Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-01 12:04 -0400 (Wed, 01 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 454/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.9.6 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: COTAN |
Version: 2.9.6 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.9.6.tar.gz |
StartedAt: 2025-09-30 20:28:26 -0400 (Tue, 30 Sep 2025) |
EndedAt: 2025-09-30 20:50:28 -0400 (Tue, 30 Sep 2025) |
EllapsedTime: 1322.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COTAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.9.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.9.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 26 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed UniformClusters 115.896 2.572 117.810 CalculatingCOEX 54.586 1.050 55.897 HandlingClusterizations 43.151 1.110 43.934 HeatmapPlots 34.147 0.824 35.160 ParametersEstimations 22.947 0.696 23.751 GenesStatistics 10.983 0.204 11.225 COTAN_ObjectCreation 10.531 0.282 10.874 RawDataCleaning 5.043 0.278 5.175 Conversions 4.998 0.112 5.130 * 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
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘COTAN’ ... ** this is package ‘COTAN’ version ‘2.9.6’ ** 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)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > > outputTestDatasetCreation <- + function(testsDir = file.path("tests", "testthat")) { + utils::data("test.dataset", package = "COTAN") + options(parallelly.fork.enable = TRUE) + setLoggingLevel(3L) + + obj <- COTAN(raw = test.dataset) + obj <- initializeMetaDataset(objCOTAN = obj, GEO = " ", + sequencingMethod = "artificial", + sampleCondition = "test") + + obj <- proceedToCoex(objCOTAN = obj, cores = 6L, saveObj = FALSE) + + if (FALSE) { + saveRDS(obj, file = file.path(testsDir,"test.COTAN.RDS")) + } + + cells.names.test <- getCells(objCOTAN = obj)[c(1L:10L, 591L:610L, 991L:1000L)] + genes.names.test <- getGenes(objCOTAN = obj)[c(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")) + + pcaRaw <- runPCA(x = getRawData(objCOTAN = obj), rank = 10L, + BSPARAM = IrlbaParam(), get.rotation = FALSE)[["x"]] + + pca.raw.test <- pcaRaw[genes.names.test, ] + saveRDS(pca.raw.test, file.path(testsDir, "pca.raw.test.RDS")) + + dispersion.test <- getDispersion(objCOTAN = obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- + getNuNormData(objCOTAN = obj)[genes.names.test, cells.names.test] + saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS")) + + coex.test <- + getGenesCoex(objCOTAN = obj, genes = genes.names.test, zeroDiagonal = FALSE) + saveRDS(coex.test, file.path(testsDir, "coex.test.RDS")) + + lambda.test <- getLambda(objCOTAN = obj)[genes.names.test] + saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS")) + + GDI.test <- calculateGDI(objCOTAN = obj) + GDI.test <- GDI.test[genes.names.test, ] + saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS")) + + nu.test <- getNu(objCOTAN = obj)[cells.names.test] + saveRDS(nu.test, file.path(testsDir, "nu.test.RDS")) + + pvalues.test <- calculatePValue(objCOTAN = obj, + geneSubsetCol = genes.names.test, + geneSubsetRow = genes.names.test) + saveRDS(pvalues.test, file.path(testsDir, "pvalues.test.RDS")) + + groupMarkers <- list(G1 = c("g-000010", "g-000020", "g-000030"), + G2 = c("g-000300", "g-000330", "g-000660"), + G3 = c("g-000510", "g-000530", "g-000550", + "g-000570", "g-000590")) + + gcsData <- genesCoexSpace(objCOTAN = obj, + primaryMarkers = unlist(groupMarkers), + numGenesPerMarker = 11L) + + genes.coex.space.test <- gcsData[["GCS"]] + saveRDS(genes.coex.space.test, + file.path(testsDir, "genes.coex.space.test.RDS")) + + genesClustersData <- + establishGenesClusters(objCOTAN = obj, + groupMarkers = groupMarkers, + numGenesPerMarker = 11L, + kCuts = 6L, distance = "cosine", + hclustMethod = "ward.D2") + + pca.genes.clusters.test <- genesClustersData[["pca_clusters"]] + saveRDS(pca.genes.clusters.test, + file.path(testsDir, "pca.genes.clusters.test.RDS")) + + # Make it a less strict check as it is only for testing + checker <- new("AdvancedGDIUniformityCheck") + checker <- shiftCheckerThresholds(checker, 0.1) + + initialResolution <- 0.8 + splitData <- cellsUniformClustering(objCOTAN = obj, + checker = checker, + initialResolution = initialResolution, + useCoexEigen = TRUE, + dataMethod = "LL", + numReducedComp = 50L, + cores = 6L, optimizeForSpeed = TRUE, + deviceStr = "cuda", saveObj = FALSE) + + split.clusters.test <- splitData[["clusters"]] + saveRDS(split.clusters.test, file.path(testsDir, "split.clusters.test.RDS")) + + obj <- addClusterization(objCOTAN = obj, + clName = "split", + clusters = splitData[["clusters"]], + coexDF = splitData[["coex"]]) + + coex.clusters.test <- splitData[["coex"]][genes.names.test, ] + saveRDS(coex.clusters.test, file.path(testsDir, "coex.clusters.test.RDS")) + + pvalDF <- pValueFromDEA(splitData[["coex"]], + getNumCells(objCOTAN = obj), + adjustmentMethod = "none") + + pvalues.clusters.test <- pvalDF[genes.names.test, ] + saveRDS(pvalues.clusters.test, + file.path(testsDir, "pvalues.clusters.test.RDS")) + + mergedData <- mergeUniformCellsClusters(objCOTAN = obj, + clusters = splitData[["clusters"]], + checkers = checker, + cores = 6L, + distance = "cosine", + hclustMethod = "ward.D2", + saveObj = FALSE) + + merge.clusters.test <- mergedData[["clusters"]] + saveRDS(merge.clusters.test, file.path(testsDir, "merge.clusters.test.RDS")) + + obj <- addClusterization(objCOTAN = obj, + clName = "merge", + clusters = mergedData[["clusters"]], + coexDF = mergedData[["coex"]]) + } > > proc.time() user system elapsed 0.264 0.089 0.350
COTAN.Rcheck/tests/spelling.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace("spelling", quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) All Done! > > proc.time() user system elapsed 0.211 0.086 0.285
COTAN.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > library(zeallot) > test_check("COTAN") Setting new log level to 4 Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.79262804985046 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.56425905227661 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000600099563598633 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00700592994689941 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.857181072235107 Total calculations elapsed time: 3.42904615402222 Calculate genes' COEX (legacy): DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 5 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 4 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 5.30543494224548 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 7 cells batches Total calculations elapsed time: 0.850084066390991 Estimate `nu`: DONE `nu` change (abs) | max: 1.75595238095238 | median: 1.07156808035714 | mean: 1.07156808035714 Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.71510910987854 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03734183779544 | max: 4.61112297272667 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.902074098587036 Estimate `nu`: DONE `nu` change (abs) | max: 0.0295487661210321 | median: 0.016072261901129 | mean: 0.016072261901129 `nu` mean: 1.69786080481514 Marginal errors | max: 1.95799528047999 | median 1.32268477389029 | mean: 1.33563364783916 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.71387314796448 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.0585450475968788 | max: 3.52739274166646 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.866261005401611 Estimate `nu`: DONE `nu` change (abs) | max: 0.417150556912302 | median: 0.240156504520849 | mean: 0.240156504520849 `nu` mean: 0.823005947608547 Marginal errors | max: 0.837672524335753 | median 0.704691669139061 | mean: 0.646575831699996 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.69157195091248 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.328845855849147 | max: 4.03031691940854 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.889678001403809 Estimate `nu`: DONE `nu` change (abs) | max: 0.164439840041 | median: 0.0957105992188852 | mean: 0.0957105992188852 `nu` mean: 1.06872924082212 Marginal errors | max: 0.260109847946692 | median 0.21392791155499 | mean: 0.197565106613055 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.77783393859863 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.229469002841045 | max: 3.87206403670079 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.886673927307129 Estimate `nu`: DONE `nu` change (abs) | max: 0.05539667181205 | median: 0.0321044921874999 | mean: 0.0321044921874999 `nu` mean: 0.97670782037545 Marginal errors | max: 0.095347789718808 | median 0.0796003827042702 | mean: 0.0725509735761708 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.69888210296631 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.263830434255107 | max: 3.92953043775907 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.899029016494751 Estimate `nu`: DONE `nu` change (abs) | max: 0.0196209299693411 | median: 0.0114037947200925 | mean: 0.0114037947200925 `nu` mean: 1.00821713524925 Marginal errors | max: 0.0329495161656741 | median 0.0273479725376307 | mean: 0.0250296751521313 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.7286069393158 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.251734659898778 | max: 3.9096133246649 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.895127058029175 Estimate `nu`: DONE `nu` change (abs) | max: 0.0069104540740097 | median: 0.0040109538496062 | mean: 0.0040109538496062 `nu` mean: 0.997100499775596 Marginal errors | max: 0.0116950057438405 | median 0.00972280144874116 | mean: 0.00889105008777609 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.78489303588867 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.256009779031907 | max: 3.91667271750655 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.863193988800049 Estimate `nu`: DONE `nu` change (abs) | max: 0.00251004753849005 | median: 0.00146484374999994 | mean: 0.00146484374999994 `nu` mean: 1.00104520378849 Marginal errors | max: 0.00430755646112857 | median 0.00358203399504298 | mean: 0.00327684342604062 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.628751039505 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.254429717857093 | max: 3.91406908073254 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.830728054046631 Estimate `nu`: DONE `nu` change (abs) | max: 0.00104629156456748 | median: 0.000592910406456731 | mean: 0.000592910406456731 `nu` mean: 0.999546618841889 Marginal errors | max: 0.00162038706091039 | median 0.00134441676098973 | mean: 0.00123030512553246 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.67194414138794 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.255022049769696 | max: 3.91504587939868 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.874594926834106 Estimate `nu`: DONE `nu` change (abs) | max: 0.000418450901304768 | median: 0.000244140625000028 | mean: 0.000244140625000028 `nu` mean: 1.0001743102763 Marginal errors | max: 0.00071569233034019 | median 0.000597297218559056 | mean: 0.000545906995079548 Total calculations elapsed time: 46.9055230617523 Estimate `dispersion`/`nu`: DONE Estimate `dispersion`/`nu`: START Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.76958799362183 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.93015313148499 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.00118780136108398 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0043492317199707 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.844621896743774 Total calculations elapsed time: 3.78031206130981 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: 2.71210384368896 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00110316276550293 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00235390663146973 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.879404067993164 Total calculations elapsed time: 3.5949649810791 Calculate cells' COEX (legacy): DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0145130157470703 Calculate `GDI`: DONE Total calculations elapsed time: 2.74815988540649 Calculate GDI dataframe: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00270485877990723 Calculate `GDI`: DONE Total calculations elapsed time: 2.67979192733765 Calculate GDI dataframe: DONE Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Selected 5 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 5 genes using HVG_Seurat selector Running genes' selection: DONE Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer data Calculating gene means 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variance to mean ratios 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Running genes' selection: START Given 5 genes as input Running genes' selection: DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 1.80813312530518 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 1.73779082298279 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Selected 8 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 1.76122903823853 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 8 genes using HVG_Seurat selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 2.80638098716736 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 2.64671492576599 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 2.7848858833313 Elaborating Reduced dimensionality Data Matrix - DONE Initializing `COTAN` meta-data Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.75560283660889 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.876368045806885 Estimate `nu`: DONE `nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 `nu` mean: 1.68489292689732 Marginal errors | max: 1.735699617106 | median 1.3799744133366 | mean: 1.32181397451301 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.80015707015991 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.0655494303592343 | max: 3.54400580804152 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.891250848770142 Estimate `nu`: DONE `nu` change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666 `nu` mean: 0.829218804209393 Marginal errors | max: 0.803248939260364 | median 0.677504196374578 | mean: 0.619386446933353 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.8840548992157 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.326019058449519 | max: 4.02612397202046 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.871612071990967 Estimate `nu`: DONE `nu` change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312 `nu` mean: 1.0660356050592 Marginal errors | max: 0.250677002875358 | median 0.206241644985115 | mean: 0.190402167377958 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.74053907394409 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.230397316576369 | max: 3.87365659194104 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.857141017913818 Estimate `nu`: DONE `nu` change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999 `nu` mean: 0.977606315852266 Marginal errors | max: 0.0916920322976189 | median 0.0765360853958157 | mean: 0.069767303009408 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.81109499931335 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.263457616228195 | max: 3.928924407347 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.949253082275391 Estimate `nu`: DONE `nu` change (abs) | max: 0.0187878665732679 | median: 0.0109155550210726 | mean: 0.0109155550210726 `nu` mean: 1.0078723115522 Marginal errors | max: 0.0315207323253404 | median 0.0261635598193228 | mean: 0.0239435763640454 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.84927797317505 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.251890641847532 | max: 3.90987172241566 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.916007995605469 Estimate `nu`: DONE `nu` change (abs) | max: 0.00649137083358098 | median: 0.00376680890457393 | mean: 0.00376680890457393 `nu` mean: 0.997275438070993 Marginal errors | max: 0.0109748802265024 | median 0.00912386940474885 | mean: 0.00834350038184297 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.7745521068573 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.255902752363649 | max: 3.91649655995187 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.899029016494751 Estimate `nu`: DONE `nu` change (abs) | max: 0.00230094227000666 | median: 0.00132529141000018 | mean: 0.00132529141000018 `nu` mean: 1.00097565086001 Marginal errors | max: 0.00376864912836616 | median 0.00313421412286008 | mean: 0.00286709489297508 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.84444999694824 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.254520292119112 | max: 3.91421850264948 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.870712995529175 Estimate `nu`: DONE `nu` change (abs) | max: 0.000837013154366462 | median: 0.000488281250000028 | mean: 0.000488281250000028 `nu` mean: 0.999651268095634 Marginal errors | max: 0.0014405532051498 | median 0.00119489364392944 | mean: 0.00109355439757195 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.77145195007324 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.255046800817985 | max: 3.91508667609651 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.875428915023804 Estimate `nu`: DONE `nu` change (abs) | max: 0.000418448154490214 | median: 0.000244140624999917 | mean: 0.000244140624999917 `nu` mean: 1.00017430752949 Marginal errors | max: 0.000715683388516908 | median 0.000597284734240588 | mean: 0.000545899916522963 Total calculations elapsed time: 48.5482540130615 Estimate `dispersion`/`nu`: DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.70386791229248 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000514030456542969 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0021369457244873 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.897745132446289 Total calculations elapsed time: 3.6042640209198 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: 2.67013883590698 Calculating cells' COEX normalization factor Calculate cells' normalization factor elapsed time: 0.000864982604980469 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00180816650390625 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.918700933456421 Total calculations elapsed time: 3.59151291847229 Calculate cells' COEX (legacy): DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00336194038391113 Calculate `GDI`: DONE Total calculations elapsed time: 2.73328614234924 Calculate GDI dataframe: DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.325 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Total calculations elapsed time: 7.36232995986938 Calculate genes' partial COEX: DONE Calculate cells' partial COEX: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial COEX Total calculations elapsed time: 7.20830416679382 Calculate cells' partial COEX: DONE Asked to drop 2 genes and 0 cells Asked to drop 0 genes and 4 cells Asked to drop 2 genes and 2 cells Attaching package: 'rlang' The following objects are masked from 'package:testthat': is_false, is_null, is_true Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating YN..NY..NN..t().. done Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.64634418487549 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 calculating NN.. done calculating NN.. done calculating NY..YN..YY..t().. done Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.65062189102173 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.0010991096496582 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00176787376403809 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.91317892074585 Total calculations elapsed time: 3.56666779518127 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.65734100341797 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000689983367919922 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00156211853027344 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.918545961380005 Total calculations elapsed time: 3.57813906669617 Calculate genes' COEX (legacy): DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.1 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Total calculations elapsed time: 7.36158394813538 Calculate genes' partial COEX: DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.4 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Total calculations elapsed time: 7.18014311790466 Calculate genes' partial COEX: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating NY..YN..NN..t().. done Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.64256405830383 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.888146877288818 Estimate `nu`: DONE `nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 `nu` mean: 1.68489292689732 Marginal errors | max: 0.255290533439036 | median 0.0807313765005375 | mean: 0.101968565509113 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.506432056427 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.884474992752075 Estimate `nu`: DONE `nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 `nu` mean: 1.69735147626627 Marginal errors | max: 0.00330148418741771 | median 0.00111713187082163 | mean: 0.00132007186543017 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.60996794700623 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.863620042800903 Estimate `nu`: DONE `nu` change (abs) | max: 0 | median: 0 | mean: 0 `nu` mean: 1.69735147626627 Marginal errors | max: 5.14174422185931e-05 | median 1.68182247684001e-07 | mean: 5.57649710817287e-06 Total calculations elapsed time: 21.5660579204559 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: 2.70602989196777 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00122308731079102 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00191903114318848 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.921705007553101 Total calculations elapsed time: 3.63087701797485 Calculate cells' COEX (legacy): DONE Calculate cells' partial COEX: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial COEX Total calculations elapsed time: 7.26223611831665 Calculate cells' partial COEX: DONE Calculate cells' partial COEX: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial COEX Total calculations elapsed time: 7.23899412155151 Calculate cells' partial COEX: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.60348296165466 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.938524007797241 Estimate `nu`: DONE `nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 `nu` mean: 1.68489292689732 Marginal errors | max: 0.255290533439036 | median 0.0807313765005375 | mean: 0.101968565509113 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.69956493377686 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.906920909881592 Estimate `nu`: DONE `nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 `nu` mean: 1.69735147626627 Marginal errors | max: 0.00330148418741771 | median 0.00111713187082163 | mean: 0.00132007186543017 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.73932409286499 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Total calculations elapsed time: 0.935425996780396 Estimate `nu`: DONE `nu` change (abs) | max: 0 | median: 0 | mean: 0 `nu` mean: 1.69735147626627 Marginal errors | max: 5.14174422185931e-05 | median 1.68182247684001e-07 | mean: 5.57649710817287e-06 Total calculations elapsed time: 21.8939669132233 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: 2.67155289649963 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000490188598632812 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00170278549194336 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.904349088668823 Total calculations elapsed time: 3.57809495925903 Calculate genes' COEX (legacy): DONE Calculating S: START Calculating S: DONE Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Total calculations elapsed time: 6.41522192955017 Calculating G: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values genome wide on columns and genome wide on rows Total calculations elapsed time: 0.00291800498962402 calculating PValues: DONE Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Total calculations elapsed time: 6.30076694488525 Calculating G: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows Total calculations elapsed time: 6.30251693725586 calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00336790084838867 Calculate `GDI`: DONE Total calculations elapsed time: 2.87756991386414 Calculate GDI dataframe: DONE Calculate GDI dataframe: START Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Total calculations elapsed time: 6.32037210464478 Calculating G: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00288701057434082 Calculate `GDI`: DONE Total calculations elapsed time: 9.09605097770691 Calculate GDI dataframe: DONE Calculate `GDI`: START Calculating S: START Calculating S: DONE Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00434589385986328 Calculate `GDI`: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00418400764465332 Calculate `GDI`: DONE Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 0.917500019073486 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.15212082862854 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.02250409126282 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.34409594535828 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00907588005065918 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0482330322265625 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.944816112518311 Total calculations elapsed time: 4.34622097015381 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.3045117855072 Dataset analysis elapsed time: 9.24451589584351 COTAN dataset analysis: DONE Initializing `COTAN` meta-data Condition test n cells 1200 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 1.00743103027344 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.20955610275269 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.08289313316345 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.32970905303955 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00676608085632324 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0481369495391846 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.866848945617676 Total calculations elapsed time: 4.25146102905273 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.15105986595154 Dataset analysis elapsed time: 9.24138402938843 COTAN dataset analysis: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows Total calculations elapsed time: 0.0278429985046387 calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0312368869781494 Calculate `GDI`: DONE Total calculations elapsed time: 2.79174304008484 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1200 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 0.884498834609985 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 1.98972296714783 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 2.8681972026825 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.31195688247681 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00873899459838867 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0481009483337402 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.927136182785034 Total calculations elapsed time: 4.29593300819397 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.20506691932678 Dataset analysis elapsed time: 8.95776295661926 COTAN dataset analysis: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows Total calculations elapsed time: 0.0201339721679688 calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0351529121398926 Calculate `GDI`: DONE Total calculations elapsed time: 2.70516490936279 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1200 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 0.893884897232056 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.08053708076477 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.00015115737915 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.3022449016571 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00645208358764648 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0442779064178467 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.891094923019409 Total calculations elapsed time: 4.24406981468201 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.11793279647827 Dataset analysis elapsed time: 9.01196885108948 COTAN dataset analysis: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows Total calculations elapsed time: 0.00623798370361328 calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0304148197174072 Calculate `GDI`: DONE Total calculations elapsed time: 2.76476407051086 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Asked to drop 0 genes and 1160 cells COTAN dataset analysis: START 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 Dataset cleaning elapsed time: 0.911492109298706 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 6 iterations Total calculations elapsed time: 1.94783592224121 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.212044752677142 | max: 85.4528331044021 | % negative: 62.2144112478032 Model parameter estimation elapsed time: 2.84502100944519 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.882973909378052 Dataset analysis elapsed time: 4.63948702812195 COTAN dataset analysis: DONE Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.72869610786438 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0058140754699707 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00619387626647949 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.90217113494873 Total calculations elapsed time: 3.64287519454956 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.74840307235718 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00752091407775879 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00639104843139648 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.932278871536255 Total calculations elapsed time: 3.69459390640259 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.75028705596924 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00670289993286133 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00829005241394043 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.920686960220337 Total calculations elapsed time: 3.68596696853638 Calculate genes' COEX (legacy): DONE Hangling COTAN object with condition: test Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows Total calculations elapsed time: 0.00606107711791992 calculating PValues: DONE Handling genes type: G2 Handling genes type: G3 Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Clean plots: START PCA: START PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Total calculations elapsed time: 2.02332019805908 Clean plots: DONE Dataset cleaning elapsed time: 4.38584399223328 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.17927598953247 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.11314582824707 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.56222891807556 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00682616233825684 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0456538200378418 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.925005197525024 Total calculations elapsed time: 4.53971409797668 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.56548595428467 Dataset analysis elapsed time: 13.064475774765 COTAN dataset analysis: DONE Saving elaborated data locally at: /tmp/RtmpRajtBc/test.cotan.RDS Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 3.13058996200562 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: 41850 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5751 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: 41850 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.3786 Number of communities: 7 Elapsed time: 0 seconds 2 singletons identified. 5 final clusters. Used resolution for Seurat clusterization is: 1.3 Total calculations elapsed time: 4.48142004013062 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 Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 3.00635290145874 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: 29356 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5763 Number of communities: 2 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 Total calculations elapsed time: 5.44142985343933 Creating new clusterization: DONE Creating PDF UMAP in file: /tmp/RtmpRajtBc/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 20:46:13 UMAP embedding parameters a = 0.9922 b = 1.112 20:46:13 Read 1200 rows and found 65 numeric columns 20:46:13 Using Annoy for neighbor search, n_neighbors = 30 20:46:13 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:46:14 Writing NN index file to temp file /tmp/RtmpRajtBc/file98653a8ce17d 20:46:14 Searching Annoy index using 1 thread, search_k = 3000 20:46:14 Annoy recall = 100% 20:46:15 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 20:46:17 Initializing from normalized Laplacian + noise (using RSpectra) 20:46:17 Commencing optimization for 500 epochs, with 48472 positive edges 20:46:17 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:46:20 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 6.475998878479 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 20:46:20 UMAP embedding parameters a = 0.9922 b = 1.112 20:46:20 Read 1200 rows and found 65 numeric columns 20:46:20 Using Annoy for neighbor search, n_neighbors = 30 20:46:20 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:46:20 Writing NN index file to temp file /tmp/RtmpRajtBc/file98655fe8335b 20:46:20 Searching Annoy index using 1 thread, search_k = 3000 20:46:21 Annoy recall = 100% 20:46:22 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 20:46:24 Initializing from normalized Laplacian + noise (using RSpectra) 20:46:24 Commencing optimization for 500 epochs, with 48472 positive edges 20:46:24 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:46:27 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 6.49862599372864 UMAP plot: DONE * checking uniformity of cluster '0' of 2 clusters Asked to drop 0 genes and 587 cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [613] cells Dataset cleaning elapsed time: 0.986097097396851 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.07796096801758 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0334270578203965 | max: 8.68674670630126 | % negative: 4.16666666666667 Model parameter estimation elapsed time: 3.09293985366821 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.22306203842163 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00737881660461426 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0398139953613281 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.985465049743652 Total calculations elapsed time: 4.25571990013123 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.18451809883118 Dataset analysis elapsed time: 9.26355504989624 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0000' with 613 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0311160087585449 Calculate `GDI`: DONE Total calculations elapsed time: 2.88352012634277 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0411360263824463 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0000, with size 613, is uniform Cluster 01_0000's shift to uniformity: -0.0159698218976119 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0333333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38103017810239, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0233333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42514299918547, 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 = 1.4503882472624, 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 = 1.5015551958585, isUniform = TRUE, clusterSize = 613 cluster 01_0000 is uniform * checking uniformity of cluster '1' of 2 clusters Asked to drop 0 genes and 613 cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [587] cells Dataset cleaning elapsed time: 0.999906778335571 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.03594899177551 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7 Model parameter estimation elapsed time: 3.03239512443542 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.29651999473572 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0075840950012207 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0348038673400879 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.04616594314575 Total calculations elapsed time: 4.38507390022278 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.34867787361145 Dataset analysis elapsed time: 9.38097977638245 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0001' with 587 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0339500904083252 Calculate `GDI`: DONE Total calculations elapsed time: 3.06525087356567 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0437018871307373 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 587, is uniform Cluster 01_0001's shift to uniformity: -0.00930197949808731 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0433333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38769802050191, 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 = 1.42646635133469, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.46799318315158, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52850104542575, isUniform = TRUE, clusterSize = 587 cluster 01_0001 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_0000, 01_0001 Differential Expression Analysis - START * DEA on cluster '1' with 613 cells * DEA on cluster '2' with 587 cells Total calculations elapsed time: 0.0493111610412598 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 52.6833348274231 Creating cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Asked to drop 0 genes and 613 cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [587] cells Dataset cleaning elapsed time: 0.998950958251953 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.13732695579529 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7 Model parameter estimation elapsed time: 3.11957406997681 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.1848611831665 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0072939395904541 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0358610153198242 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.996855974197388 Total calculations elapsed time: 4.22487211227417 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.21084594726562 Dataset analysis elapsed time: 9.32937097549438 COTAN dataset analysis: DONE Checking uniformity for the cluster 'Cluster_2' with 587 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0368101596832275 Calculate `GDI`: DONE Total calculations elapsed time: 3.05970001220703 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0476429462432861 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster Cluster_2, with size 587, is uniform Cluster Cluster_2's shift to uniformity: -0.00930197949808731 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0433333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38769802050191, 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 = 1.42646635133469, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.46799318315158, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52850104542575, isUniform = TRUE, clusterSize = 587 Differential Expression Analysis - START * DEA on cluster '-1' with 50 cells * DEA on cluster '1' with 611 cells * DEA on cluster '2' with 539 cells Total calculations elapsed time: 0.0535070896148682 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 2, 2 -> 1, -1 -> -1 Applied reordering to clusterization is: 1 -> 1, 2 -> 2, -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 Total calculations elapsed time: 0.0326879024505615 Calculate `GDI`: DONE Total calculations elapsed time: 3.05191493034363 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 Total calculations elapsed time: 6.02401399612427 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 Total calculations elapsed time: 7.14529609680176 Creating new clusterization: DONE Using passed in clusterization Creating PDF UMAP in file: /tmp/RtmpRajtBc/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 20:47:25 UMAP embedding parameters a = 0.9922 b = 1.112 20:47:25 Read 1200 rows and found 40 numeric columns 20:47:25 Using Annoy for neighbor search, n_neighbors = 30 20:47:25 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:47:25 Writing NN index file to temp file /tmp/RtmpRajtBc/file98656cb3b746 20:47:25 Searching Annoy index using 1 thread, search_k = 3000 20:47:25 Annoy recall = 100% 20:47:26 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 20:47:28 Initializing from normalized Laplacian + noise (using RSpectra) 20:47:28 Commencing optimization for 500 epochs, with 42644 positive edges 20:47:28 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:47:31 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 6.19120717048645 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 20:47:31 UMAP embedding parameters a = 0.9922 b = 1.112 20:47:31 Read 1200 rows and found 40 numeric columns 20:47:31 Using Annoy for neighbor search, n_neighbors = 30 20:47:31 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:47:31 Writing NN index file to temp file /tmp/RtmpRajtBc/file98652f85ca53 20:47:31 Searching Annoy index using 1 thread, search_k = 3000 20:47:31 Annoy recall = 100% 20:47:32 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 20:47:34 Initializing from normalized Laplacian + noise (using RSpectra) 20:47:34 Commencing optimization for 500 epochs, with 42644 positive edges 20:47:34 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:47:37 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 6.40902018547058 UMAP plot: DONE * checking uniformity of cluster '1' of 2 clusters Asked to drop 0 genes and 600 cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [600] cells Dataset cleaning elapsed time: 1.0042781829834 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.07725095748901 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0387079873074399 | max: 19.3963889884382 | % negative: 6.5 Model parameter estimation elapsed time: 3.02012801170349 COTAN genes' COEX estimation: START Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.16442799568176 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00902485847473145 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0311009883880615 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.960546016693115 Total calculations elapsed time: 4.16509985923767 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.16576790809631 Dataset analysis elapsed time: 9.1901741027832 COTAN dataset analysis: DONE 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 Total calculations elapsed time: 0.030109167098999 Calculate `GDI`: DONE Total calculations elapsed time: 3.04636096954346 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0458989143371582 Clean plots: 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: -0.0123041937718968 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 = 1.3846958062281, 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 = 1.42417208332107, 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 = 1.45335006989431, 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 = 1.51519118633036, 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 dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [600] cells Dataset cleaning elapsed time: 0.92455792427063 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.09534311294556 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0329292435898063 | max: 10.0824885336881 | % negative: 3.66666666666667 Model parameter estimation elapsed time: 3.04257106781006 COTAN genes' COEX estimation: START Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.27435398101807 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00847721099853516 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0394189357757568 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.968050003051758 Total calculations elapsed time: 4.29030013084412 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.23195886611938 Dataset analysis elapsed time: 9.19908785820007 COTAN dataset analysis: DONE 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 Total calculations elapsed time: 0.0292811393737793 Calculate `GDI`: DONE Total calculations elapsed time: 2.70460295677185 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0443210601806641 Clean plots: 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: -0.0203364702469133 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 = 1.37666352975309, 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 = 1.42307834225193, 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 = 1.43781655605474, 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 = 1.50180130506577, 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 Total calculations elapsed time: 0.0600621700286865 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 53.3228750228882 Creating cells' uniform clustering: DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 1.84418106079102 Log Fold Change Analysis - DONE Total calculations elapsed time: 1.85426592826843 findClustersMarkers - DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 2.022057056427 Log Fold Change Analysis - DONE Total calculations elapsed time: 2.03143501281738 findClustersMarkers - DONE findClustersMarkers - START Differential Expression Analysis - START * DEA on cluster '1' with 613 cells * DEA on cluster '2' with 587 cells Total calculations elapsed time: 0.090785026550293 Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 1.78315901756287 Log Fold Change Analysis - DONE Total calculations elapsed time: 1.87956190109253 findClustersMarkers - DONE [1] "Tested cluster: 1" Asked to drop 0 genes and 587 cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [613] cells Dataset cleaning elapsed time: 0.984498023986816 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.1325740814209 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0334270578203965 | max: 8.68674670630126 | % negative: 4.16666666666667 Model parameter estimation elapsed time: 3.09778714179993 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.25446701049805 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00848889350891113 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0657179355621338 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.02245807647705 Total calculations elapsed time: 4.35113191604614 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.36154198646545 Dataset analysis elapsed time: 9.4438271522522 COTAN dataset analysis: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0315768718719482 Calculate `GDI`: DONE Total calculations elapsed time: 3.0491931438446 Calculate GDI dataframe: DONE [1] "Tested cluster: 2" Asked to drop 0 genes and 613 cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [587] cells Dataset cleaning elapsed time: 1.03971695899963 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.02173495292664 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7 Model parameter estimation elapsed time: 3.00460386276245 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.33419895172119 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00925898551940918 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0366320610046387 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.00453901290894 Total calculations elapsed time: 4.38462901115417 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.36079120635986 Dataset analysis elapsed time: 9.40511202812195 COTAN dataset analysis: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0359840393066406 Calculate `GDI`: DONE Total calculations elapsed time: 2.95060801506042 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 Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.34090399742126 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 1.06554794311523 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.43792080879211 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.39797711372375 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.867626905441284 Dataset analysis elapsed time: 5.33115196228027 COTAN dataset analysis: DONE Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 PC_ 2 Positive: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 Negative: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 PC_ 5 Positive: g-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: 55940 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5920 Number of communities: 4 Elapsed time: 0 seconds Clusterizations found: RNA_snn_res.0.8, seurat_clusters Conditions found: orig.ident COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 0.949526071548462 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.20941114425659 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.18796586990356 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.980536222457886 Dataset analysis elapsed time: 5.11802816390991 COTAN dataset analysis: DONE COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 0.986557960510254 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.28862190246582 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.25973701477051 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.56803703308105 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00847387313842773 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0430171489715576 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.00269985198975 Total calculations elapsed time: 4.62222790718079 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.58534407615662 Dataset analysis elapsed time: 9.83163905143738 COTAN dataset analysis: DONE Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows Total calculations elapsed time: 0.00516009330749512 calculating PValues: DONE Number of selected secondary markers: 6 Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.010267972946167 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 6 Number of rows (U set): 60 Total calculations elapsed time: 1.04546999931335 Calculating gene co-expression space - DONE Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows Total calculations elapsed time: 0.0104808807373047 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 Total calculations elapsed time: 0.00905704498291016 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 109 Number of rows (U set): 60 Total calculations elapsed time: 1.06538391113281 Calculating gene co-expression space - DONE Establishing gene clusters - START Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows Total calculations elapsed time: 0.0108349323272705 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 Total calculations elapsed time: 0.0123071670532227 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 109 Number of rows (U set): 60 Total calculations elapsed time: 1.12054491043091 Calculating gene co-expression space - DONE Total calculations elapsed time: 1.20851898193359 Establishing gene clusters - DONE Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 1.00325202941895 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.20958113670349 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.14148902893066 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.939450979232788 Dataset analysis elapsed time: 5.0841920375824 COTAN dataset analysis: DONE Differential Expression Analysis - START * DEA on cluster '1' with 608 cells * DEA on cluster '2' with 592 cells Total calculations elapsed time: 0.0590789318084717 Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 1.8828239440918 Log Fold Change Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.09087489420394 Handling cluster '2' with mean UDE 0.906669027574328 clustersDeltaExpression - DONE In group G1 there are 3 detected over 3 genes In group G2 there are 2 detected over 3 genes In group G3 there are 5 detected over 5 genes Merging cells' uniform clustering: START The merge algorithm will use 2 passes Start merging nearest clusters - the main threshold is: 1.297 Start merging nearest clusters: iteration 1 Differential Expression Analysis - START * DEA on cluster '1' with 608 cells * DEA on cluster '2' with 592 cells Total calculations elapsed time: 0.0609550476074219 Differential Expression Analysis - DONE Updating check results for the 0 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("1", "2") *1_2-merge Asked to drop no genes or cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Dataset cleaning elapsed time: 0.925225973129272 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.19388794898987 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 3.05944800376892 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.44768190383911 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00721192359924316 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0437109470367432 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.96655011177063 Total calculations elapsed time: 4.46515488624573 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.44110298156738 Dataset analysis elapsed time: 9.42577695846558 COTAN dataset analysis: DONE Checking uniformity for the cluster '1_2-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 Total calculations elapsed time: 0.0323030948638916 Calculate `GDI`: DONE Total calculations elapsed time: 2.97911715507507 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0476241111755371 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge, with size 1200, is not uniform Cluster 1_2-merge's shift to uniformity: 0.273171158219277 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.696666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017115821928, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.665, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61241976619328, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.411666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64049230721132, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 247, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66511539543561, isUniform = FALSE, clusterSize = 1200 Clusters 1 and 2 cannot be merged Finished the first batch - no merges were executed Loop calculations elapsed time: 17.4503741264343 Start merging nearest clusters: iteration 2 Differential Expression Analysis - START * DEA on cluster '1' with 608 cells * DEA on cluster '2' with 592 cells Total calculations elapsed time: 0.0491330623626709 Differential Expression Analysis - DONE Updating check results for the 1 already tested pairs to align to new checker 0 new clusters pairs to be tested for merging: No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.297 out of 1 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 608 cells * DEA on cluster '2' with 592 cells Total calculations elapsed time: 0.0519239902496338 Differential Expression Analysis - DONE Updating check results for the 1 already tested pairs to align to new checker 0 new clusters pairs to be tested for merging: No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.397 out of 1 checks The final merged clusterization contains [2] different clusters: 1, 2 Differential Expression Analysis - START * DEA on cluster '1' with 608 cells * DEA on cluster '2' with 592 cells Total calculations elapsed time: 0.0601770877838135 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 19.7404408454895 Merging cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 2.02263212203979 Log Fold Change Analysis - DONE [1] "Tested cluster: 1" Asked to drop 0 genes and 592 cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [608] cells Dataset cleaning elapsed time: 0.997963905334473 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 1.95865297317505 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0337582853418583 | max: 10.9273420652533 | % negative: 4.33333333333333 Model parameter estimation elapsed time: 2.90249991416931 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.29195094108582 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0081639289855957 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0374619960784912 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.953860998153687 Total calculations elapsed time: 4.29143786430359 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.25420308113098 Dataset analysis elapsed time: 9.15466690063477 COTAN dataset analysis: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0374319553375244 Calculate `GDI`: DONE Total calculations elapsed time: 3.03716993331909 Calculate GDI dataframe: DONE [1] "Tested cluster: 2" Asked to drop 0 genes and 608 cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [592] cells Dataset cleaning elapsed time: 0.968024015426636 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 4 iterations Total calculations elapsed time: 2.03452396392822 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0390500444479481 | max: 19.2061656068405 | % negative: 7.33333333333333 Model parameter estimation elapsed time: 3.00000905990601 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.2127959728241 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00844097137451172 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0361120700836182 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.73504090309143 Total calculations elapsed time: 4.99238991737366 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 7.06005907058716 Dataset analysis elapsed time: 11.0280921459198 COTAN dataset analysis: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.063291072845459 Calculate `GDI`: DONE Total calculations elapsed time: 3.70287489891052 Calculate GDI dataframe: DONE Dispersion bisection: straddling used 2 iterations Dispersion bisection: used 8 iterations Dispersion bisection: straddling used 1 iterations Dispersion bisection: used 9 iterations Dispersion Newton-Raphson: used up to 4 iterations Dispersion Newton-Raphson: used up to 4 iterations parallel dispersion bisection: straddling used up to 2 iterations Parallel dispersion bisection: used up to 9 iterations Parallel dispersion Newton-Raphson: used up to 4 iterations [ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ] > > proc.time() user system elapsed 648.147 10.010 665.322
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN_Legacy | 0.002 | 0.001 | 0.005 | |
COTAN_ObjectCreation | 10.531 | 0.282 | 10.874 | |
CalculatingCOEX | 54.586 | 1.050 | 55.897 | |
ClustersList | 0.010 | 0.003 | 0.013 | |
Conversions | 4.998 | 0.112 | 5.130 | |
GenesStatistics | 10.983 | 0.204 | 11.225 | |
HandleMetaData | 0.096 | 0.005 | 0.102 | |
HandlingClusterizations | 43.151 | 1.110 | 43.934 | |
HandlingConditions | 0.117 | 0.006 | 0.123 | |
HeatmapPlots | 34.147 | 0.824 | 35.160 | |
Installing_torch | 0.001 | 0.000 | 0.002 | |
LoggingFunctions | 0.003 | 0.001 | 0.004 | |
ParametersEstimations | 22.947 | 0.696 | 23.751 | |
RawDataCleaning | 5.043 | 0.278 | 5.175 | |
RawDataGetters | 0.102 | 0.006 | 0.108 | |
UniformClusters | 115.896 | 2.572 | 117.810 | |
getColorsVector | 0.001 | 0.014 | 0.001 | |