Multiple platform build/check report for BioC 3.22 - CHECK results for COTAN on nebbiolo2

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
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 nebbiolo2

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: 2.10.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings COTAN_2.10.0.tar.gz

StartedAt: 2025-10-31 22:34:36 -0400 (Fri, 31 Oct 2025)

EndedAt: 2025-10-31 23:02:33 -0400 (Fri, 31 Oct 2025)

EllapsedTime: 1677.4 seconds

RetCode: 0

Status: OK

CheckDir: COTAN.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings COTAN_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.10.0’
* 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 loading without being on the library search path ... 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         66.276  0.115  65.614
CalculatingCOEX         52.788  0.484  52.210
HandlingClusterizations 42.904  0.325  42.890
HeatmapPlots            32.074  0.518  31.828
ParametersEstimations   21.545  0.277  21.806
GenesStatistics         10.819  0.038  10.575
COTAN_ObjectCreation     9.292  0.193   9.206
Conversions              5.042  0.041   5.084
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

COTAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL COTAN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘COTAN’ ...
** this is package ‘COTAN’ version ‘2.10.0’
** 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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.160   0.033   0.181

COTAN.Rcheck/tests/spelling.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.136   0.040   0.165

COTAN.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: 1.61511278152466
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: 2.2444806098938
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000627279281616211
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00727009773254395
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.873154640197754
Total calculations elapsed time: 3.12553262710571
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: 4.98948168754578
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: 0.911617040634155
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: 1.68664026260376
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: 0.830230236053467
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0295487661210321 | median:  0.016072261901129 | mean:  0.016072261901129
`nu` mean: 1.69786080481514
Marginal errors | max: 1.95799528048 | 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: 1.80776238441467
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: 0.742103576660156
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: 1.5582218170166
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: 0.795255661010742
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: 1.56138586997986
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: 0.846961736679077
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: 1.7007691860199
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: 0.805440664291382
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 0.0273479725376324 | mean: 0.025029675152131
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: 1.63060140609741
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251734659898779 | max: 3.9096133246649 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.746954202651978
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 0.00972280144873849 | mean: 0.00889105008777538
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: 1.52221822738647
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: 0.843477487564087
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00251004753849005 | median:  0.00146484374999994 | mean:  0.00146484374999994
`nu` mean: 1.00104520378849
Marginal errors | max: 0.00430755646112857 | median 0.00358203399504298 | mean: 0.00327684342604062
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.52057886123657
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: 0.83569598197937
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: 1.68607401847839
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: 0.737399339675903
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: 0.00054590699507937
Total calculations elapsed time: 43.6187963485718
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: 1.59190988540649
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: 2.68515419960022
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000659942626953125
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00314474105834961
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.864321708679199
Total calculations elapsed time: 3.55328059196472
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: 2.87116003036499
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000716447830200195
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00247740745544434
Estimating cells' COEX
Calculate cells' COEX elapsed time: 1.05761528015137
Total calculations elapsed time: 3.931969165802
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: 0.0107595920562744
Calculate `GDI`: DONE
Total calculations elapsed time: 2.85630011558533
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: 0.00319314002990723
Calculate `GDI`: DONE
Total calculations elapsed time: 2.72321820259094
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: 1.77541875839233
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: 1.80769991874695
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: 1.76470375061035
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: 3.05149602890015
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: 2.69724011421204
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: 2.70962071418762
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: 1.75870108604431
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: 0.884084939956665
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: 1.99310731887817
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: 1.00137448310852
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: 1.63203263282776
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: 0.758939027786255
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: 1.9154064655304
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: 0.866820812225342
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: 1.63027453422546
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: 0.787787914276123
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: 1.77188348770142
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251890641847533 | max: 3.90987172241566 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.860250949859619
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 0.00912386940474796 | mean: 0.00834350038184244
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: 1.64720845222473
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: 0.871506452560425
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00230094227000666 | median:  0.00132529141000018 | mean:  0.00132529141000018
`nu` mean: 1.00097565086001
Marginal errors | max: 0.00376864912836616 | median 0.00313421412286008 | mean: 0.00286709489297579
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: 1.96666073799133
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: 0.959990501403809
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837013154366462 | median:  0.000488281250000028 | mean:  0.000488281250000028
`nu` mean: 0.999651268095634
Marginal errors | max: 0.00144055320514802 | median 0.00119489364392944 | mean: 0.00109355439757213
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: 1.85146427154541
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255046800817986 | max: 3.9150866760965 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.824752569198608
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: 47.8717715740204
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: 2.50051212310791
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000495195388793945
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00131487846374512
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.784724473953247
Total calculations elapsed time: 3.2870466709137
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: 2.46365785598755
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.000535726547241211
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00138378143310547
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.844521999359131
Total calculations elapsed time: 3.31009936332703
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: 0.00306153297424316
Calculate `GDI`: DONE
Total calculations elapsed time: 2.73926091194153
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: 6.80594515800476
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: 7.11338639259338
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: 3.63368391990662
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: 2.73491263389587
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000649452209472656
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00134921073913574
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.837384939193726
Total calculations elapsed time: 3.57429623603821
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: 2.7440779209137
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000592231750488281
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00155448913574219
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.932998895645142
Total calculations elapsed time: 3.67922353744507
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: 6.97792887687683
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: 7.10935258865356
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: 3.41880226135254
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: 0.859034538269043
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 0.080731376500534 | mean: 0.101968565509112
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: 3.30597329139709
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: 0.853852987289429
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: 3.17445707321167
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: 0.843544244766235
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: 19.6107313632965
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: 2.54743432998657
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000644683837890625
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00133252143859863
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.798913717269897
Total calculations elapsed time: 3.34832525253296
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: 7.57649350166321
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: 7.41663432121277
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: 3.7545599937439
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: 0.951039552688599
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 0.080731376500534 | mean: 0.101968565509112
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: 3.68306684494019
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: 1.26666450500488
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: 3.92246651649475
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: 0.892482995986938
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: 23.17742395401
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: 2.61563801765442
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000565290451049805
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00150871276855469
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.911727905273438
Total calculations elapsed time: 3.52943992614746
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: 7.10789823532104
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: 0.00219297409057617
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: 8.03933262825012
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: 8.04057335853577
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: 0.00327634811401367
Calculate `GDI`: DONE
Total calculations elapsed time: 2.77936363220215
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: 6.73141551017761
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00349593162536621
Calculate `GDI`: DONE
Total calculations elapsed time: 9.56987857818604
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: 0.00481653213500977
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00369524955749512
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: 1.01258444786072
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: 1.91865086555481
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.8521888256073
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: 3.18509769439697
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00600171089172363
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0619001388549805
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.872398614883423
Total calculations elapsed time: 4.1253981590271
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.13381266593933
Dataset analysis elapsed time: 8.99858593940735
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: 0.948820114135742
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: 2.21001482009888
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.23373603820801
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: 3.28144788742065
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00643587112426758
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0630817413330078
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.959944486618042
Total calculations elapsed time: 4.31090998649597
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.14862871170044
Dataset analysis elapsed time: 9.33118486404419
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: 0.0192785263061523
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: 0.0302419662475586
Calculate `GDI`: DONE
Total calculations elapsed time: 2.66501069068909
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: 1.03918790817261
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: 1.99952292442322
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.87563943862915
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: 2.80543923377991
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00539422035217285
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0610291957855225
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.802239418029785
Total calculations elapsed time: 3.67410206794739
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.54525327682495
Dataset analysis elapsed time: 8.46008062362671
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: 0.0152387619018555
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: 0.0303375720977783
Calculate `GDI`: DONE
Total calculations elapsed time: 2.92212677001953
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: 0.91640043258667
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: 2.25888919830322
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.25698900222778
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: 3.41748714447021
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0073704719543457
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.063812255859375
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.10435771942139
Total calculations elapsed time: 4.59302759170532
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.67159628868103
Dataset analysis elapsed time: 9.84498572349548
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: 0.00561237335205078
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: 0.0319633483886719
Calculate `GDI`: DONE
Total calculations elapsed time: 3.2623405456543
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: 1.06200385093689
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: 2.1161322593689
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.267567793681876 | max: 101.923257389521 | % negative: 52.6112185686654
Model parameter estimation elapsed time: 3.15259099006653
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 1.12687993049622
Dataset analysis elapsed time: 5.34147477149963
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: 3.39600372314453
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0061030387878418
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0137214660644531
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.12623763084412
Total calculations elapsed time: 4.54206585884094
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: 3.35739135742188
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0049898624420166
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0125014781951904
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.01309204101562
Total calculations elapsed time: 4.38797473907471
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: 3.00986337661743
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0048365592956543
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0125496387481689
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.937679290771484
Total calculations elapsed time: 3.96492886543274
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: 0.00486326217651367
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: 2.22094702720642
Clean plots: DONE
Dataset cleaning elapsed time: 4.58428430557251
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: 2.17128920555115
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.34135317802429
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: 3.50922703742981
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00723481178283691
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0659580230712891
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.03630805015564
Total calculations elapsed time: 4.61872792243958
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.86385726928711
Dataset analysis elapsed time: 13.7894947528839
COTAN dataset analysis: DONE
Saving elaborated data locally at: /tmp/Rtmpc2v9QB/test.cotan.RDS
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 3.07139086723328
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: 3.98387408256531
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: 3.39941453933716
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: 4.25938057899475
Creating new clusterization: DONE
Creating PDF UMAP in file:  /tmp/Rtmpc2v9QB/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
22:50:16 UMAP embedding parameters a = 0.9922 b = 1.112
22:50:16 Read 1000 rows and found 65 numeric columns
22:50:16 Using Annoy for neighbor search, n_neighbors = 30
22:50:17 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:50:17 Writing NN index file to temp file /tmp/Rtmpc2v9QB/file1d17834a1c17f
22:50:17 Searching Annoy index using 1 thread, search_k = 3000
22:50:17 Annoy recall = 100%
22:50:18 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:50:20 Initializing from normalized Laplacian + noise (using RSpectra)
22:50:20 Commencing optimization for 500 epochs, with 39044 positive edges
22:50:20 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:50:22 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.80638027191162
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
22:50:23 UMAP embedding parameters a = 0.9922 b = 1.112
22:50:23 Read 1000 rows and found 65 numeric columns
22:50:23 Using Annoy for neighbor search, n_neighbors = 30
22:50:23 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:50:23 Writing NN index file to temp file /tmp/Rtmpc2v9QB/file1d17831cf053d7
22:50:23 Searching Annoy index using 1 thread, search_k = 3000
22:50:23 Annoy recall = 100%
22:50:24 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:50:25 Initializing from normalized Laplacian + noise (using RSpectra)
22:50:26 Commencing optimization for 500 epochs, with 39044 positive edges
22:50:26 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:50:28 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.24168109893799
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: 1.02803730964661
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: 2.03573727607727
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.126565269702225 | max: 788.372048308528 | % negative: 38.5996409335727
Model parameter estimation elapsed time: 2.91676950454712
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: 3.16846513748169
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0063629150390625
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0317881107330322
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.19180846214294
Total calculations elapsed time: 4.39842462539673
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.46014666557312
Dataset analysis elapsed time: 9.40495347976685
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: 0.0293364524841309
Calculate `GDI`: DONE
Total calculations elapsed time: 3.13777422904968
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0365357398986816
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: -0.0175178017151365
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 = 1.43089123341141, 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 = 1.44383613651627, 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: 0.902653694152832
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: 1.93054556846619
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.93720674514771
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: 3.35042500495911
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00553393363952637
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0282473564147949
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.14494132995605
Total calculations elapsed time: 4.52914762496948
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.6183774471283
Dataset analysis elapsed time: 9.45823788642883
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: 0.0281386375427246
Calculate `GDI`: DONE
Total calculations elapsed time: 3.44458246231079
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0407137870788574
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: -0.0466523594846431
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 = 1.35034764051536, 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 = 1.37278730407697, 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 = 1.38664163146849, 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: 1.08307361602783
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: 1.90813589096069
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.166254045792573 | max: 224.924342782861 | % negative: 42.6386233269598
Model parameter estimation elapsed time: 2.863525390625
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: 3.03882122039795
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00461363792419434
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0255720615386963
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.04027843475342
Total calculations elapsed time: 4.10928535461426
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.23810148239136
Dataset analysis elapsed time: 9.18470048904419
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: 0.0254602432250977
Calculate `GDI`: DONE
Total calculations elapsed time: 2.7727689743042
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0346343517303467
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: -0.0473527936300242
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 = 1.38771313919654, 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 = 1.43097703442027, 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: 1.10749912261963
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: 2.05891036987305
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 3.04997134208679
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: 3.18154072761536
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00542926788330078
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0234239101409912
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.03576517105103
Total calculations elapsed time: 4.24615907669067
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.36328744888306
Dataset analysis elapsed time: 9.52075791358948
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: 0.0256013870239258
Calculate `GDI`: DONE
Total calculations elapsed time: 3.37095737457275
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0377914905548096
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: -0.0672912272435866
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 = 1.32970877275641, 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 = 1.35752445041521, 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 = 1.37495297633956, 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 = 1.4014884302523, 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: 0.0343630313873291
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  3, 2  ->  1, 3  ->  2, 4  ->  4
Total calculations elapsed time: 83.2779862880707
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: 1.27826070785522
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: 2.26793599128723
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 3.31957101821899
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: 3.37935280799866
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00571322441101074
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0240018367767334
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.09452176094055
Total calculations elapsed time: 4.50358963012695
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.6611635684967
Dataset analysis elapsed time: 10.2589952945709
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: 0.0256538391113281
Calculate `GDI`: DONE
Total calculations elapsed time: 3.12167572975159
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.03513503074646
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: -0.0672912272435866
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 = 1.32970877275641, 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 = 1.35752445041521, 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 = 1.37495297633956, 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 = 1.4014884302523, 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: 0.0338459014892578
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: 3.5731463432312
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: 4.41693139076233
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file:  /tmp/Rtmpc2v9QB/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
22:51:58 UMAP embedding parameters a = 0.9922 b = 1.112
22:51:58 Read 1000 rows and found 40 numeric columns
22:51:58 Using Annoy for neighbor search, n_neighbors = 30
22:51:58 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:51:58 Writing NN index file to temp file /tmp/Rtmpc2v9QB/file1d178355850575
22:51:58 Searching Annoy index using 1 thread, search_k = 3000
22:51:58 Annoy recall = 100%
22:51:59 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:52:01 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
22:52:01 Using 'irlba' for PCA
22:52:01 PCA: 2 components explained 36.15% variance
22:52:01 Scaling init to sdev = 1
22:52:01 Commencing optimization for 500 epochs, with 41630 positive edges
22:52:01 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:52:03 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.87108826637268
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
22:52:04 UMAP embedding parameters a = 0.9922 b = 1.112
22:52:04 Read 1000 rows and found 40 numeric columns
22:52:04 Using Annoy for neighbor search, n_neighbors = 30
22:52:04 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:52:04 Writing NN index file to temp file /tmp/Rtmpc2v9QB/file1d17835c4384e8
22:52:04 Searching Annoy index using 1 thread, search_k = 3000
22:52:04 Annoy recall = 100%
22:52:05 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:52:07 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
22:52:07 Using 'irlba' for PCA
22:52:07 PCA: 2 components explained 36.15% variance
22:52:07 Scaling init to sdev = 1
22:52:07 Commencing optimization for 500 epochs, with 41630 positive edges
22:52:07 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:52:09 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.77463340759277
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: 0.985238075256348
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: 2.42053699493408
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.108871643378045 | max: 295.971778839086 | % negative: 35.0533807829181
Model parameter estimation elapsed time: 3.32344126701355
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: 3.21767449378967
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00596809387207031
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0384171009063721
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.977527618408203
Total calculations elapsed time: 4.23958730697632
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.21230864524841
Dataset analysis elapsed time: 9.52098798751831
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: 0.0291657447814941
Calculate `GDI`: DONE
Total calculations elapsed time: 2.93484163284302
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0391838550567627
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: -0.041730199066494
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 = 1.35526980093351, 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 = 1.38536328181495, 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 = 1.40346106115492, 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: 0.847983360290527
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: 1.82281827926636
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0636486786621688 | max: 141.389145035675 | % negative: 36.1510791366906
Model parameter estimation elapsed time: 2.85868191719055
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: 3.29561853408813
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00557088851928711
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0389168262481689
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.00139427185059
Total calculations elapsed time: 4.34150052070618
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.30650639533997
Dataset analysis elapsed time: 9.01317167282104
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: 0.0283439159393311
Calculate `GDI`: DONE
Total calculations elapsed time: 3.13029503822327
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0407323837280273
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: -0.0413872276843505
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 = 1.35561277231565, 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 = 1.38757136821537, 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: 0.0291531085968018
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 50.2948427200317
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: 3.65311312675476
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.66452264785767
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: 3.60460543632507
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.61508274078369
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: 0.0280396938323975
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: 3.70152163505554
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.73833250999451
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: 1.06634187698364
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: 1.80615997314453
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.73697352409363
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: 2.82552766799927
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00481057167053223
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0278053283691406
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.01261234283447
Total calculations elapsed time: 3.87075591087341
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.86768412590027
Dataset analysis elapsed time: 8.67099952697754
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: 0.0269744396209717
Calculate `GDI`: DONE
Total calculations elapsed time: 2.92183876037598
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: 2.19379925727844
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % 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: 1.03761529922485
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: 2.21477127075195
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.24277377128601
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 1.0169575214386
Dataset analysis elapsed time: 5.29734659194946
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-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 
Negative:  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 
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: 68107

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: 2
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: 0.964696407318115
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: 2.09745264053345
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.12777042388916
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 1.04737114906311
Dataset analysis elapsed time: 5.13983798027039
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: 0.965642213821411
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: 2.13798999786377
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.00831866264343
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: 3.19127917289734
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00644111633300781
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0645034313201904
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.946678876876831
Total calculations elapsed time: 4.20890259742737
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.2042772769928
Dataset analysis elapsed time: 9.17823815345764
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: 0.00463390350341797
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: 0.00875186920166016
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Total calculations elapsed time: 0.964784145355225
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: 0.00686454772949219
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: 0.00789451599121094
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 0.970828294754028
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: 0.00616216659545898
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: 0.00794291496276855
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 1.07144093513489
Calculating gene co-expression space - DONE
Total calculations elapsed time: 1.13584423065186
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: 0.877327442169189
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: 2.14031600952148
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.08669805526733
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 1.03938913345337
Dataset analysis elapsed time: 5.00341463088989
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: 0.0416996479034424
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: 4.36451458930969
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: 0.0405399799346924
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: 1.13335251808167
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: 2.61031436920166
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 3.77047634124756
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: 3.20879483222961
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00798153877258301
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0421895980834961
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.10130333900452
Total calculations elapsed time: 4.36026930809021
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.25122666358948
Dataset analysis elapsed time: 10.1550555229187
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: 0.0307595729827881
Calculate `GDI`: DONE
Total calculations elapsed time: 2.82801532745361
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0373961925506592
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: 0.0566581136434114
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 = 1.38256306292787, 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 = 1.42111642638124, isUniform = FALSE, clusterSize = 499
Clusters 1 and 2 cannot be merged
Finished the first batch - no merges were executed
Loop calculations elapsed time: 17.874826669693
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: 0.0288429260253906
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: 1.00080728530884
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: 2.01288032531738
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.107568326617881 | max: 698.639334552754 | % negative: 32.1492007104796
Model parameter estimation elapsed time: 2.97841477394104
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: 2.96067237854004
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00516510009765625
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0383784770965576
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.929839134216309
Total calculations elapsed time: 3.93405508995056
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.93758153915405
Dataset analysis elapsed time: 8.91680359840393
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: 0.0284063816070557
Calculate `GDI`: DONE
Total calculations elapsed time: 2.90295696258545
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0354864597320557
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: 0.0813107504723223
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 = 1.37831075047232, 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 = 1.41473792188166, 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 = 1.43341610223243, 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 = 1.46173948790285, 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: 0.0361230373382568
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: 0.930269479751587
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: 1.98483896255493
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0739592351622374 | max: 400.051960722894 | % negative: 25.7191201353638
Model parameter estimation elapsed time: 3.07950377464294
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: 3.17563009262085
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0088508129119873
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0424306392669678
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.965020418167114
Total calculations elapsed time: 4.19193196296692
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.09854364395142
Dataset analysis elapsed time: 9.10831689834595
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: 0.030311107635498
Calculate `GDI`: DONE
Total calculations elapsed time: 2.89445495605469
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0382413864135742
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: 16.8477344512939
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: 0.0285117626190186
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: 0.933824062347412
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: 1.99711728096008
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.86603808403015
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: 3.15384817123413
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00579500198364258
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.060744047164917
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.878028631210327
Total calculations elapsed time: 4.09841585159302
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.03989887237549
Dataset analysis elapsed time: 8.83976101875305
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: 0.0303990840911865
Calculate `GDI`: DONE
Total calculations elapsed time: 2.85849761962891
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0355956554412842
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: 0.0290675163269043
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 67.807133436203
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: 1.85629773139954
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: 0.857202768325806
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: 1.83935308456421
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.74000906944275
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: 2.86978554725647
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00694632530212402
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0410585403442383
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.949492931365967
Total calculations elapsed time: 3.8672833442688
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.80121254920959
Dataset analysis elapsed time: 8.39842438697815
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: 0.0313353538513184
Calculate `GDI`: DONE
Total calculations elapsed time: 2.83343195915222
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 
710.177   3.380 709.803

Example timings

COTAN.Rcheck/COTAN-Ex.timings

name	user	system	elapsed
COTAN_Legacy	0.001	0.000	0.001
COTAN_ObjectCreation	9.292	0.193	9.206
CalculatingCOEX	52.788	0.484	52.210
ClustersList	0.008	0.000	0.008
Conversions	5.042	0.041	5.084
GenesStatistics	10.819	0.038	10.575
HandleMetaData	0.040	0.000	0.039
HandlingClusterizations	42.904	0.325	42.890
HandlingConditions	0.074	0.001	0.075
HeatmapPlots	32.074	0.518	31.828
Installing_torch	0	0	0
LoggingFunctions	0.002	0.000	0.002
ParametersEstimations	21.545	0.277	21.806
RawDataCleaning	4.411	0.011	4.358
RawDataGetters	0.038	0.000	0.038
UniformClusters	66.276	0.115	65.614
getColorsVector	0.001	0.000	0.000