Multiple platform build/check report for BioC 3.21 - CHECK results for COTAN on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for COTAN on nebbiolo1

To the developers/maintainers of the COTAN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: COTAN

Version: 2.8.5

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings COTAN_2.8.5.tar.gz

StartedAt: 2025-10-15 22:04:16 -0400 (Wed, 15 Oct 2025)

EndedAt: 2025-10-15 22:38:29 -0400 (Wed, 15 Oct 2025)

EllapsedTime: 2053.5 seconds

RetCode: 0

Status: OK

CheckDir: COTAN.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings COTAN_2.8.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.8.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 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 ... NOTE
'library' or 'require' call to ‘torch’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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         200.729  0.693 199.470
CalculatingCOEX          57.646  0.551  56.834
HandlingClusterizations  45.251  0.416  45.279
HeatmapPlots             36.617  0.473  36.095
ParametersEstimations    26.795  0.120  26.899
GenesStatistics          12.538  0.074  12.256
COTAN_ObjectCreation     11.032  0.252  10.945
Conversions               6.598  0.070   6.668
RawDataCleaning           5.850  0.100   5.812
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘outputTestDatasetCreation.R’
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck/00check.log’
for details.

Installation output

COTAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL COTAN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘COTAN’ ...
** this is package ‘COTAN’ version ‘2.8.5’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COTAN)

Tests output

COTAN.Rcheck/tests/outputTestDatasetCreation.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> # Creates the files to be reloaded by the tests for comparisons
> library(zeallot)
> 
> outputTestDatasetCreation <- function(testsDir = file.path("tests",
+                                                            "testthat")) {
+   utils::data("test.dataset", package = "COTAN")
+   options(parallelly.fork.enable = TRUE)
+ 
+   obj <- COTAN(raw = test.dataset)
+   obj <- initializeMetaDataset(obj, GEO = " ",
+                                sequencingMethod = "artificial",
+                                sampleCondition = "test")
+ 
+   obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE)
+   #saveRDS(obj, file = file.path(testsDir,"temp.RDS"))
+ 
+   cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+   genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)]
+   saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS"))
+   saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS"))
+ 
+   dispersion.test <- getDispersion(obj)[genes.names.test]
+   saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+ 
+   raw.norm.test <- getNuNormData(obj)[genes.names.test, cells.names.test]
+   saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+ 
+   coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE)
+   saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+ 
+   lambda.test <- getLambda(obj)[genes.names.test]
+   saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+ 
+   GDI.test <- calculateGDI(obj)
+   GDI.test <- GDI.test[genes.names.test, ]
+   saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+ 
+   nu.test <- getNu(obj)[cells.names.test]
+   saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+ 
+   pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test)
+   saveRDS(pval.test, file.path(testsDir, "pval.test.RDS"))
+ 
+   GDIThreshold <- 1.46
+   initialResolution <- 0.8
+   clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold,
+                                      initialResolution   = initialResolution,
+                                      cores = 6L, saveObj = FALSE)[["clusters"]]
+   saveRDS(clusters, file.path(testsDir, "clusters1.RDS"))
+ 
+   coexDF <- DEAOnClusters(obj, clusters = clusters)
+   obj <- addClusterization(obj, clName = "clusters",
+                            clusters = clusters, coexDF = coexDF)
+ 
+   saveRDS(coexDF[genes.names.test, ],
+           file.path(testsDir, "coex.test.cluster1.RDS"))
+ 
+   pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), adjustmentMethod = "none")
+ 
+   saveRDS(pvalDF[genes.names.test, ],
+           file.path(testsDir, "pval.test.cluster1.RDS"))
+ 
+   c(mergedClusters, mCoexDF) %<-%
+     mergeUniformCellsClusters(objCOTAN = obj,
+                               clusters = NULL,
+                               GDIThreshold = GDIThreshold,
+                               cores = 6L,
+                               distance = "cosine",
+                               hclustMethod = "ward.D2",
+                               saveObj = FALSE)
+ 
+   saveRDS(mergedClusters[genes.names.test],
+           file.path(testsDir, "cluster_data_merged.RDS"))
+ }
> 
> proc.time()
   user  system elapsed 
  0.164   0.031   0.183

COTAN.Rcheck/tests/spelling.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace("spelling", quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.149   0.035   0.171

COTAN.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> 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
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % 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: 2.78011894226074
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000995874404907227
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00605297088623047
Estimating genes' coex
Calculate genes' coex elapsed time: 0.829318284988403
Total calculations elapsed time: 3.61648607254028
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
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 7 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75595238095238 | median:  1.07174634176587 | mean:  1.07174634176587
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0265938895089288 | median:  0.0144680038331048 | mean:  0.0144680038331048
`nu` mean: 1.69633192486233
Marginal errors | max: 1.95570586131367 | median 1.32068160171502 | mean: 1.33375826507259
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.058837890625 | max: 3.528076171875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.416683423613994 | median:  0.239880630367975 | mean:  0.239880630367975
`nu` mean: 0.823197206753982
Marginal errors | max: 0.836359531101206 | median 0.703684202571891 | mean: 0.645537958989614
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.164237872898673 | median:  0.0955985184389135 | mean:  0.0955985184389135
`nu` mean: 1.06863935445976
Marginal errors | max: 0.259872988828242 | median 0.213703042752633 | mean: 0.197386407582083
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2294921875 | max: 3.8720703125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.055185575120883 | median:  0.0319991762044448 | mean:  0.0319991762044448
`nu` mean: 0.976813601083562
Marginal errors | max: 0.0951586919577032 | median 0.079429703709466 | mean: 0.0724140148396648
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0196211148938294 | median:  0.01138609597457 | mean:  0.01138609597457
`nu` mean: 1.00823501891926
Marginal errors | max: 0.0327747321002292 | median 0.0272104747849538 | mean: 0.0248963830312038
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00670099066960717 | median:  0.00388888266671264 | mean:  0.00388888266671264
`nu` mean: 0.997187891997105
Marginal errors | max: 0.0114324509186883 | median 0.0094232649770607 | mean: 0.00863113610779571
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00230093811689414 | median:  0.00132529122122246 | mean:  0.00132529122122246
`nu` mean: 1.00097564689567
Marginal errors | max: 0.00387133150664631 | median 0.0031091017608853 | mean: 0.00286071175800213
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837011646904529 | median:  0.000470837393363011 | mean:  0.000470837393363011
`nu` mean: 0.999633825746458
Marginal errors | max: 0.00122501723202006 | median 0.00102126435760308 | mean: 0.000943992659051318
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000209227351122054 | median:  0.000122070312500028 | mean:  0.000122070312500028
`nu` mean: 1.00008715703862
Marginal errors | max: 0.000364602956581805 | median 0.000313956936819793 | mean: 0.000282899574318485
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
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % 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 avalable 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: 2.466472864151
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000690937042236328
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00306415557861328
Estimating genes' coex
Calculate genes' coex elapsed time: 0.823208332061768
Total calculations elapsed time: 3.29343628883362
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: 2.59477138519287
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000768661499023438
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00236821174621582
Estimating cells' coex
Calculate cells' coex elapsed time: 0.873992919921875
Total calculations elapsed time: 3.47190117835999
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
Calculate `GDI`: DONE
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
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
Calculate `GDI`: DONE
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
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
Calculate `GDI`: DONE
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
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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
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
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
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 1.73564890252257 | median 1.37996360874076 | mean: 1.32180348113228
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.402649984216273 | median:  0.231868788425666 | mean:  0.231868788425666
`nu` mean: 0.829218804209393
Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.619375430892821
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.158004893526231 | median:  0.0919692884670312 | mean:  0.0919692884670312
`nu` mean: 1.0660356050592
Marginal errors | max: 0.250724014302326 | median 0.206232152124436 | mean: 0.190425623677198
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0532774732102337 | median:  0.0308837890624999 | mean:  0.0308837890624999
`nu` mean: 0.977606315852266
Marginal errors | max: 0.0916983669060123 | median 0.0765266929824948 | mean: 0.0697593208689684
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0189966206463044 | median:  0.0110199320575908 | mean:  0.0110199320575908
`nu` mean: 1.00797668858871
Marginal errors | max: 0.0317151207459254 | median 0.0262702142278251 | mean: 0.0240886952086962
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00670088501353994 | median:  0.00388888101583662 | mean:  0.00388888101583662
`nu` mean: 0.997187996002297
Marginal errors | max: 0.0113693316356223 | median 0.00939669372836249 | mean: 0.00860715734056932
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00251007446998996 | median:  0.00144735987374958 | mean:  0.00144735987374958
`nu` mean: 1.00106271459624
Marginal errors | max: 0.00406746973787442 | median 0.00343393462175534 | mean: 0.00313496757119527
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25445556640625 | max: 3.9140625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837027590858019 | median:  0.000488281249999889 | mean:  0.000488281249999889
`nu` mean: 0.999651253659142
Marginal errors | max: 0.00143433714371533 | median 0.00116636244706747 | mean: 0.00109289166947839
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000209227688885871 | median:  0.0001220703125 | mean:  0.0001220703125
`nu` mean: 1.00008715737639
Marginal errors | max: 0.000379524846207957 | median 0.000325685250686547 | mean: 0.000295532844332236
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 avalable 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: 2.49488258361816
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000568389892578125
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00139975547790527
Estimating genes' coex
Calculate genes' coex elapsed time: 0.814221858978271
Total calculations elapsed time: 3.31107258796692
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: 2.3975670337677
Calculating cells' coex normalization factor
Calculate cells' normalization factor elapsed time: 0.000544309616088867
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.0013740062713623
Estimating cells' coex
Calculate cells' coex elapsed time: 0.83548641204834
Total calculations elapsed time: 3.23497176170349
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
Calculate `GDI`: DONE
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
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
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
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % 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: 2.67275094985962
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000725984573364258
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00144863128662109
Estimating genes' coex
Calculate genes' coex elapsed time: 0.885864973068237
Total calculations elapsed time: 3.56079053878784
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 avalable 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: 2.74446630477905
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000570535659790039
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00157046318054199
Estimating genes' coex
Calculate genes' coex elapsed time: 0.934082746505737
Total calculations elapsed time: 3.68069005012512
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
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
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
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
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: 3.35192465782166
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000768661499023438
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00142931938171387
Estimating cells' coex
Calculate cells' coex elapsed time: 0.896370410919189
Total calculations elapsed time: 4.25049304962158
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
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
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
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
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: 3.06784629821777
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000642776489257812
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00168681144714355
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12356209754944
Total calculations elapsed time: 4.19373798370361
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
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
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
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
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
Calculate `GDI`: DONE
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
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 3.56007170677185
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.54014825820923
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00652456283569336
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0498988628387451
Estimating genes' coex
Calculate genes' coex elapsed time: 1.09551095962524
Total calculations elapsed time: 4.69208264350891
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.79369950294495
Total elapsed time: 11.3338241577148
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 3.77514410018921
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.35813450813293
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00755143165588379
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0525023937225342
Estimating genes' coex
Calculate genes' coex elapsed time: 1.05554366111755
Total calculations elapsed time: 4.47373199462891
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.39281606674194
Total elapsed time: 11.3801822662354
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
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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.54844379425049
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.40655994415283
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00699377059936523
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0497512817382812
Estimating genes' coex
Calculate genes' coex elapsed time: 0.969305515289307
Total calculations elapsed time: 4.43261051177979
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.29214978218079
Total elapsed time: 12.3299291133881
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
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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.44747829437256
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.4783980846405
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00563359260559082
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0484776496887207
Estimating genes' coex
Calculate genes' coex elapsed time: 0.832233428955078
Total calculations elapsed time: 4.36474275588989
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.20380926132202
Total elapsed time: 11.8288342952728
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
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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 1160 cells
Cotan analysis functions started
Asked to drop 31 genes and 0 cells
Genes/cells selection done: dropped [31] genes and [0] cells
Working on [569] genes and [40] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032
Cotan genes' coex estimation not requested
Total elapsed time: 5.62758421897888
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.01700448989868
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00539088249206543
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00709128379821777
Estimating genes' coex
Calculate genes' coex elapsed time: 1.06840348243713
Total calculations elapsed time: 4.0978901386261
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.13707494735718
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00623798370361328
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0070650577545166
Estimating genes' coex
Calculate genes' coex elapsed time: 0.893091917037964
Total calculations elapsed time: 4.04346990585327
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 avalable 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: 2.99075102806091
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00585365295410156
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00687217712402344
Estimating genes' coex
Calculate genes' coex elapsed time: 1.00969886779785
Total calculations elapsed time: 4.01317572593689
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
calculating PValues: DONE
Handling genes type: G2
Handling genes type: G3
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 10.3980181217194
Saving elaborated data locally at: /tmp/RtmpnFecPl/test.cotan.RDS
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
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
Creating Seurat object: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Creating Seurat object: DONE
Creating PDF UMAP in file:  /tmp/RtmpnFecPl/test/reclustering/pdf_umap_1.pdf
UMAP plot
Calculating UMAP: START
22:22:57 UMAP embedding parameters a = 0.9922 b = 1.112
22:22:57 Read 1200 rows and found 40 numeric columns
22:22:57 Using Annoy for neighbor search, n_neighbors = 30
22:22:57 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:22:57 Writing NN index file to temp file /tmp/RtmpnFecPl/file27897b7c2898a
22:22:57 Searching Annoy index using 1 thread, search_k = 3000
22:22:57 Annoy recall = 100%
22:22:59 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:23:02 Initializing from normalized Laplacian + noise (using RSpectra)
22:23:02 Commencing optimization for 500 epochs, with 42618 positive edges
22:23:02 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:23:05 Optimization finished
Calculating UMAP: DONE
UMAP plot
Calculating UMAP: START
22:23:05 UMAP embedding parameters a = 0.9922 b = 1.112
22:23:05 Read 1200 rows and found 40 numeric columns
22:23:05 Using Annoy for neighbor search, n_neighbors = 30
22:23:05 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:23:05 Writing NN index file to temp file /tmp/RtmpnFecPl/file27897b38c689c
22:23:05 Searching Annoy index using 1 thread, search_k = 3000
22:23:06 Annoy recall = 100%
22:23:07 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:23:09 Initializing from normalized Laplacian + noise (using RSpectra)
22:23:09 Commencing optimization for 500 epochs, with 42618 positive edges
22:23:09 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:23:12 Optimization finished
Calculating UMAP: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 847 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [353] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 3.11567687988281
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.74362182617188
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00886225700378418
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0425689220428467
Estimating genes' coex
Calculate genes' coex elapsed time: 1.19376134872437
Total calculations elapsed time: 4.98881435394287
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.99143123626709
Total elapsed time: 11.6659235954285
Checking uniformity for the cluster '01_0000' with 353 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 353, is uniform
Cluster 01_0000's shift to uniformity: -0.0160990564073067
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.00833333333333333, check.thresholdRank = 0, check.quantileAtRatio = 1.44390094359269, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 353
cluster 01_0000 is uniform

* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 4.60655498504639
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.56352972984314
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00661158561706543
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0356690883636475
Estimating genes' coex
Calculate genes' coex elapsed time: 1.14023971557617
Total calculations elapsed time: 4.74605011940002
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.0344705581665
Total elapsed time: 13.4354827404022
Checking uniformity for the cluster '01_0001' with 321 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 321, is uniform
Cluster 01_0001's shift to uniformity: -0.029501740796509
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.005, check.thresholdRank = 0, check.quantileAtRatio = 1.43049825920349, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 321
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.75755023956299
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.40129852294922
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00664496421813965
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0171699523925781
Estimating genes' coex
Calculate genes' coex elapsed time: 1.11666131019592
Total calculations elapsed time: 4.54177474975586
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.70355606079102
Total elapsed time: 12.0104429721832
Checking uniformity for the cluster '01_0002' with 295 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 295, is uniform
Cluster 01_0002's shift to uniformity: -0.0675248136510636
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.39247518634894, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 295
cluster 01_0002 is uniform

* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 4.75071930885315
Cotan genes' coex estimation started
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 avalable 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: 4.49741172790527
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0118758678436279
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.021153450012207
Estimating genes' coex
Calculate genes' coex elapsed time: 1.33418416976929
Total calculations elapsed time: 5.8646252155304
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.25951814651489
Total elapsed time: 14.9503743648529
Checking uniformity for the cluster '01_0003' with 231 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 231, is uniform
Cluster 01_0003's shift to uniformity: -0.0869783653733056
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.37302163462669, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 231
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 353 cells
* DEA on cluster '2' with 321 cells
* DEA on cluster '3' with 295 cells
* DEA on cluster '4' with 231 cells

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  3, 2  ->  1, 3  ->  2, 4  ->  4
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2, 3  ->  3, 4  ->  4
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 4.46612334251404
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.78740811347961
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00611591339111328
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0168766975402832
Estimating genes' coex
Calculate genes' coex elapsed time: 1.01644682884216
Total calculations elapsed time: 4.82684755325317
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.90742540359497
Total elapsed time: 13.0562558174133
Checking uniformity for the cluster 'Cluster_2' with 295 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_2, with size 295, is uniform
Cluster Cluster_2's shift to uniformity: -0.00560790972802017
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0416666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.29139209027198, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.34700400911787, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.39247518634894, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4279762218014, isUniform = TRUE, clusterSize = 295
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 321 cells
* DEA on cluster '2' with 245 cells
* DEA on cluster '3' with 353 cells
* DEA on cluster '4' with 231 cells

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  2, 2  ->  1, 3  ->  4, 4  ->  3, -1  ->  -1
Applied reordering to clusterization is:
1  ->  2, 2  ->  3, 3  ->  1, 4  ->  4, -1  ->  -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.61939716339111
Cotan genes' coex estimation started
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: 4.98160219192505
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00889301300048828
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0553219318389893
Estimating genes' coex
Calculate genes' coex elapsed time: 1.64632821083069
Total calculations elapsed time: 6.69214534759521
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.99853467941284
Total elapsed time: 15.2290189266205
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Included 186 genes with GDI below 1.3
Selected 600 genes using HGDI selector
Running genes' selection: DONE
Creating Seurat object: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Creating Seurat object: DONE
Using passed in clusterization
Creating PDF UMAP in file:  /tmp/RtmpnFecPl/test/reclustering/pdf_umap_1.pdf
UMAP plot
Calculating UMAP: START
22:25:24 UMAP embedding parameters a = 0.9922 b = 1.112
22:25:24 Read 1200 rows and found 40 numeric columns
22:25:24 Using Annoy for neighbor search, n_neighbors = 30
22:25:24 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:25:24 Writing NN index file to temp file /tmp/RtmpnFecPl/file27897b674db6e
22:25:24 Searching Annoy index using 1 thread, search_k = 3000
22:25:25 Annoy recall = 100%
22:25:26 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:25:28 Initializing from normalized Laplacian + noise (using RSpectra)
22:25:28 Commencing optimization for 500 epochs, with 42618 positive edges
22:25:28 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:25:31 Optimization finished
Calculating UMAP: DONE
UMAP plot
Calculating UMAP: START
22:25:32 UMAP embedding parameters a = 0.9922 b = 1.112
22:25:32 Read 1200 rows and found 40 numeric columns
22:25:32 Using Annoy for neighbor search, n_neighbors = 30
22:25:32 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:25:32 Writing NN index file to temp file /tmp/RtmpnFecPl/file27897b700bf285
22:25:32 Searching Annoy index using 1 thread, search_k = 3000
22:25:32 Annoy recall = 100%
22:25:33 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:25:36 Initializing from normalized Laplacian + noise (using RSpectra)
22:25:36 Commencing optimization for 500 epochs, with 42618 positive edges
22:25:36 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:25:39 Optimization finished
Calculating UMAP: DONE
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5
Only analysis elapsed time: 3.54159736633301
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.67675304412842
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0062263011932373
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0384535789489746
Estimating genes' coex
Calculate genes' coex elapsed time: 1.13470768928528
Total calculations elapsed time: 4.85614061355591
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.99920749664307
Total elapsed time: 11.6051406860352
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 600, is uniform
Cluster 01_0001's shift to uniformity: -0.012256083873327
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38474391612667, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42418110276821, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00666666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45338035249414, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 4, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.51521594648007, isUniform = TRUE, clusterSize = 600
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667
Only analysis elapsed time: 4.17891716957092
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.84524130821228
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00559663772583008
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0424587726593018
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12765669822693
Total calculations elapsed time: 5.02095341682434
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.23956680297852
Total elapsed time: 13.6668996810913
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 600, is uniform
Cluster 01_0002's shift to uniformity: -0.0203445505533575
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37665544944664, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42305229982216, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43783135828069, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50182972335853, isUniform = TRUE, clusterSize = 600
cluster 01_0002 is uniform


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

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
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'

Log Fold Change Analysis - DONE
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'

Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1' with 321 cells
* DEA on cluster '2' with 295 cells
* DEA on cluster '3' with 353 cells
* DEA on cluster '4' with 231 cells

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'

Log Fold Change Analysis - DONE
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 4.04687786102295
Cotan genes' coex estimation started
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 avalable 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: 4.04296636581421
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00680923461914062
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.03529953956604
Estimating genes' coex
Calculate genes' coex elapsed time: 1.27148056030273
Total calculations elapsed time: 5.35655570030212
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.60977625846863
Total elapsed time: 13.1601049900055
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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
[1] "Tested cluster: 4"
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 3.42473649978638
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.83425164222717
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00762629508972168
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0189399719238281
Estimating genes' coex
Calculate genes' coex elapsed time: 1.38719487190247
Total calculations elapsed time: 5.24801278114319
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.38002991676331
Total elapsed time: 11.980339050293
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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 9.06502413749695
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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

Number of nodes: 1200
Number of edges: 55884

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5927
Number of communities: 4
Elapsed time: 0 seconds
Clusterizations found: RNA_snn_res.0.8, seurat_clusters
Conditions found: orig.ident
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 8.64303612709045
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.42938828468323
Cotan genes' coex estimation started
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: 4.63334274291992
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00592660903930664
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0507090091705322
Estimating genes' coex
Calculate genes' coex elapsed time: 1.19530606269836
Total calculations elapsed time: 5.88528442382812
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.14861869812012
Total elapsed time: 14.3265857696533
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
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
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
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
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
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
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 9.79909682273865
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

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'

Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.43530796540674
Handling cluster '2' with mean UDE 0.640931107489519
Handling cluster '3' with mean UDE 0.546546914955575
Handling cluster '4' with mean UDE 1.22034802329657
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 2 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 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("1", "2") c("3", "4")
*1_2-merge
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 7.16049885749817
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 6.70546126365662
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0084068775177002
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0519790649414062
Estimating genes' coex
Calculate genes' coex elapsed time: 2.04829573631287
Total calculations elapsed time: 8.81414294242859
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 10.7110624313354
Total elapsed time: 22.2926862239838
Checking uniformity for the cluster '1_2-merge' with 574 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 574, is not uniform
Cluster 1_2-merge's shift to uniformity: 0.0820221369127518
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.326666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37902213691275, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.28, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41724738266283, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.42971854140312, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 20, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.5067755752749, isUniform = FALSE, clusterSize = 574
Clusters 1 and 2 cannot be merged
*3_4-merge
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 4.51894354820251
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.96753120422363
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00704288482666016
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0401725769042969
Estimating genes' coex
Calculate genes' coex elapsed time: 1.02190160751343
Total calculations elapsed time: 5.03664827346802
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.02706384658813
Total elapsed time: 13.9958753585815
Checking uniformity for the cluster '3_4-merge' with 626 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 626, is not uniform
Cluster 3_4-merge's shift to uniformity: 0.0914611744346074
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.248333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38846117443461, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.218333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42066795244751, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0366666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45442688129939, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 22, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52592182249635, isUniform = FALSE, clusterSize = 626
Clusters 3 and 4 cannot be merged
Finished the first batch - no merges were executed
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Updating check results for the 2 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("2", "3") c("2", "4")
*2_3-merge
Asked to drop 0 genes and 664 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [536] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0390625 | max: 12.59375 | % negative: 9.16666666666667
Only analysis elapsed time: 3.46914172172546
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.41853356361389
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00645065307617188
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0297293663024902
Estimating genes' coex
Calculate genes' coex elapsed time: 1.15724110603333
Total calculations elapsed time: 4.61195468902588
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.6368293762207
Total elapsed time: 11.2838535308838
Checking uniformity for the cluster '2_3-merge' with 536 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_3-merge, with size 536, is not uniform
Cluster 2_3-merge's shift to uniformity: 0.102213698003777
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.29, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.39921369800378, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.251666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.45276697088286, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.05, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.49016449535422, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 30, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.54477108741147, isUniform = FALSE, clusterSize = 536
Clusters 2 and 3 cannot be merged
*2_4-merge
Asked to drop 0 genes and 668 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [532] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.04754638671875 | max: 10.234375 | % negative: 5
Only analysis elapsed time: 3.23440098762512
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.18416166305542
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00587916374206543
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0393812656402588
Estimating genes' coex
Calculate genes' coex elapsed time: 0.988357305526733
Total calculations elapsed time: 4.21777939796448
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.35781955718994
Total elapsed time: 10.6396129131317
Checking uniformity for the cluster '2_4-merge' with 532 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_4-merge, with size 532, is not uniform
Cluster 2_4-merge's shift to uniformity: 0.213129217682233
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.39, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.51012921768223, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.361666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55599610798341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.181666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59088431608469, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 109, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68475283375668, isUniform = FALSE, clusterSize = 532
Clusters 2 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 4 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 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Updating check results for the 4 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("1", "3") c("1", "4")
*1_3-merge
Asked to drop 0 genes and 532 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [668] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.046630859375 | max: 9.03515625 | % negative: 1.33333333333333
Only analysis elapsed time: 3.10471749305725
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.10689854621887
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00603461265563965
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0420501232147217
Estimating genes' coex
Calculate genes' coex elapsed time: 1.05612826347351
Total calculations elapsed time: 4.21111154556274
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.23448848724365
Total elapsed time: 10.2973701953888
Checking uniformity for the cluster '1_3-merge' with 668 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_3-merge, with size 668, is not uniform
Cluster 1_3-merge's shift to uniformity: 0.177923707405303
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.33, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.5749237074053, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.31, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.6368755707341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.128333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.65704996173771, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 77, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68881338289977, isUniform = FALSE, clusterSize = 668
Clusters 1 and 3 cannot be merged
*1_4-merge
Asked to drop 0 genes and 536 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [664] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0164794921875 | max: 5.5595703125 | % negative: 0.166666666666667
Only analysis elapsed time: 3.06160044670105
Cotan genes' coex estimation started
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 avalable 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: 2.87553858757019
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00547504425048828
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0463259220123291
Estimating genes' coex
Calculate genes' coex elapsed time: 1.0223982334137
Total calculations elapsed time: 3.9497377872467
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.95625829696655
Total elapsed time: 9.91541504859924
Checking uniformity for the cluster '1_4-merge' with 664 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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_4-merge, with size 664, is not uniform
Cluster 1_4-merge's shift to uniformity: 0.138277355686157
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.348333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.53527735568616, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55951216335001, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0983333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59105696847609, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 59, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.64605433203111, isUniform = FALSE, clusterSize = 664
Clusters 1 and 4 cannot be merged
Clusters 2 and 1 will be merged
Clusters 3 and 4 will be merged
Executed 2 merges
Start merging nearest clusters: iteration 4
Differential Expression Analysis - START
* DEA on cluster '1_2-merge' with 574 cells
* DEA on cluster '3_4-merge' with 626 cells

Differential Expression Analysis - DONE
Updating check results for the 6 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 analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 3.24312663078308
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.08694124221802
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00545549392700195
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0483946800231934
Estimating genes' coex
Calculate genes' coex elapsed time: 0.955036401748657
Total calculations elapsed time: 4.09582781791687
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.98590278625488
Total elapsed time: 10.1141541004181
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: 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 1200, is not uniform
Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 0.173174985379327
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.415, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017498537933, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.388333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61240081401504, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.15, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64046660675367, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 90, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66512085964758, isUniform = FALSE, clusterSize = 1200
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 7 checks
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1' with 574 cells
* DEA on cluster '2' with 626 cells

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
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'

Log Fold Change Analysis - DONE
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 2.82453227043152
Cotan genes' coex estimation started
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 avalable 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: 2.74461102485657
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00728797912597656
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0438785552978516
Estimating genes' coex
Calculate genes' coex elapsed time: 0.81477952003479
Total calculations elapsed time: 3.61055707931519
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.52755069732666
Total elapsed time: 9.18627715110779
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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 2.9214174747467
Cotan genes' coex estimation started
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 avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.00771188735962
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00537681579589844
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0406866073608398
Estimating genes' coex
Calculate genes' coex elapsed time: 0.916479587554932
Total calculations elapsed time: 3.97025489807129
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.93058228492737
Total elapsed time: 9.63743352890015
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
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 562 ]
> 
> proc.time()
   user  system elapsed 
935.226   5.710 935.541

Example timings

COTAN.Rcheck/COTAN-Ex.timings

name	user	system	elapsed
COTAN_Legacy	0.002	0.001	0.003
COTAN_ObjectCreation	11.032	0.252	10.945
CalculatingCOEX	57.646	0.551	56.834
ClustersList	0.006	0.003	0.009
Conversions	6.598	0.070	6.668
GenesStatistics	12.538	0.074	12.256
HandleMetaData	0.069	0.000	0.070
HandlingClusterizations	45.251	0.416	45.279
HandlingConditions	0.092	0.002	0.095
HeatmapPlots	36.617	0.473	36.095
LoggingFunctions	0.003	0.000	0.003
ParametersEstimations	26.795	0.120	26.899
RawDataCleaning	5.850	0.100	5.812
RawDataGetters	0.071	0.004	0.075
UniformClusters	200.729	0.693	199.470
getColorsVector	0.001	0.000	0.001