | max: 400.051960722886 | % negative: 25.7191201353638
Model parameter estimation elapsed time: 2.92412114143372
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: 3.060467004776
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00808906555175781
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0374150276184082
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02412295341492
Total calculations elapsed time: 4.13009405136108
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.08370590209961
Dataset analysis elapsed time: 8.96265602111816
COTAN dataset analysis: DONE
Checking uniformity for the cluster '2_4-merge' with 430 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: 0.027656078338623
Calculate `GDI`: DONE
Total calculations elapsed time: 2.89953398704529
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0429329872131348
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_4-merge, with size 430, is not uniform
Cluster 2_4-merge's shift to uniformity: 3.07228472969514
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.583756345177665, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 3.7954982715656, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.576988155668359, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.08354952912925, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.524534686971235, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 4.42722016730736, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 310, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 4.57228472969514, isUniform = FALSE, clusterSize = 430
Clusters 2 and 4 cannot be merged
Clusters 1 and 2 will be merged
Clusters 4 and 3 will be merged
Executed 2 merges
Loop calculations elapsed time: 16.8595128059387
Start merging nearest clusters: iteration 4
Differential Expression Analysis - START
* DEA on cluster '1_2-merge' with 499 cells
* DEA on cluster '3_4-merge' with 501 cells

Total calculations elapsed time: 0.029932975769043
Differential Expression Analysis - DONE
Updating check results for the 3 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1_2-merge", "3_4-merge")
*1_2-merge_3_4-merge-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 [1000] cells
Dataset cleaning elapsed time: 0.953765869140625
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.12684512138367
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418991 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.06308317184448
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: 3.37255883216858
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00864410400390625
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0545918941497803
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.984722137451172
Total calculations elapsed time: 4.42051696777344
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.37482094764709
Dataset analysis elapsed time: 9.3916699886322
COTAN dataset analysis: DONE
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1000 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: 0.028770923614502
Calculate `GDI`: DONE
Total calculations elapsed time: 2.92812013626099
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0507309436798096
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge_3_4-merge-merge, with size 1000, is not uniform
Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 3.86988385120409
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.69, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 4.54596809454193, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.678333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.93144728766684, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.593333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 5.2532296852478, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 356, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 5.36988385120409, isUniform = FALSE, clusterSize = 1000
Clusters 1_2-merge and 3_4-merge cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.397 out of 4 checks
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1' with 499 cells
* DEA on cluster '2' with 501 cells

Total calculations elapsed time: 0.0294690132141113
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 68.9079740047455
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: 1.8884060382843
Log Fold Change Analysis - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 501 cells
COTAN dataset analysis: START
Asked to drop 16 genes and 0 cells
Genes/cells selection done: dropped [16] genes and [0] cells
Working on [584] genes and [499] cells
Dataset cleaning elapsed time: 0.937102794647217
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 2.04467678070068
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.97255706787109
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: 3.1083447933197
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00626516342163086
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0390298366546631
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.937339067459106
Total calculations elapsed time: 4.0909788608551
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.04081201553345
Dataset analysis elapsed time: 8.95047187805176
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: 0.03183913230896
Calculate `GDI`: DONE
Total calculations elapsed time: 2.8520679473877
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 
694.577  10.043 706.392

Example timings

COTAN.Rcheck/COTAN-Ex.timings

name	user	system	elapsed
COTAN_Legacy	0.002	0.001	0.004
COTAN_ObjectCreation	10.225	0.261	10.550
CalculatingCOEX	52.342	1.003	53.609
ClustersList	0.009	0.002	0.011
Conversions	4.805	0.098	4.932
GenesStatistics	10.605	0.291	10.801
HandleMetaData	0.035	0.002	0.036
HandlingClusterizations	41.629	1.129	42.403
HandlingConditions	0.071	0.003	0.074
HeatmapPlots	30.788	0.813	31.768
Installing_torch	0.001	0.000	0.001
LoggingFunctions	0.001	0.001	0.003
ParametersEstimations	21.042	0.626	21.778
RawDataCleaning	4.693	0.291	4.780
RawDataGetters	0.030	0.003	0.033
UniformClusters	66.259	1.890	67.478
getColorsVector	0.001	0.015	0.001