##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.9.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.9.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘COTAN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
UniformClusters         181.135  0.435 181.010
CalculatingCOEX          50.412  0.185  49.979
HandlingClusterizations  41.181  0.201  41.357
HeatmapPlots             32.588  0.366  32.497
ParametersEstimations    23.631  0.034  23.746
COTAN_ObjectCreation     11.223  0.208  11.271
GenesStatistics          10.573  0.050  10.467
Conversions               5.606  0.028   5.651
RawDataCleaning           5.062  0.016   5.101
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘outputTestDatasetCreation.R’
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘COTAN’ ...
** this is package ‘COTAN’ version ‘2.9.5’
** 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)

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

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

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

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

> 
> # Creates the files to be reloaded by the tests for comparisons
> 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 
  0.214   0.023   0.222 

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

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

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

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

> if (requireNamespace("spelling", quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.192   0.031   0.208 

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

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

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

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

> Sys.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> 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: 2.17114424705505
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0013120174407959
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00851297378540039
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.730889081954956
Total calculations elapsed time: 2.91185832023621
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: 2.22583413124084
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000898838043212891
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0038306713104248
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.812620639801025
Total calculations elapsed time: 3.04318428039551
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: 2.25269389152527
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.0010526180267334
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00280237197875977
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.753515243530273
Total calculations elapsed time: 3.01006412506104
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 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
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Selected 5 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 5 genes using HVG_Seurat selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer data
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Running genes' selection: START
Given 5 genes as input
Running genes' selection: DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Selected 8 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 8 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Initializing `COTAN` meta-data
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`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: 2.40543794631958
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000835180282592773
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00218582153320312
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.758108377456665
Total calculations elapsed time: 3.16656732559204
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: 2.38270235061646
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.00076603889465332
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00192093849182129
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.786106109619141
Total calculations elapsed time: 3.17149543762207
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: 2.32361149787903
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000918149948120117
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00188374519348145
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.783907651901245
Total calculations elapsed time: 3.11032104492188
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: 2.27931189537048
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000667810440063477
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00185275077819824
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.753583431243896
Total calculations elapsed time: 3.03541588783264
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: 2.39023542404175
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.00107908248901367
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00214338302612305
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.841642618179321
Total calculations elapsed time: 3.23510050773621
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: 2.29826712608337
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000692844390869141
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00184273719787598
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.767585039138794
Total calculations elapsed time: 3.06838774681091
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: 3.18685293197632
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: 2.6559534072876
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0141544342041016
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0492615699768066
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.837281703948975
Total calculations elapsed time: 3.55665111541748
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.36324310302734
Total elapsed time: 9.14042353630066
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: 3.14842319488525
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: 2.68776416778564
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0132162570953369
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.047269344329834
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.80786395072937
Total calculations elapsed time: 3.55611371994019
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.30662846565247
Total elapsed time: 9.04934167861938
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: 3.11673951148987
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: 2.62751483917236
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0125637054443359
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0474324226379395
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.791788339614868
Total calculations elapsed time: 3.47929930686951
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.2910795211792
Total elapsed time: 8.97705078125
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: 3.07148623466492
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: 2.62160706520081
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0134963989257812
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0468747615814209
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.773830652236938
Total calculations elapsed time: 3.45580887794495
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.20693111419678
Total elapsed time: 8.83421993255615
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: 4.54808020591736
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: 2.28036975860596
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0120043754577637
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00786685943603516
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.75870156288147
Total calculations elapsed time: 3.05894255638123
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: 2.34494543075562
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0119009017944336
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00752735137939453
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.789305686950684
Total calculations elapsed time: 3.15367937088013
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: 2.37640070915222
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0124421119689941
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00774312019348145
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.78292989730835
Total calculations elapsed time: 3.17951583862305
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
Elaborating PCA - START
Elaborating PCA - DONE
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
Only analysis elapsed time: 3.26728200912476
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: 2.72939443588257
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0129909515380859
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0486772060394287
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.830721855163574
Total calculations elapsed time: 3.62178444862366
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.42434668540955
Total elapsed time: 12.3129932880402
Saving elaborated data locally at: /home/biocbuild/tmp/RtmpFwaJ3l/test.cotan.RDS
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 37723

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5827
Number of communities: 2
Elapsed time: 0 seconds
Number of clusters is too small. Reclustering at resolution higher than: 0.8
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 37723

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3954
Number of communities: 5
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Creating new clusterization: DONE
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 600 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Creating new clusterization: DONE
Creating PDF UMAP in file:  /home/biocbuild/tmp/RtmpFwaJ3l/test/reclustering/pdf_umap_1.pdf
UMAP plot
Calculating UMAP: START
05:57:25 UMAP embedding parameters a = 0.9922 b = 1.112
05:57:25 Read 1200 rows and found 40 numeric columns
05:57:25 Using Annoy for neighbor search, n_neighbors = 30
05:57:25 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
05:57:25 Writing NN index file to temp file /home/biocbuild/tmp/RtmpFwaJ3l/file342497191ac5c8
05:57:25 Searching Annoy index using 1 thread, search_k = 3000
05:57:25 Annoy recall = 100%
05:57:26 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
05:57:28 Initializing from normalized Laplacian + noise (using RSpectra)
05:57:28 Commencing optimization for 500 epochs, with 42674 positive edges
05:57:28 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
05:57:31 Optimization finished
Calculating UMAP: DONE
UMAP plot
Calculating UMAP: START
05:57:31 UMAP embedding parameters a = 0.9922 b = 1.112
05:57:31 Read 1200 rows and found 40 numeric columns
05:57:31 Using Annoy for neighbor search, n_neighbors = 30
05:57:31 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
05:57:31 Writing NN index file to temp file /home/biocbuild/tmp/RtmpFwaJ3l/file3424971b7505e3
05:57:31 Searching Annoy index using 1 thread, search_k = 3000
05:57:32 Annoy recall = 100%
05:57:33 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
05:57:34 Initializing from normalized Laplacian + noise (using RSpectra)
05:57:34 Commencing optimization for 500 epochs, with 42674 positive edges
05:57:34 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
05:57:37 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: 2.81192350387573
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: 2.62988805770874
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0122401714324951
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0345861911773682
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.80408787727356
Total calculations elapsed time: 3.48080229759216
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.35644960403442
Total elapsed time: 8.85993218421936
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: -0.0160990564073278
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 = 1.44390094359267, 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: 2.66700124740601
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: 2.61659789085388
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.01340651512146
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0324399471282959
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.855118989944458
Total calculations elapsed time: 3.5175633430481
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.41770792007446
Total elapsed time: 8.78359842300415
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: -0.0295017407965217
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 = 1.43049825920348, 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: 2.52637791633606
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: 2.47583723068237
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0119330883026123
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0154304504394531
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.791034698486328
Total calculations elapsed time: 3.29423546791077
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.1105170249939
Total elapsed time: 8.30134296417236
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: -0.0675248136510651
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.39247518634893, 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: 2.62002038955688
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: 2.66089367866516
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0127885341644287
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.01639723777771
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.835062265396118
Total calculations elapsed time: 3.52514171600342
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.30911111831665
Total elapsed time: 8.56704163551331
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: -0.0869783653733431
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.37302163462666, 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: 2.65042686462402
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: 2.58461689949036
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.012714147567749
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0157649517059326
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.865600347518921
Total calculations elapsed time: 3.47869634628296
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.2935266494751
Total elapsed time: 8.58301877975464
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: -0.00560790972808967
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 = 1.29139209027191, 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 = 1.34700400911793, 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 = 1.39247518634893, 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 = 1.42797622180124, 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
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
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
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file:  /home/biocbuild/tmp/RtmpFwaJ3l/test/reclustering/pdf_umap_1.pdf
UMAP plot
Calculating UMAP: START
05:58:58 UMAP embedding parameters a = 0.9922 b = 1.112
05:58:58 Read 1200 rows and found 40 numeric columns
05:58:58 Using Annoy for neighbor search, n_neighbors = 30
05:58:58 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
05:58:59 Writing NN index file to temp file /home/biocbuild/tmp/RtmpFwaJ3l/file3424974ad06f8c
05:58:59 Searching Annoy index using 1 thread, search_k = 3000
05:58:59 Annoy recall = 100%
05:59:00 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
05:59:02 Initializing from normalized Laplacian + noise (using RSpectra)
05:59:02 Commencing optimization for 500 epochs, with 42644 positive edges
05:59:02 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
05:59:05 Optimization finished
Calculating UMAP: DONE
UMAP plot
Calculating UMAP: START
05:59:05 UMAP embedding parameters a = 0.9922 b = 1.112
05:59:05 Read 1200 rows and found 40 numeric columns
05:59:05 Using Annoy for neighbor search, n_neighbors = 30
05:59:05 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
05:59:05 Writing NN index file to temp file /home/biocbuild/tmp/RtmpFwaJ3l/file3424977bcbad1a
05:59:05 Searching Annoy index using 1 thread, search_k = 3000
05:59:05 Annoy recall = 100%
05:59:06 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
05:59:08 Initializing from normalized Laplacian + noise (using RSpectra)
05:59:08 Commencing optimization for 500 epochs, with 42644 positive edges
05:59:08 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
05:59:11 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: 2.96118593215942
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: 2.74055862426758
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0128355026245117
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0367019176483154
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.84699010848999
Total calculations elapsed time: 3.6370861530304
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.49344253540039
Total elapsed time: 9.16279816627502
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: -0.0122560838732164
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 = 1.38474391612678, 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 = 1.42418110276816, 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 = 1.4533803524942, 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 = 1.5152159464801, 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: 2.9183337688446
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: 2.86648654937744
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0137252807617188
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0386765003204346
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.908895015716553
Total calculations elapsed time: 3.82778334617615
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.69306778907776
Total elapsed time: 9.38424372673035
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: -0.0203445505533857
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 = 1.37665544944661, 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 = 1.42305229982225, 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 = 1.43783135828053, 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: 2.73126292228699
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: 2.66306591033936
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0123329162597656
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.031574010848999
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.874288082122803
Total calculations elapsed time: 3.58126091957092
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.39830422401428
Total elapsed time: 8.86538481712341
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: 2.78389835357666
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: 2.55699920654297
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0123460292816162
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0159680843353271
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.851885318756104
Total calculations elapsed time: 3.43719863891602
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.32258486747742
Total elapsed time: 8.83989191055298
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: 5.71969056129456
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-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-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 
	   g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 
	   g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 
Negative:  g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 
	   g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 
	   g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 
PC_ 5 
Positive:  g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 
	   g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 
	   g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 
Negative:  g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 
	   g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 
	   g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55864

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5945
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: 6.01523590087891
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: 3.3303918838501
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: 2.88672089576721
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0140142440795898
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.04862380027771
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.874050855636597
Total calculations elapsed time: 3.82340979576111
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.72051692008972
Total elapsed time: 9.79341387748718
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: 5.86084604263306
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: 2.79813241958618
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: 2.69656372070312
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.013566255569458
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0381958484649658
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.848529100418091
Total calculations elapsed time: 3.59685492515564
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.47891759872437
Total elapsed time: 9.02416038513184
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: 0.0820221369127296
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 = 1.37902213691273, 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 = 1.41724738266277, 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 = 1.42971854140314, 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 = 1.50677557527475, 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: 2.86824011802673
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: 2.61079621315002
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0133345127105713
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0346605777740479
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.809897184371948
Total calculations elapsed time: 3.46868848800659
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.27853775024414
Total elapsed time: 8.86237907409668
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: 0.0914611744346732
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 = 1.38846117443467, 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 = 1.4206679524475, 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 = 1.45442688129937, 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 = 1.52592182249624, 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: 2.869220495224
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: 2.78565073013306
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0136098861694336
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0261781215667725
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.873150587081909
Total calculations elapsed time: 3.69858932495117
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.59667611122131
Total elapsed time: 9.15780162811279
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: 0.102213698004012
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 = 1.39921369800401, 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 = 1.45276697088276, 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 = 1.49016449535431, 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 = 1.54477108741164, 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: 2.89505839347839
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: 2.73502564430237
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0129084587097168
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0360016822814941
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.871670722961426
Total calculations elapsed time: 3.655606508255
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.50819540023804
Total elapsed time: 9.15589952468872
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: 0.213129217682169
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 = 1.51012921768217, 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 = 1.55599610798334, 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 = 1.59088431608462, 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 = 1.68475283375659, 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: 3.06307554244995
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: 2.81402182579041
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0136253833770752
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0395796298980713
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.871903657913208
Total calculations elapsed time: 3.73913049697876
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.65354824066162
Total elapsed time: 9.53355741500854
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: 0.177923707405312
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 = 1.57492370740531, 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 = 1.6368755707342, 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 = 1.65704996173763, 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 = 1.68881338289992, 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: 3.06221580505371
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: 2.9094762802124
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0135996341705322
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0438697338104248
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.890352010726929
Total calculations elapsed time: 3.85729765892029
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.74010491371155
Total elapsed time: 9.51341199874878
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: 0.138277355686092
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 = 1.53527735568609, 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 = 1.55951216335002, 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 = 1.59105696847611, 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 = 1.64605433203105, 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: 3.36701130867004
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: 2.95489883422852
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0143082141876221
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0487039089202881
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.893913507461548
Total calculations elapsed time: 3.91182446479797
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.79166173934937
Total elapsed time: 9.93464660644531
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: 0.173174985379335
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 = 1.61240081401493, 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 = 1.64046660675371, 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 = 1.66512085964769, 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: 2.97369933128357
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: 2.75375366210938
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0142698287963867
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.038456916809082
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.89658784866333
Total calculations elapsed time: 3.70306825637817
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.59133362770081
Total elapsed time: 9.40722584724426
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: 2.70436596870422
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: 2.62658476829529
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0133571624755859
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0343818664550781
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.834131956100464
Total calculations elapsed time: 3.50845575332642
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.35942578315735
Total elapsed time: 8.79779839515686
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 1 | SKIP 0 | PASS 572 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 572 ]
> 
> proc.time()
   user  system elapsed 
737.223   2.817 739.257