Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-09 12:06 -0400 (Thu, 09 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" | 4854 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4642 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4584 |
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 455/2341 | 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: 2025-10-08 19:00:21 -0400 (Wed, 08 Oct 2025) |
EndedAt: 2025-10-08 19:09:53 -0400 (Wed, 08 Oct 2025) |
EllapsedTime: 571.8 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: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * 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 55.047 0.478 56.655 CalculatingCOEX 25.974 0.337 26.911 HandlingClusterizations 19.245 0.190 19.861 HeatmapPlots 15.795 0.367 16.313 ParametersEstimations 10.346 0.298 10.769 COTAN_ObjectCreation 5.215 0.086 5.503 GenesStatistics 5.198 0.101 5.412 * 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-arm64/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: aarch64-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 0.086 0.024 0.105
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: aarch64-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 0.067 0.019 0.088
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: aarch64-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: 0.849795818328857 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: 1.18031096458435 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000216960906982422 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0023190975189209 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.420815944671631 Total calculations elapsed time: 1.60366296768188 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: 2.45314383506775 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: 0.381652116775513 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: 0.76979398727417 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: 0.395055055618286 Estimate `nu`: DONE `nu` change (abs) | max: 0.0295487661210321 | median: 0.016072261901129 | mean: 0.016072261901129 `nu` mean: 1.69786080481514 Marginal errors | max: 1.95799528048 | median 1.32268477389029 | mean: 1.33563364783916 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 0.77230715751648 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: 0.38205099105835 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: 0.787094831466675 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: 0.395535945892334 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: 0.814798831939697 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: 0.413403034210205 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: 0.770153999328613 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: 0.426481008529663 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: 0.0250296751521299 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: 0.804731130599976 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.251734659898779 | max: 3.9096133246649 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.405665159225464 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 0.00972280144874027 | mean: 0.00889105008777591 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: 0.778089046478271 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: 0.417917013168335 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: 0.00327684342603955 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: 0.797842025756836 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: 0.422631025314331 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: 0.849169969558716 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: 0.438127040863037 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: 21.7658801078796 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: 0.847720146179199 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: 1.25478005409241 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000256061553955078 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00120782852172852 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.436576128005981 Total calculations elapsed time: 1.69282007217407 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: 1.30168414115906 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000268936157226562 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.000792026519775391 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.436363935470581 Total calculations elapsed time: 1.73910903930664 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: 0.00394797325134277 Calculate `GDI`: DONE Total calculations elapsed time: 1.33929395675659 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: 0.000930070877075195 Calculate `GDI`: DONE Total calculations elapsed time: 1.21257305145264 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: 0.876356840133667 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: 0.994004011154175 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: 0.883319139480591 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: 1.38691091537476 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: 1.3099479675293 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: 1.3472900390625 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: 0.89923906326294 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: 0.470869064331055 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: 0.893054962158203 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: 0.417320013046265 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: 0.870805978775024 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: 0.421833038330078 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: 0.868150949478149 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: 0.469680070877075 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: 0.0697673030094073 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: 0.876754999160767 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: 0.454375982284546 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: 0.90743899345398 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.251890641847533 | max: 3.90987172241566 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.531492948532104 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: 0.00834350038184262 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: 0.835509061813354 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: 0.434266090393066 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: 0.00286709489297543 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: 0.823011159896851 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: 0.455037832260132 Estimate `nu`: DONE `nu` change (abs) | max: 0.000837013154366462 | median: 0.000488281250000028 | mean: 0.000488281250000028 `nu` mean: 0.999651268095634 Marginal errors | max: 0.00144055320514802 | median 0.00119489364392944 | mean: 0.00109355439757213 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 0.922506093978882 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.255046800817986 | max: 3.91508667609651 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 0.43019700050354 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: 0.000545899916524739 Total calculations elapsed time: 23.9357359409332 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: 1.29193902015686 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000220060348510742 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.000504016876220703 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.440884113311768 Total calculations elapsed time: 1.73354721069336 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: 1.23597979545593 Calculating cells' COEX normalization factor Calculate cells' normalization factor elapsed time: 0.000217199325561523 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.000478982925415039 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.425058841705322 Total calculations elapsed time: 1.66173481941223 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: 0.000986099243164062 Calculate `GDI`: DONE Total calculations elapsed time: 1.27873992919922 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: 3.4735848903656 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: 3.5273449420929 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: 1.7773871421814 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: 1.3519561290741 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000272989273071289 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.000467061996459961 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.423032999038696 Total calculations elapsed time: 1.77572917938232 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: 1.34784603118896 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000213861465454102 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.000477075576782227 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.49720287322998 Total calculations elapsed time: 1.84573984146118 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: 3.59130907058716 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: 3.51332807540894 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: 1.7140908241272 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: 0.478127956390381 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: 1.62908697128296 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: 0.426668167114258 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: 1.624342918396 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: 0.395917177200317 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: 9.94064998626709 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: 1.24694895744324 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000274896621704102 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.000488996505737305 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.386282205581665 Total calculations elapsed time: 1.63399505615234 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: 3.380863904953 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: 3.27653312683105 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: 1.70774793624878 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: 0.395391941070557 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: 1.58737993240356 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: 0.432102918624878 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: 1.75419783592224 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: 0.414260864257812 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: 10.0089828968048 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: 1.20591402053833 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000204086303710938 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00049281120300293 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.421379089355469 Total calculations elapsed time: 1.62799000740051 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: 2.7844660282135 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: 0.000633001327514648 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: 2.92250323295593 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: 2.92306518554688 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: 0.000910043716430664 Calculate `GDI`: DONE Total calculations elapsed time: 1.28139400482178 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: 2.98844194412231 Calculating G: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0010380744934082 Calculate `GDI`: DONE Total calculations elapsed time: 4.24337601661682 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: 0.00148892402648926 Calculate `GDI`: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.000938892364501953 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: 0.483853101730347 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: 1.0144259929657 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.48458290100098 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: 1.74463081359863 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00342512130737305 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0222289562225342 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.407156944274902 Total calculations elapsed time: 2.17744183540344 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.58578205108643 Dataset analysis elapsed time: 4.55421805381775 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: 0.417156934738159 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: 0.965468883514404 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.39788007736206 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: 1.82503604888916 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00349307060241699 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0301589965820312 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.474415063858032 Total calculations elapsed time: 2.33310317993164 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.82098603248596 Dataset analysis elapsed time: 4.63602304458618 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: 0.0112810134887695 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: 0.0188260078430176 Calculate `GDI`: DONE Total calculations elapsed time: 1.285236120224 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: 0.424095869064331 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: 0.936928033828735 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.34486198425293 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: 1.81372690200806 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00297212600708008 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0216670036315918 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.417701005935669 Total calculations elapsed time: 2.2560670375824 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.6892421245575 Dataset analysis elapsed time: 4.45819997787476 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: 0.00653505325317383 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: 0.0180139541625977 Calculate `GDI`: DONE Total calculations elapsed time: 1.34461188316345 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: 0.419832944869995 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: 0.932780981063843 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.32064294815063 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: 1.87408804893494 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00355982780456543 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0363090038299561 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.423489093780518 Total calculations elapsed time: 2.33744597434998 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.78579592704773 Dataset analysis elapsed time: 4.52627182006836 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: 0.00298619270324707 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: 0.0181930065155029 Calculate `GDI`: DONE Total calculations elapsed time: 1.2811291217804 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: 0.404173135757446 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: 0.860899925231934 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.212044752677142 | max: 85.4528331044018 | % negative: 62.2144112478032 Model parameter estimation elapsed time: 1.26631283760071 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.420136213302612 Dataset analysis elapsed time: 2.09062218666077 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: 1.22391486167908 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00301194190979004 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00281119346618652 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.415915966033936 Total calculations elapsed time: 1.64565396308899 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: 1.26622700691223 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00397896766662598 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00320315361022949 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.427574872970581 Total calculations elapsed time: 1.70098400115967 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: 1.29568195343018 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00304007530212402 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00277280807495117 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.403561115264893 Total calculations elapsed time: 1.70505595207214 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: 0.00224494934082031 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: 0.916481971740723 Clean plots: DONE Dataset cleaning elapsed time: 1.78069281578064 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: 0.96135401725769 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.37694311141968 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: 1.74177002906799 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00310492515563965 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.022104024887085 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.44476318359375 Total calculations elapsed time: 2.21174216270447 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.66302704811096 Dataset analysis elapsed time: 5.82066297531128 COTAN dataset analysis: DONE Saving elaborated data locally at: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpeB9w9D/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: 1.41084289550781 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: 1.9369261264801 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: 1.45585489273071 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: 1.8105309009552 Creating new clusterization: DONE Creating PDF UMAP in file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpeB9w9D/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 19:07:57 UMAP embedding parameters a = 0.9922 b = 1.112 19:07:57 Read 1200 rows and found 65 numeric columns 19:07:57 Using Annoy for neighbor search, n_neighbors = 30 19:07:57 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:07:58 Writing NN index file to temp file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpeB9w9D/file5c324d2c147a 19:07:58 Searching Annoy index using 1 thread, search_k = 3000 19:07:58 Annoy recall = 100% 19:07:58 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 19:07:59 Initializing from normalized Laplacian + noise (using RSpectra) 19:07:59 Commencing optimization for 500 epochs, with 48472 positive edges 19:07:59 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:08:00 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 2.9428768157959 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 19:08:00 UMAP embedding parameters a = 0.9922 b = 1.112 19:08:00 Read 1200 rows and found 65 numeric columns 19:08:00 Using Annoy for neighbor search, n_neighbors = 30 19:08:00 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:08:01 Writing NN index file to temp file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpeB9w9D/file5c326b4596a4 19:08:01 Searching Annoy index using 1 thread, search_k = 3000 19:08:01 Annoy recall = 100% 19:08:01 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 19:08:02 Initializing from normalized Laplacian + noise (using RSpectra) 19:08:02 Commencing optimization for 500 epochs, with 48472 positive edges 19:08:02 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:08:04 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 3.04298210144043 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: 0.447281122207642 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: 0.916957139968872 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0334270578204022 | max: 8.68674670630065 | % negative: 4.16666666666667 Model parameter estimation elapsed time: 1.34806299209595 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: 1.54732489585876 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00360608100891113 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0189769268035889 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.441660165786743 Total calculations elapsed time: 2.01156806945801 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.47385096549988 Dataset analysis elapsed time: 4.26919507980347 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: 0.0186989307403564 Calculate `GDI`: DONE Total calculations elapsed time: 1.34261417388916 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0118880271911621 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: -0.0159698218976567 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 = 1.38103017810234, 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 = 1.4251429991854, 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 = 1.50155519585851, 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: 0.459871053695679 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: 0.95881986618042 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.03833779917087 | max: 19.013469852534 | % negative: 7 Model parameter estimation elapsed time: 1.43835496902466 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: 1.61569404602051 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00295400619506836 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0170388221740723 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.45605206489563 Total calculations elapsed time: 2.09173893928528 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.5738410949707 Dataset analysis elapsed time: 4.47206711769104 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: 0.0183460712432861 Calculate `GDI`: DONE Total calculations elapsed time: 1.39433407783508 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0114660263061523 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: -0.00930197949813882 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 = 1.38769802050186, 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 = 1.42646635133474, 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 = 1.46799318315139, 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 = 1.52850104542569, 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: 0.0214130878448486 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 23.2765429019928 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: 0.426548957824707 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: 0.924036026000977 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.03833779917087 | max: 19.013469852534 | % negative: 7 Model parameter estimation elapsed time: 1.34065794944763 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: 1.50028777122498 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00418615341186523 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0183930397033691 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.450237035751343 Total calculations elapsed time: 1.97310400009155 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.4002480506897 Dataset analysis elapsed time: 4.16745495796204 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: 0.0192511081695557 Calculate `GDI`: DONE Total calculations elapsed time: 1.38682103157043 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0115840435028076 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: -0.00930197949813882 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 = 1.38769802050186, 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 = 1.42646635133474, 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 = 1.46799318315139, 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 = 1.52850104542569, 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: 0.0217330455780029 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: 0.0179710388183594 Calculate `GDI`: DONE Total calculations elapsed time: 1.42411613464355 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: 2.74190902709961 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: 3.0868649482727 Creating new clusterization: DONE Using passed in clusterization Creating PDF UMAP in file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpeB9w9D/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 19:08:29 UMAP embedding parameters a = 0.9922 b = 1.112 19:08:29 Read 1200 rows and found 40 numeric columns 19:08:29 Using Annoy for neighbor search, n_neighbors = 30 19:08:29 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:08:29 Writing NN index file to temp file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpeB9w9D/file5c32178bba1f 19:08:29 Searching Annoy index using 1 thread, search_k = 3000 19:08:30 Annoy recall = 100% 19:08:30 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 19:08:31 Initializing from normalized Laplacian + noise (using RSpectra) 19:08:31 Commencing optimization for 500 epochs, with 42644 positive edges 19:08:31 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:08:32 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 2.87700796127319 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 19:08:32 UMAP embedding parameters a = 0.9922 b = 1.112 19:08:32 Read 1200 rows and found 40 numeric columns 19:08:32 Using Annoy for neighbor search, n_neighbors = 30 19:08:32 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:08:32 Writing NN index file to temp file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpeB9w9D/file5c325bb81ce5 19:08:32 Searching Annoy index using 1 thread, search_k = 3000 19:08:32 Annoy recall = 100% 19:08:33 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 19:08:34 Initializing from normalized Laplacian + noise (using RSpectra) 19:08:34 Commencing optimization for 500 epochs, with 42644 positive edges 19:08:34 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:08:35 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 2.8944890499115 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: 0.461618900299072 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: 0.986337900161743 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0387079873074399 | max: 19.3963889884382 | % negative: 6.5 Model parameter estimation elapsed time: 1.45322895050049 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: 1.63560795783997 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00357389450073242 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0178220272064209 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.440759897232056 Total calculations elapsed time: 2.09776377677917 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.60925912857056 Dataset analysis elapsed time: 4.52410697937012 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: 0.0200650691986084 Calculate `GDI`: DONE Total calculations elapsed time: 1.46462297439575 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0129220485687256 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: -0.0123041937719663 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 = 1.38469580622803, 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 = 1.4241720833211, 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 = 1.45335006989435, 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 = 1.51519118633037, 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: 0.44196891784668 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: 0.981308937072754 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0329292435898051 | max: 10.082488533688 | % negative: 3.66666666666667 Model parameter estimation elapsed time: 1.4355161190033 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: 1.56110596656799 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00372505187988281 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0197010040283203 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.445883989334106 Total calculations elapsed time: 2.0304160118103 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.4764678478241 Dataset analysis elapsed time: 4.35395288467407 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: 0.0220839977264404 Calculate `GDI`: DONE Total calculations elapsed time: 1.47467517852783 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0119431018829346 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: -0.0203364702473958 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 = 1.3766635297526, 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 = 1.423078342252, 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 = 1.43781655605483, 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: 0.0220718383789062 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 24.7316489219666 Creating cells' uniform clustering: DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 0.862169981002808 Log Fold Change Analysis - DONE Total calculations elapsed time: 0.865005016326904 findClustersMarkers - DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 0.867439031600952 Log Fold Change Analysis - DONE Total calculations elapsed time: 0.870023965835571 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: 0.0201301574707031 Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 0.851282119750977 Log Fold Change Analysis - DONE Total calculations elapsed time: 0.87360692024231 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: 0.437280178070068 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: 0.933573961257935 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0334270578204022 | max: 8.68674670630065 | % negative: 4.16666666666667 Model parameter estimation elapsed time: 1.37015891075134 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: 1.52678990364075 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00435805320739746 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0204000473022461 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.472852945327759 Total calculations elapsed time: 2.02440094947815 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.47845196723938 Dataset analysis elapsed time: 4.28589105606079 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: 0.0201499462127686 Calculate `GDI`: DONE Total calculations elapsed time: 1.34847283363342 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: 0.470161914825439 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: 0.956756830215454 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.03833779917087 | max: 19.013469852534 | % negative: 7 Model parameter estimation elapsed time: 1.42717409133911 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: 1.6093590259552 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00316596031188965 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0172159671783447 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.46635103225708 Total calculations elapsed time: 2.09609198570251 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.56724095344543 Dataset analysis elapsed time: 4.46457695960999 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: 0.0227320194244385 Calculate `GDI`: DONE Total calculations elapsed time: 1.40939092636108 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: 1.04655981063843 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | 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: 0.482223033905029 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: 0.995114088058472 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.47473406791687 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.455167055130005 Dataset analysis elapsed time: 2.4121241569519 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-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 Negative: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 PC_ 4 Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 PC_ 5 Positive: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Negative: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55689 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5922 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: 0.468260049819946 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: 1.01961588859558 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.47033309936523 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.455164909362793 Dataset analysis elapsed time: 2.39375805854797 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: 0.473073959350586 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: 1.07943105697632 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.58763885498047 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.03381109237671 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00384688377380371 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0230541229248047 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.477778911590576 Total calculations elapsed time: 2.53849101066589 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 3.01033115386963 Dataset analysis elapsed time: 5.07104396820068 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: 0.00319480895996094 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: 0.00382518768310547 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 6 Number of rows (U set): 60 Total calculations elapsed time: 0.521878957748413 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: 0.00371909141540527 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: 0.00454092025756836 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 109 Number of rows (U set): 60 Total calculations elapsed time: 0.471267938613892 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: 0.00341916084289551 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: 0.00717902183532715 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 109 Number of rows (U set): 60 Total calculations elapsed time: 0.47657299041748 Calculating gene co-expression space - DONE Total calculations elapsed time: 0.500587940216064 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: 0.473855018615723 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: 1.10790491104126 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.57482481002808 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.47544002532959 Dataset analysis elapsed time: 2.52411985397339 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: 0.0201270580291748 Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 0.942054986953735 Log Fold Change Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.09087489420394 Handling cluster '2' with mean UDE 0.906669027574326 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: 0.0189669132232666 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: 0.479241847991943 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: 1.07568597793579 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.219880139527932 | max: 6.08024473714308 | % negative: 0 Model parameter estimation elapsed time: 1.5629391670227 COTAN genes' COEX estimation: START While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.03010106086731 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0033719539642334 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0229928493499756 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.471456050872803 Total calculations elapsed time: 2.52792191505432 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 3.01172995567322 Dataset analysis elapsed time: 5.05391097068787 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: 0.0217421054840088 Calculate `GDI`: DONE Total calculations elapsed time: 1.4038679599762 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0115201473236084 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: 0.273171158219312 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 = 1.57017115821931, 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 = 1.61241976619327, 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 = 1.64049230721139, 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 = 1.66511539543559, isUniform = FALSE, clusterSize = 1200 Clusters 1 and 2 cannot be merged Finished the first batch - no merges were executed Loop calculations elapsed time: 8.72030901908875 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: 0.0197668075561523 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: 0.02109694480896 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: 0.019866943359375 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 9.74070191383362 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: 0.9186110496521 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: 0.455328941345215 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: 0.962831020355225 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0337582853418571 | max: 10.9273420652531 | % negative: 4.33333333333333 Model parameter estimation elapsed time: 1.46214509010315 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: 1.66663408279419 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00399589538574219 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0194451808929443 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.465557813644409 Total calculations elapsed time: 2.15563297271729 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.59300708770752 Dataset analysis elapsed time: 4.51048111915588 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: 0.0182220935821533 Calculate `GDI`: DONE Total calculations elapsed time: 1.35537195205688 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: 0.475232124328613 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: 0.997606992721558 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0390500444479457 | max: 19.2061656068404 | % negative: 7.33333333333333 Model parameter estimation elapsed time: 1.41835904121399 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: 1.67499399185181 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00402593612670898 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0189950466156006 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.48528790473938 Total calculations elapsed time: 2.1833028793335 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.65537190437317 Dataset analysis elapsed time: 4.54896306991577 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: 0.0185778141021729 Calculate `GDI`: DONE Total calculations elapsed time: 1.44916391372681 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 298.711 1.901 307.149
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN_Legacy | 0.001 | 0.001 | 0.002 | |
COTAN_ObjectCreation | 5.215 | 0.086 | 5.503 | |
CalculatingCOEX | 25.974 | 0.337 | 26.911 | |
ClustersList | 0.002 | 0.001 | 0.003 | |
Conversions | 2.252 | 0.041 | 2.351 | |
GenesStatistics | 5.198 | 0.101 | 5.412 | |
HandleMetaData | 0.024 | 0.006 | 0.029 | |
HandlingClusterizations | 19.245 | 0.190 | 19.861 | |
HandlingConditions | 0.034 | 0.004 | 0.039 | |
HeatmapPlots | 15.795 | 0.367 | 16.313 | |
Installing_torch | 0 | 0 | 0 | |
LoggingFunctions | 0.001 | 0.000 | 0.001 | |
ParametersEstimations | 10.346 | 0.298 | 10.769 | |
RawDataCleaning | 1.808 | 0.051 | 1.869 | |
RawDataGetters | 0.023 | 0.006 | 0.029 | |
UniformClusters | 55.047 | 0.478 | 56.655 | |
getColorsVector | 0 | 0 | 0 | |