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This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 457/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COTAN 2.9.7  (landing page)
Galfrè Silvia Giulia
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/COTAN
git_branch: devel
git_last_commit: f624c05
git_last_commit_date: 2025-10-11 16:40:33 -0400 (Sat, 11 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for COTAN on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: COTAN
Version: 2.9.7
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.9.7.tar.gz
StartedAt: 2025-10-17 07:38:49 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 07:59:49 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 1259.9 seconds
RetCode: 0
Status:   OK  
CheckDir: COTAN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.9.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.9.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘COTAN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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         62.636  0.176  62.579
CalculatingCOEX         48.092  0.263  47.896
HandlingClusterizations 42.241  0.187  42.386
HeatmapPlots            30.856  0.256  30.765
ParametersEstimations   20.482  0.133  20.672
GenesStatistics          9.859  0.016   9.740
COTAN_ObjectCreation     8.763  0.116   8.737
RawDataCleaning          5.546  0.008   5.574
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘outputTestDatasetCreation.R’
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

COTAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL COTAN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘COTAN’ ...
** this is package ‘COTAN’ version ‘2.9.7’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COTAN)

Tests output

COTAN.Rcheck/tests/outputTestDatasetCreation.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  0.221   0.033   0.238 

COTAN.Rcheck/tests/spelling.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  0.205   0.031   0.224 

COTAN.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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: 1.63788890838623
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: 2.32010674476624
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000705242156982422
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00826930999755859
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.778205394744873
Total calculations elapsed time: 3.10728669166565
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: 4.63618969917297
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: 0.782323360443115
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: 1.5675790309906
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: 0.839959144592285
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: 1.58457517623901
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: 0.825355529785156
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: 1.63669013977051
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: 0.756616353988647
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: 1.58213210105896
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: 0.819705724716187
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: 1.69429779052734
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: 0.776134252548218
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: 1.5958456993103
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: 0.769160509109497
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: 1.55468082427979
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: 0.753223419189453
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: 1.55319213867188
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: 0.78314733505249
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: 1.52928996086121
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: 0.764874458312988
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: 42.6893920898438
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: 1.5422158241272
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: 2.51404213905334
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000963449478149414
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00400829315185547
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.789704322814941
Total calculations elapsed time: 3.30871820449829
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: 2.46272873878479
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000949382781982422
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.0028688907623291
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.800674200057983
Total calculations elapsed time: 3.26722121238708
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: 0.0136189460754395
Calculate `GDI`: DONE
Total calculations elapsed time: 2.53062605857849
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: 0.00434494018554688
Calculate `GDI`: DONE
Total calculations elapsed time: 2.42401218414307
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: 1.72337436676025
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: 1.70172023773193
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: 1.75191044807434
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 8 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 2.72356271743774
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: 2.41051912307739
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: 2.45038962364197
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: 1.64085459709167
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: 0.816735506057739
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: 1.76586651802063
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0655494303592343 | max: 3.54400580804152 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.848588705062866
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: 1.75962400436401
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: 0.851942539215088
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: 1.58985733985901
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: 0.790919303894043
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: 1.61671614646912
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: 0.818102359771729
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: 1.54233717918396
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: 0.855113744735718
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: 1.6700587272644
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: 0.855845212936401
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: 1.65186977386475
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: 0.814258098602295
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: 1.51743626594543
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: 0.839398860931396
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: 44.5625612735748
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: 2.42100405693054
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000724554061889648
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00186038017272949
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.751272678375244
Total calculations elapsed time: 3.17486166954041
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: 2.30920648574829
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.000751018524169922
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.0018622875213623
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.789966344833374
Total calculations elapsed time: 3.1017861366272
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: 0.00407242774963379
Calculate `GDI`: DONE
Total calculations elapsed time: 2.27031874656677
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: 5.90866899490356
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: 6.20119118690491
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: 3.25297617912292
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: 2.43967604637146
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.00100970268249512
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00206971168518066
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.825705289840698
Total calculations elapsed time: 3.26846075057983
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: 2.43310642242432
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000689983367919922
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00191211700439453
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.859461307525635
Total calculations elapsed time: 3.29516983032227
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: 6.60838317871094
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: 6.53240871429443
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: 3.32585287094116
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: 0.855634450912476
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: 3.3067581653595
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: 0.866069555282593
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: 3.32476258277893
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: 0.847028970718384
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: 19.9684658050537
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: 2.50706028938293
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000982999801635742
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.0020902156829834
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.808800935745239
Total calculations elapsed time: 3.31893444061279
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: 6.70284104347229
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: 6.48560428619385
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: 3.32233595848083
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: 0.802030563354492
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: 3.18187236785889
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: 0.848121404647827
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: 3.14289975166321
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: 0.797053575515747
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: 19.2954125404358
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: 2.34979629516602
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000726699829101562
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00200796127319336
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.829311847686768
Total calculations elapsed time: 3.18184280395508
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: 5.85338401794434
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: 0.00310921669006348
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: 5.65731525421143
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: 5.65901017189026
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: 0.00423860549926758
Calculate `GDI`: DONE
Total calculations elapsed time: 2.48112511634827
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: 5.69244575500488
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00413393974304199
Calculate `GDI`: DONE
Total calculations elapsed time: 8.07841110229492
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: 0.00659012794494629
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00559806823730469
Calculate `GDI`: DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.836714506149292
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: 1.87701010704041
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.70802855491638
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: 2.6212477684021
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0130491256713867
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.064265251159668
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.800915718078613
Total calculations elapsed time: 3.49947786331177
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.31559777259827
Dataset analysis elapsed time: 7.86034083366394
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: 0.806251287460327
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: 1.89030814170837
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.76077604293823
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: 2.67488050460815
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0128934383392334
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0643370151519775
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.804858922958374
Total calculations elapsed time: 3.55696988105774
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.37268257141113
Dataset analysis elapsed time: 7.93970990180969
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: 0.0220346450805664
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: 0.0316026210784912
Calculate `GDI`: DONE
Total calculations elapsed time: 2.40057420730591
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: 0.830211639404297
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: 1.89973521232605
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.69419002532959
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: 2.61210584640503
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0128929615020752
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0641605854034424
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.833991765975952
Total calculations elapsed time: 3.5231511592865
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.35474324226379
Dataset analysis elapsed time: 7.87914490699768
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: 0.0210165977478027
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: 0.0323078632354736
Calculate `GDI`: DONE
Total calculations elapsed time: 2.57767295837402
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: 0.801541090011597
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: 1.83733558654785
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.64542698860168
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: 2.64679002761841
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0129320621490479
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0646042823791504
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.772773742675781
Total calculations elapsed time: 3.49710011482239
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.30561804771423
Dataset analysis elapsed time: 7.75258612632751
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: 0.00823616981506348
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: 0.0332615375518799
Calculate `GDI`: DONE
Total calculations elapsed time: 2.4260847568512
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 960 cells
COTAN dataset analysis: START
Asked to drop 83 genes and 0 cells
Genes/cells selection done: dropped [83] genes and [0] cells
Working on [517] genes and [40] cells
Dataset cleaning elapsed time: 0.838498592376709
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: 1.68661546707153
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.267567793681876 | max: 101.923257389521 | % negative: 52.6112185686654
Model parameter estimation elapsed time: 2.4879584312439
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.870809316635132
Dataset analysis elapsed time: 4.19726634025574
COTAN dataset analysis: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.50612902641296
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0102002620697021
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.011876106262207
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.853234529495239
Total calculations elapsed time: 3.38143992424011
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: 2.55164909362793
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0102124214172363
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0118868350982666
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.841322422027588
Total calculations elapsed time: 3.41507077217102
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: 2.59306144714355
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0100734233856201
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0119321346282959
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.884713649749756
Total calculations elapsed time: 3.49978065490723
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: 0.00622105598449707
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: 2.05647754669189
Clean plots: DONE
Dataset cleaning elapsed time: 4.68331098556519
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: 2.0307137966156
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.90662860870361
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: 2.86645030975342
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0144824981689453
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0679090023040771
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.843170642852783
Total calculations elapsed time: 3.79201245307922
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.67756223678589
Dataset analysis elapsed time: 12.2675018310547
COTAN dataset analysis: DONE
Saving elaborated data locally at: /home/biocbuild/tmp/Rtmpz7SjYJ/test.cotan.RDS
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.79039287567139
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: 3.99227595329285
Creating new clusterization: DONE
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.90056729316711
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1000
Number of edges: 36652

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3743
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 3.9958975315094
Creating new clusterization: DONE
Creating PDF UMAP in file:  /home/biocbuild/tmp/Rtmpz7SjYJ/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
07:55:11 UMAP embedding parameters a = 0.9922 b = 1.112
07:55:11 Read 1000 rows and found 65 numeric columns
07:55:11 Using Annoy for neighbor search, n_neighbors = 30
07:55:11 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:55:11 Writing NN index file to temp file /home/biocbuild/tmp/Rtmpz7SjYJ/file13d80c7bdcbe61
07:55:11 Searching Annoy index using 1 thread, search_k = 3000
07:55:12 Annoy recall = 100%
07:55:13 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
07:55:14 Initializing from normalized Laplacian + noise (using RSpectra)
07:55:14 Commencing optimization for 500 epochs, with 39044 positive edges
07:55:14 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:55:17 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.89189291000366
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
07:55:17 UMAP embedding parameters a = 0.9922 b = 1.112
07:55:17 Read 1000 rows and found 65 numeric columns
07:55:17 Using Annoy for neighbor search, n_neighbors = 30
07:55:17 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:55:18 Writing NN index file to temp file /home/biocbuild/tmp/Rtmpz7SjYJ/file13d80c4c0f7249
07:55:18 Searching Annoy index using 1 thread, search_k = 3000
07:55:18 Annoy recall = 100%
07:55:19 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
07:55:21 Initializing from normalized Laplacian + noise (using RSpectra)
07:55:21 Commencing optimization for 500 epochs, with 39044 positive edges
07:55:21 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:55:23 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.75819706916809
UMAP plot: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 687 cells
COTAN dataset analysis: START
Asked to drop 43 genes and 0 cells
Genes/cells selection done: dropped [43] genes and [0] cells
Working on [557] genes and [313] cells
Dataset cleaning elapsed time: 0.910665035247803
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 11 iterations
Total calculations elapsed time: 1.80436897277832
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.126565269702225 | max: 788.372048308528 | % negative: 38.5996409335727
Model parameter estimation elapsed time: 2.68458437919617
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: 2.67582535743713
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0119955539703369
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0300164222717285
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.90632176399231
Total calculations elapsed time: 3.62415909767151
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.51547431945801
Dataset analysis elapsed time: 8.11072373390198
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: 0.030390739440918
Calculate `GDI`: DONE
Total calculations elapsed time: 2.67916011810303
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0517427921295166
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: -0.0175178017151116
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 = 1.37948219828489, 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 = 1.43089123341142, 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 = 1.47612588512219, 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: 0.866795539855957
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: 1.67612552642822
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.53756976127625
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: 2.64619469642639
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0114371776580811
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0261392593383789
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.874396562576294
Total calculations elapsed time: 3.55816769599915
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.41931056976318
Dataset analysis elapsed time: 7.82367587089539
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: 0.0292346477508545
Calculate `GDI`: DONE
Total calculations elapsed time: 2.65598750114441
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0563704967498779
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: -0.0466523594846466
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 = 1.35034764051535, 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 = 1.37278730407695, 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 = 1.38664163146848, 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 = 1.45240567481125, isUniform = TRUE, clusterSize = 257
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 758 cells
COTAN dataset analysis: START
Asked to drop 77 genes and 0 cells
Genes/cells selection done: dropped [77] genes and [0] cells
Working on [523] genes and [242] cells
Dataset cleaning elapsed time: 0.875179767608643
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: 1.78501892089844
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.166254045792573 | max: 224.924342782861 | % negative: 42.6386233269598
Model parameter estimation elapsed time: 2.68145704269409
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: 2.65434908866882
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0100374221801758
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0240931510925293
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.938806533813477
Total calculations elapsed time: 3.627286195755
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.48196530342102
Dataset analysis elapsed time: 8.03860211372375
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: 0.0274229049682617
Calculate `GDI`: DONE
Total calculations elapsed time: 2.73120760917664
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0572447776794434
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: -0.0473527936300073
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 = 1.34964720636999, 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 = 1.37472946305403, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38771313919655, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.43097703442028, isUniform = TRUE, clusterSize = 242
cluster 01_0002 is uniform

* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 812 cells
COTAN dataset analysis: START
Asked to drop 79 genes and 0 cells
Genes/cells selection done: dropped [79] genes and [0] cells
Working on [521] genes and [188] cells
Dataset cleaning elapsed time: 0.914257764816284
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 6 iterations
Total calculations elapsed time: 1.78124284744263
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 2.62948250770569
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: 2.64262652397156
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0103862285614014
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0216000080108643
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.865008354187012
Total calculations elapsed time: 3.53962111473083
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.38870716094971
Dataset analysis elapsed time: 7.93244743347168
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: 0.0266292095184326
Calculate `GDI`: DONE
Total calculations elapsed time: 2.53855657577515
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0527667999267578
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: -0.0672912272436044
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 = 1.3297087727564, 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 = 1.37495297633957, 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: 0.0496022701263428
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  3, 2  ->  1, 3  ->  2, 4  ->  4
Total calculations elapsed time: 75.6854858398438
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2, 3  ->  3, 4  ->  4
Asked to drop 0 genes and 812 cells
COTAN dataset analysis: START
Asked to drop 79 genes and 0 cells
Genes/cells selection done: dropped [79] genes and [0] cells
Working on [521] genes and [188] cells
Dataset cleaning elapsed time: 0.906322956085205
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 6 iterations
Total calculations elapsed time: 1.76598119735718
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 2.60769033432007
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: 2.50840258598328
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00986242294311523
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0212912559509277
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.806090116500854
Total calculations elapsed time: 3.34564638137817
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.19620656967163
Dataset analysis elapsed time: 7.7102198600769
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: 0.0273935794830322
Calculate `GDI`: DONE
Total calculations elapsed time: 2.55891060829163
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0536143779754639
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: -0.0672912272436044
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 = 1.3297087727564, 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 = 1.37495297633957, 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: 0.0468339920043945
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: 3.11913657188416
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: 4.22791409492493
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file:  /home/biocbuild/tmp/Rtmpz7SjYJ/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
07:56:41 UMAP embedding parameters a = 0.9922 b = 1.112
07:56:41 Read 1000 rows and found 40 numeric columns
07:56:41 Using Annoy for neighbor search, n_neighbors = 30
07:56:41 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:56:42 Writing NN index file to temp file /home/biocbuild/tmp/Rtmpz7SjYJ/file13d80c10fe9849
07:56:42 Searching Annoy index using 1 thread, search_k = 3000
07:56:42 Annoy recall = 100%
07:56:43 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
07:56:44 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
07:56:44 Using 'irlba' for PCA
07:56:44 PCA: 2 components explained 36.15% variance
07:56:44 Scaling init to sdev = 1
07:56:45 Commencing optimization for 500 epochs, with 41630 positive edges
07:56:45 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:56:47 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.8088743686676
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
07:56:48 UMAP embedding parameters a = 0.9922 b = 1.112
07:56:48 Read 1000 rows and found 40 numeric columns
07:56:48 Using Annoy for neighbor search, n_neighbors = 30
07:56:48 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:56:48 Writing NN index file to temp file /home/biocbuild/tmp/Rtmpz7SjYJ/file13d80c31d93578
07:56:48 Searching Annoy index using 1 thread, search_k = 3000
07:56:48 Annoy recall = 100%
07:56:49 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
07:56:51 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
07:56:51 Using 'irlba' for PCA
07:56:51 PCA: 2 components explained 36.15% variance
07:56:51 Scaling init to sdev = 1
07:56:51 Commencing optimization for 500 epochs, with 41630 positive edges
07:56:51 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:56:53 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.78952717781067
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: 0.917710542678833
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: 1.91313028335571
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.108871643378045 | max: 295.971778839086 | % negative: 35.0533807829181
Model parameter estimation elapsed time: 2.86735582351685
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: 2.76776385307312
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0120954513549805
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0378460884094238
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.90216064453125
Total calculations elapsed time: 3.71986603736877
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.56971549987793
Dataset analysis elapsed time: 8.35478186607361
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: 0.030811071395874
Calculate `GDI`: DONE
Total calculations elapsed time: 2.7231183052063
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0542812347412109
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: -0.0417301990664185
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 = 1.35526980093358, 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 = 1.40346106115496, 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 = 1.42565794715039, 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: 0.924238681793213
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: 1.85721063613892
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0636486786621688 | max: 141.389145035675 | % negative: 36.1510791366906
Model parameter estimation elapsed time: 2.75303792953491
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: 2.7936224937439
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0119094848632812
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0377471446990967
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.961352109909058
Total calculations elapsed time: 3.80463123321533
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.71762990951538
Dataset analysis elapsed time: 8.39490652084351
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: 0.0299451351165771
Calculate `GDI`: DONE
Total calculations elapsed time: 2.70198225975037
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0552604198455811
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: -0.0413872276843519
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 = 1.37204026755189, 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 = 1.40876953414112, 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: 0.0399703979492188
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 47.499086856842
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: 3.64901900291443
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.66567730903625
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: 3.42660069465637
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.442538022995
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: 0.0460312366485596
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: 3.50105452537537
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.56075310707092
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 743 cells
COTAN dataset analysis: START
Asked to drop 51 genes and 0 cells
Genes/cells selection done: dropped [51] genes and [0] cells
Working on [549] genes and [257] cells
Dataset cleaning elapsed time: 0.930532693862915
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: 1.85482883453369
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.81925892829895
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: 2.74609136581421
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0106656551361084
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0261156558990479
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.874545574188232
Total calculations elapsed time: 3.6574182510376
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.52166485786438
Dataset analysis elapsed time: 8.27145648002625
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: 0.0292723178863525
Calculate `GDI`: DONE
Total calculations elapsed time: 2.7103853225708
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: 2.01183271408081
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: 0.897327423095703
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: 2.08279609680176
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.00105595588684
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.845970153808594
Dataset analysis elapsed time: 4.74435353279114
COTAN dataset analysis: DONE
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
PC_ 1 
Positive:  g-000397, g-000525, g-000460, g-000458, g-000535, g-000217, g-000194, g-000497, g-000432, g-000383 
	   g-000318, g-000486, g-000464, g-000588, g-000549, g-000368, g-000252, g-000151, g-000209, g-000538 
	   g-000325, g-000514, g-000524, g-000244, g-000320, g-000201, g-000499, g-000309, g-000290, g-000483 
Negative:  g-000415, g-000506, g-000496, g-000579, g-000572, g-000421, g-000455, g-000328, g-000178, g-000567 
	   g-000405, g-000296, g-000387, g-000501, g-000493, g-000481, g-000343, g-000528, g-000551, g-000414 
	   g-000367, g-000594, g-000159, g-000517, g-000574, g-000229, g-000222, g-000533, g-000243, g-000306 
PC_ 2 
Positive:  g-000141, g-000093, g-000089, g-000033, g-000123, g-000557, g-000330, g-000156, g-000142, g-000095 
	   g-000061, g-000235, g-000032, g-000186, g-000056, g-000259, g-000027, g-000041, g-000333, g-000386 
	   g-000009, g-000395, g-000048, g-000116, g-000340, g-000418, g-000035, g-000332, g-000086, g-000040 
Negative:  g-000088, g-000158, g-000255, g-000115, g-000054, g-000472, g-000554, g-000391, g-000253, g-000226 
	   g-000051, g-000147, g-000541, g-000077, g-000224, g-000194, g-000290, g-000293, g-000313, g-000118 
	   g-000121, g-000220, g-000467, g-000500, g-000341, g-000039, g-000091, g-000249, g-000426, g-000288 
PC_ 3 
Positive:  g-000126, g-000083, g-000086, g-000117, g-000130, g-000010, g-000498, g-000333, g-000047, g-000179 
	   g-000340, g-000035, g-000531, g-000140, g-000527, g-000049, g-000316, g-000031, g-000014, g-000073 
	   g-000218, g-000445, g-000129, g-000175, g-000105, g-000581, g-000404, g-000025, g-000266, g-000354 
Negative:  g-000096, g-000575, g-000370, g-000337, g-000319, g-000364, g-000308, g-000293, g-000147, g-000307 
	   g-000038, g-000492, g-000541, g-000185, g-000008, g-000482, g-000562, g-000097, g-000222, g-000084 
	   g-000141, g-000377, g-000224, g-000223, g-000136, g-000434, g-000277, g-000426, g-000139, g-000093 
PC_ 4 
Positive:  g-000006, g-000043, g-000462, g-000279, g-000180, g-000576, g-000087, g-000584, g-000498, g-000333 
	   g-000189, g-000088, g-000451, g-000059, g-000135, g-000281, g-000106, g-000429, g-000316, g-000578 
	   g-000303, g-000031, g-000581, g-000026, g-000122, g-000561, g-000546, g-000164, g-000353, g-000300 
Negative:  g-000072, g-000012, g-000129, g-000052, g-000097, g-000262, g-000080, g-000056, g-000025, g-000092 
	   g-000354, g-000334, g-000423, g-000228, g-000002, g-000010, g-000086, g-000147, g-000185, g-000172 
	   g-000124, g-000009, g-000077, g-000476, g-000126, g-000145, g-000065, g-000268, g-000152, g-000348 
PC_ 5 
Positive:  g-000051, g-000150, g-000088, g-000476, g-000344, g-000116, g-000428, g-000012, g-000523, g-000394 
	   g-000101, g-000127, g-000069, g-000214, g-000049, g-000357, g-000075, g-000081, g-000576, g-000342 
	   g-000439, g-000018, g-000070, g-000079, g-000015, g-000550, g-000600, g-000247, g-000218, g-000331 
Negative:  g-000105, g-000037, g-000110, g-000054, g-000090, g-000389, g-000022, g-000578, g-000289, g-000147 
	   g-000547, g-000011, g-000477, g-000433, g-000200, g-000348, g-000404, g-000003, g-000250, g-000109 
	   g-000402, g-000241, g-000595, g-000341, g-000560, g-000385, g-000413, g-000352, g-000573, g-000265 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1000
Number of edges: 67836

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: 0.849077939987183
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: 1.89909052848816
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.71962809562683
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.849930286407471
Dataset analysis elapsed time: 4.41863632202148
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: 0.809880971908569
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: 1.8771755695343
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.74821448326111
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: 2.8741888999939
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0129268169403076
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0655770301818848
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.841296195983887
Total calculations elapsed time: 3.79398894309998
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.6684398651123
Dataset analysis elapsed time: 8.22653532028198
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: 0.00593805313110352
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: 0.0101299285888672
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Total calculations elapsed time: 0.871552467346191
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: 0.00868606567382812
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: 0.00957393646240234
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 0.913389205932617
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: 0.00927090644836426
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: 0.0101761817932129
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 0.908308744430542
Calculating gene co-expression space - DONE
Total calculations elapsed time: 1.00354504585266
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: 0.888771772384644
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: 2.05603766441345
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.99166655540466
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.91890811920166
Dataset analysis elapsed time: 4.79934644699097
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: 0.0469787120819092
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: 3.56415247917175
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: 0.0470545291900635
Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1", "2")
*1_2-merge
Asked to drop 0 genes and 501 cells
COTAN dataset analysis: START
Asked to drop 16 genes and 0 cells
Genes/cells selection done: dropped [16] genes and [0] cells
Working on [584] genes and [499] cells
Dataset cleaning elapsed time: 0.879148006439209
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: 1.87634134292603
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.73525524139404
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: 2.73421931266785
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0125486850738525
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0394802093505859
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.887137889862061
Total calculations elapsed time: 3.67338609695435
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.54507517814636
Dataset analysis elapsed time: 8.15947842597961
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: 0.0328183174133301
Calculate `GDI`: DONE
Total calculations elapsed time: 2.67647171020508
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0548062324523926
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: 0.0566581136434268
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 = 1.35365811364343, 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 = 1.37149326865969, 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 = 1.42111642638122, isUniform = FALSE, clusterSize = 499
Clusters 1 and 2 cannot be merged
Finished the first batch - no merges were executed
Loop calculations elapsed time: 15.6645908355713
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: 0.0449070930480957
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: 0.889568090438843
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 11 iterations
Total calculations elapsed time: 1.87851357460022
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.107568326617881 | max: 698.639334552754 | % negative: 32.1492007104796
Model parameter estimation elapsed time: 2.77990174293518
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: 2.78718781471252
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0119664669036865
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0376119613647461
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.889639616012573
Total calculations elapsed time: 3.72640585899353
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.6036958694458
Dataset analysis elapsed time: 8.27316570281982
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: 0.0314123630523682
Calculate `GDI`: DONE
Total calculations elapsed time: 2.71394658088684
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.054940938949585
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: 0.0813107504723543
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 = 1.37831075047235, 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 = 1.41473792188167, 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: 0.0477573871612549
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: 0.948305606842041
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: 1.93062806129456
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0739592351622374 | max: 400.051960722894 | % negative: 25.7191201353638
Model parameter estimation elapsed time: 2.85286736488342
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: 2.74950528144836
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0128018856048584
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0373775959014893
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.912914276123047
Total calculations elapsed time: 3.71259903907776
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.5887131690979
Dataset analysis elapsed time: 8.38988614082336
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: 0.0318479537963867
Calculate `GDI`: DONE
Total calculations elapsed time: 2.72661662101746
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0551900863647461
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: 16.2602360248566
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: 0.0443286895751953
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: 0.973092794418335
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: 2.19736361503601
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.1093418598175
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: 2.80527234077454
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.012521505355835
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0637471675872803
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.846646308898926
Total calculations elapsed time: 3.72818732261658
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.64004516601562
Dataset analysis elapsed time: 8.72247982025146
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: 0.0321574211120605
Calculate `GDI`: DONE
Total calculations elapsed time: 2.68804049491882
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0559728145599365
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: 3.8698838512041
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 = 4.54596809454194, 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 = 5.25322968524779, 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 = 5.3698838512041, 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: 0.0419387817382812
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Total calculations elapsed time: 64.5137267112732
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: 1.73134517669678
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: 0.934406280517578
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: 1.88422560691833
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.7980649471283
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: 2.74657607078552
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0129857063293457
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0399644374847412
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.911604881286621
Total calculations elapsed time: 3.71113109588623
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.60497164726257
Dataset analysis elapsed time: 8.33744287490845
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: 0.032764196395874
Calculate `GDI`: DONE
Total calculations elapsed time: 2.65464663505554
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 
653.156   3.113 656.150 

Example timings

COTAN.Rcheck/COTAN-Ex.timings

nameusersystemelapsed
COTAN_Legacy0.0020.0000.002
COTAN_ObjectCreation8.7630.1168.737
CalculatingCOEX48.092 0.26347.896
ClustersList0.0080.0040.011
Conversions4.4430.0124.469
GenesStatistics9.8590.0169.740
HandleMetaData0.0400.0030.043
HandlingClusterizations42.241 0.18742.386
HandlingConditions0.0920.0040.096
HeatmapPlots30.856 0.25630.765
Installing_torch000
LoggingFunctions0.0000.0020.002
ParametersEstimations20.482 0.13320.672
RawDataCleaning5.5460.0085.574
RawDataGetters0.0450.0000.045
UniformClusters62.636 0.17662.579
getColorsVector0.0010.0000.001