Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:05 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 455/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.9.7 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 2.9.7 |
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_2.9.7.tar.gz |
StartedAt: 2025-10-10 18:52:42 -0400 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 19:01:54 -0400 (Fri, 10 Oct 2025) |
EllapsedTime: 551.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: COTAN.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_2.9.7.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 ‘2.9.7’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 26 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 31.576 0.247 31.824 CalculatingCOEX 24.453 0.371 25.000 HandlingClusterizations 18.657 0.163 18.916 HeatmapPlots 14.200 0.406 14.618 ParametersEstimations 9.859 0.365 10.238 COTAN_ObjectCreation 5.070 0.079 5.265 GenesStatistics 4.962 0.062 5.019 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘outputTestDatasetCreation.R’ Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: actual$4 | expected$4 [1] 0.5371388180944 | 0.5371388180944 [1] [2] 0.2738893632548 - 0.2738893632547 [2] [3] 0.2583567237534 | 0.2583567237534 [3] [4] 0.4893139226499 | 0.4893139226499 [4] [5] 0.0323031738549 | 0.0323031738549 [5] [6] 0.3139658627130 | 0.3139658627130 [6] [7] 0.2214564371627 - 0.2214564371736 [7] [8] 0.0778174753379 | 0.0778174753379 [8] [9] 0.1495024524018 | 0.1495024524018 [9] [10] 0.9395496327399 | 0.9395496327399 [10] [ FAIL 2 | WARN 3 | SKIP 0 | PASS 571 ] Error: Test failures Execution halted * 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: 1 ERROR See ‘/Users/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck/00check.log’ for details.
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 ‘2.9.7’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
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(131L:140L, 291L:310L, 591L: 600L)] + saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS")) + saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS")) + + pcaRaw <- runPCA(x = getRawData(objCOTAN = obj), rank = 10L, + BSPARAM = IrlbaParam(), get.rotation = FALSE)[["x"]] + + pca.raw.test <- pcaRaw[genes.names.test, ] + saveRDS(pca.raw.test, file.path(testsDir, "pca.raw.test.RDS")) + + dispersion.test <- getDispersion(objCOTAN = obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- + getNuNormData(objCOTAN = obj)[genes.names.test, cells.names.test] + saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS")) + + coex.test <- + getGenesCoex(objCOTAN = obj, genes = genes.names.test, zeroDiagonal = FALSE) + saveRDS(coex.test, file.path(testsDir, "coex.test.RDS")) + + lambda.test <- getLambda(objCOTAN = obj)[genes.names.test] + saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS")) + + GDI.test <- calculateGDI(objCOTAN = obj) + GDI.test <- GDI.test[genes.names.test, ] + saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS")) + + nu.test <- getNu(objCOTAN = obj)[cells.names.test] + saveRDS(nu.test, file.path(testsDir, "nu.test.RDS")) + + pvalues.test <- calculatePValue(objCOTAN = obj, + geneSubsetCol = genes.names.test, + geneSubsetRow = genes.names.test) + saveRDS(pvalues.test, file.path(testsDir, "pvalues.test.RDS")) + + groupMarkers <- list(G1 = c("g-000010", "g-000020", "g-000138"), + G2 = c("g-000300", "g-000330", "g-000660"), + G3 = c("g-000510", "g-000530", "g-000550", + "g-000570", "g-000590")) + + gcsData <- genesCoexSpace(objCOTAN = obj, + primaryMarkers = unlist(groupMarkers), + numGenesPerMarker = 11L) + + genes.coex.space.test <- gcsData[["GCS"]] + saveRDS(genes.coex.space.test, + file.path(testsDir, "genes.coex.space.test.RDS")) + + genesClustersData <- + establishGenesClusters(objCOTAN = obj, + groupMarkers = groupMarkers, + numGenesPerMarker = 11L, + kCuts = 6L, distance = "cosine", + hclustMethod = "ward.D2") + + pca.genes.clusters.test <- genesClustersData[["pca_clusters"]] + saveRDS(pca.genes.clusters.test, + file.path(testsDir, "pca.genes.clusters.test.RDS")) + + # Make it a less strict check as it is only for testing + checker <- new("AdvancedGDIUniformityCheck") + checker <- shiftCheckerThresholds(checker, 0.1) + + initialResolution <- 1.3 + splitData <- cellsUniformClustering(objCOTAN = obj, + checker = checker, + initialResolution = initialResolution, + useCoexEigen = TRUE, + dataMethod = "LL", + numReducedComp = 50L, + cores = 6L, optimizeForSpeed = TRUE, + deviceStr = "cuda", saveObj = FALSE) + + split.clusters.test <- splitData[["clusters"]] + saveRDS(split.clusters.test, + file = file.path(testsDir, "split.clusters.test.RDS")) + + test.dataset.clusters1 <- split.clusters.test + save(test.dataset.clusters1, compress = TRUE, + file = file.path("data", "test.dataset.clusters1.rda")) + + obj <- addClusterization(objCOTAN = obj, + clName = "split", + clusters = splitData[["clusters"]], + coexDF = splitData[["coex"]]) + + coex.clusters.test <- splitData[["coex"]][genes.names.test, ] + saveRDS(coex.clusters.test, file.path(testsDir, "coex.clusters.test.RDS")) + + pvalDF <- pValueFromDEA(splitData[["coex"]], + getNumCells(objCOTAN = obj), + adjustmentMethod = "none") + + pvalues.clusters.test <- pvalDF[genes.names.test, ] + saveRDS(pvalues.clusters.test, + file.path(testsDir, "pvalues.clusters.test.RDS")) + + mergedData <- mergeUniformCellsClusters(objCOTAN = obj, + clusters = splitData[["clusters"]], + checkers = checker, + batchSize = 1L, + cores = 6L, + distance = "cosine", + hclustMethod = "ward.D2", + saveObj = FALSE) + + merge.clusters.test <- mergedData[["clusters"]] + saveRDS(merge.clusters.test, + file = file.path(testsDir, "merge.clusters.test.RDS")) + + test.dataset.clusters2 <- merge.clusters.test + save(test.dataset.clusters2, compress = TRUE, + file = file.path("data", "test.dataset.clusters2.rda")) + + obj <- addClusterization(objCOTAN = obj, + clName = "merge", + clusters = mergedData[["clusters"]], + coexDF = mergedData[["coex"]]) + } > > proc.time() user system elapsed 0.081 0.017 0.095
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 0.066 0.017 0.080
COTAN.Rcheck/tests/testthat.Rout.fail
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: 0.869282007217407 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: 1.21364808082581 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000223875045776367 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00233602523803711 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.458659172058105 Total calculations elapsed time: 1.67486715316772 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: 2.26352906227112 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: 0.385215997695923 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: 0.747208118438721 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: 0.382127046585083 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: 0.753267049789429 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: 0.409923076629639 Estimate `nu`: DONE `nu` change (abs) | max: 0.417150556912302 | median: 0.240156504520849 | mean: 0.240156504520849 `nu` mean: 0.823005947608547 Marginal errors | max: 0.837672524335755 | median 0.704691669139065 | mean: 0.646575831699997 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 0.764796018600464 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: 0.385053873062134 Estimate `nu`: DONE `nu` change (abs) | max: 0.164439840041 | median: 0.0957105992188852 | mean: 0.0957105992188852 `nu` mean: 1.06872924082212 Marginal errors | max: 0.260109847946692 | median 0.21392791155499 | mean: 0.197565106613054 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 0.742990016937256 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: 0.366491079330444 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: 0.768815040588379 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: 0.366949081420898 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: 0.0250296751521306 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: 0.835054159164429 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: 0.38844108581543 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 0.00972280144873938 | mean: 0.00889105008777555 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: 0.750542879104614 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: 0.389652967453003 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: 0.00327684342604027 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: 0.882574081420898 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: 0.400162935256958 Estimate `nu`: DONE `nu` change (abs) | max: 0.00104629156456748 | median: 0.000592910406456731 | mean: 0.000592910406456731 `nu` mean: 0.999546618841889 Marginal errors | max: 0.00162038706091039 | median 0.00134441676098973 | mean: 0.00123030512553282 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 0.806778907775879 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: 0.369158029556274 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: 0.000545906995079193 Total calculations elapsed time: 20.8368000984192 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: 0.728787899017334 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: 1.25743007659912 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000255107879638672 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00119400024414062 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.398653984069824 Total calculations elapsed time: 1.65753316879272 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: 1.30834412574768 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000292062759399414 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.000908851623535156 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.423156976699829 Total calculations elapsed time: 1.73270201683044 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: 0.00400495529174805 Calculate `GDI`: DONE Total calculations elapsed time: 1.22894883155823 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: 0.000929117202758789 Calculate `GDI`: DONE Total calculations elapsed time: 1.23034191131592 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: 0.883241891860962 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: 0.845267057418823 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: 0.876343965530396 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: 1.29598307609558 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: 1.21005892753601 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: 1.1858389377594 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: 0.776029109954834 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: 0.427112817764282 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: 0.798144817352295 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: 0.376596927642822 Estimate `nu`: DONE `nu` change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666 `nu` mean: 0.829218804209393 Marginal errors | max: 0.803248939260364 | median 0.677504196374571 | mean: 0.619386446933351 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 0.770423889160156 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: 0.383973836898804 Estimate `nu`: DONE `nu` change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312 `nu` mean: 1.0660356050592 Marginal errors | max: 0.25067700287536 | median 0.206241644985115 | mean: 0.190402167377958 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 0.80220103263855 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: 0.396673202514648 Estimate `nu`: DONE `nu` change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999 `nu` mean: 0.977606315852266 Marginal errors | max: 0.0916920322976189 | median 0.0765360853958175 | mean: 0.0697673030094082 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: 0.789767980575562 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: 0.422065019607544 Estimate `nu`: DONE `nu` change (abs) | max: 0.0187878665732679 | median: 0.0109155550210726 | mean: 0.0109155550210726 `nu` mean: 1.0078723115522 Marginal errors | max: 0.0315207323253404 | median 0.0261635598193228 | mean: 0.0239435763640456 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 0.774189949035645 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: 0.37465500831604 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: 0.794395923614502 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: 0.411868810653687 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: 0.00286709489297596 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: 0.819888114929199 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: 0.443314075469971 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: 0.831952810287476 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: 0.42816686630249 Estimate `nu`: DONE `nu` change (abs) | max: 0.000418448154490214 | median: 0.000244140624999917 | mean: 0.000244140624999917 `nu` mean: 1.00017430752949 Marginal errors | max: 0.000715683388516908 | median 0.0005972847342397 | mean: 0.00054589991652314 Total calculations elapsed time: 21.7687702178955 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: 1.27910208702087 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000224113464355469 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.000483989715576172 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.456573963165283 Total calculations elapsed time: 1.73638415336609 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: 1.28750085830688 Calculating cells' COEX normalization factor Calculate cells' normalization factor elapsed time: 0.000240087509155273 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00053095817565918 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.434400081634521 Total calculations elapsed time: 1.72267198562622 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: 0.000996112823486328 Calculate `GDI`: DONE Total calculations elapsed time: 1.28715395927429 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: 3.4350368976593 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: 3.42464804649353 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: 1.73374795913696 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: 1.27882695198059 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000262022018432617 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.000464916229248047 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.417066097259521 Total calculations elapsed time: 1.69661998748779 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: 1.19110107421875 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000199079513549805 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00046086311340332 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.410650014877319 Total calculations elapsed time: 1.60241103172302 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: 3.48752188682556 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: 3.38364601135254 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: 1.80769896507263 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: 0.453171968460083 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: 1.58285999298096 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: 0.44598913192749 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: 0.00132007186542999 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: 1.66815209388733 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: 0.435747861862183 Estimate `nu`: DONE `nu` change (abs) | max: 0 | median: 0 | mean: 0 `nu` mean: 1.69735147626627 Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06 Total calculations elapsed time: 10.3483271598816 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: 1.28975892066956 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000256061553955078 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.000467061996459961 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.401047945022583 Total calculations elapsed time: 1.69152998924255 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: 3.23520684242249 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: 3.37918400764465 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: 1.73124098777771 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: 0.433865070343018 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: 1.64760279655457 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: 0.401415109634399 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: 0.00132007186542999 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: 1.54831194877625 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: 0.383792161941528 Estimate `nu`: DONE `nu` change (abs) | max: 0 | median: 0 | mean: 0 `nu` mean: 1.69735147626627 Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06 Total calculations elapsed time: 9.94433999061584 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: 1.2368221282959 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000211954116821289 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.000488996505737305 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.427678108215332 Total calculations elapsed time: 1.66520118713379 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: 2.91587710380554 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: 0.000724077224731445 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: 2.94037318229675 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: 2.94095015525818 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: 0.000866174697875977 Calculate `GDI`: DONE Total calculations elapsed time: 1.23736691474915 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: 2.91590905189514 Calculating G: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00100302696228027 Calculate `GDI`: DONE Total calculations elapsed time: 4.16011810302734 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: 0.00146889686584473 Calculate `GDI`: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.000936031341552734 Calculate `GDI`: DONE Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.416938066482544 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.881882905960083 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.29581499099731 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: 1.68734312057495 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00351309776306152 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0270259380340576 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.436179876327515 Total calculations elapsed time: 2.15406203269958 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.56236815452576 Dataset analysis elapsed time: 4.27512121200562 COTAN dataset analysis: DONE Initializing `COTAN` meta-data Condition test n cells 1000 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.450500965118408 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.928156137466431 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.34557914733887 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: 1.65089893341064 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00331521034240723 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0282337665557861 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.390643119812012 Total calculations elapsed time: 2.07309103012085 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.47194790840149 Dataset analysis elapsed time: 4.26802802085876 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: 0.00985383987426758 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: 0.0166440010070801 Calculate `GDI`: DONE Total calculations elapsed time: 1.27777695655823 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1000 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.394449234008789 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.872885942459106 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.27390599250793 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: 1.64410901069641 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00337600708007812 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0284478664398193 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.413995027542114 Total calculations elapsed time: 2.08992791175842 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.50558686256409 Dataset analysis elapsed time: 4.17394208908081 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: 0.00682783126831055 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: 0.016855001449585 Calculate `GDI`: DONE Total calculations elapsed time: 1.26189184188843 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1000 COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.403275966644287 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.897428035736084 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.32003593444824 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: 1.68199586868286 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00336217880249023 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.031019926071167 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.415817975997925 Total calculations elapsed time: 2.13219594955444 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.53342199325562 Dataset analysis elapsed time: 4.25673389434814 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: 0.00283694267272949 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: 0.0169999599456787 Calculate `GDI`: DONE Total calculations elapsed time: 1.23940801620483 Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Asked to drop 0 genes and 960 cells COTAN dataset analysis: START Asked to drop 83 genes and 0 cells Genes/cells selection done: dropped [83] genes and [0] cells Working on [517] genes and [40] cells Dataset cleaning elapsed time: 0.379786968231201 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.818328857421875 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.267567793681876 | max: 101.923257389521 | % negative: 52.6112185686654 Model parameter estimation elapsed time: 1.22775602340698 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.432878017425537 Dataset analysis elapsed time: 2.04042100906372 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: 1.31310796737671 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00337386131286621 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00614619255065918 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.415776014328003 Total calculations elapsed time: 1.73840403556824 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: 1.25009202957153 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00292205810546875 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00549197196960449 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.448279857635498 Total calculations elapsed time: 1.7067859172821 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: 1.22091817855835 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00267291069030762 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00535202026367188 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.417687892913818 Total calculations elapsed time: 1.64663100242615 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: 0.00198197364807129 calculating PValues: DONE Handling genes type: G2 Handling genes type: G3 Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Clean plots: START PCA: START PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Total calculations elapsed time: 0.937512159347534 Clean plots: DONE Dataset cleaning elapsed time: 1.77266812324524 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.900707006454468 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.3924458026886 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: 1.68162202835083 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00427889823913574 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0273239612579346 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.42963695526123 Total calculations elapsed time: 2.14286184310913 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.59853720664978 Dataset analysis elapsed time: 5.76365113258362 COTAN dataset analysis: DONE Saving elaborated data locally at: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpr4G5Sx/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: 1.39918899536133 Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1000 Number of edges: 44886 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.4008 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 1.3 Total calculations elapsed time: 1.80676007270813 Creating new clusterization: DONE Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters Asked to drop no genes or cells Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 1.40056705474854 Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1000 Number of edges: 36652 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.3743 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 1.3 Total calculations elapsed time: 1.75981903076172 Creating new clusterization: DONE Creating PDF UMAP in file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpr4G5Sx/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 18:59:38 UMAP embedding parameters a = 0.9922 b = 1.112 18:59:38 Read 1000 rows and found 65 numeric columns 18:59:38 Using Annoy for neighbor search, n_neighbors = 30 18:59:38 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 18:59:38 Writing NN index file to temp file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpr4G5Sx/filea9b112d75cbe 18:59:38 Searching Annoy index using 1 thread, search_k = 3000 18:59:38 Annoy recall = 100% 18:59:38 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 18:59:39 Initializing from normalized Laplacian + noise (using RSpectra) 18:59:39 Commencing optimization for 500 epochs, with 39044 positive edges 18:59:39 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 18:59:41 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 2.9293520450592 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 18:59:41 UMAP embedding parameters a = 0.9922 b = 1.112 18:59:41 Read 1000 rows and found 65 numeric columns 18:59:41 Using Annoy for neighbor search, n_neighbors = 30 18:59:41 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 18:59:41 Writing NN index file to temp file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpr4G5Sx/filea9b1710fcf31 18:59:41 Searching Annoy index using 1 thread, search_k = 3000 18:59:41 Annoy recall = 100% 18:59:41 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 18:59:42 Initializing from normalized Laplacian + noise (using RSpectra) 18:59:42 Commencing optimization for 500 epochs, with 39044 positive edges 18:59:42 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 18:59:44 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 2.78282690048218 UMAP plot: DONE * checking uniformity of cluster '0' of 4 clusters Asked to drop 0 genes and 687 cells COTAN dataset analysis: START Asked to drop 43 genes and 0 cells Genes/cells selection done: dropped [43] genes and [0] cells Working on [557] genes and [313] cells Dataset cleaning elapsed time: 0.418062925338745 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 11 iterations Total calculations elapsed time: 0.857860803604126 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.126565269702225 | max: 788.372048308529 | % negative: 38.5996409335727 Model parameter estimation elapsed time: 1.30320715904236 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: 1.41490411758423 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0035099983215332 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0150129795074463 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.468940019607544 Total calculations elapsed time: 1.90236711502075 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.42517590522766 Dataset analysis elapsed time: 4.14644598960876 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0000' with 313 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0157849788665771 Calculate `GDI`: DONE Total calculations elapsed time: 1.28970694541931 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0111048221588135 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0000, with size 313, is uniform Cluster 01_0000's shift to uniformity: -0.0175178017152766 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0412926391382406, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37948219828472, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0323159784560144, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.43089123341067, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00179533213644524, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.4438361365159, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 1, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.47612588512221, isUniform = TRUE, clusterSize = 313 cluster 01_0000 is uniform * checking uniformity of cluster '1' of 4 clusters Asked to drop 0 genes and 743 cells COTAN dataset analysis: START Asked to drop 51 genes and 0 cells Genes/cells selection done: dropped [51] genes and [0] cells Working on [549] genes and [257] cells Dataset cleaning elapsed time: 0.419658899307251 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 10 iterations Total calculations elapsed time: 0.921510934829712 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998 Model parameter estimation elapsed time: 1.33673405647278 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: 1.45093011856079 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00283479690551758 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.012829065322876 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.442252159118652 Total calculations elapsed time: 1.90884613990784 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.33881688117981 Dataset analysis elapsed time: 4.09520983695984 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0001' with 257 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0158059597015381 Calculate `GDI`: DONE Total calculations elapsed time: 1.37055611610413 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0113370418548584 Clean plots: DONE GDI plot Removed 1 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 257, is uniform Cluster 01_0001's shift to uniformity: -0.0466523594845982 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00910746812386157, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3503476405154, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00728597449908925, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37278730407693, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.3866416314687, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.45240567481124, isUniform = TRUE, clusterSize = 257 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 4 clusters Asked to drop 0 genes and 758 cells COTAN dataset analysis: START Asked to drop 77 genes and 0 cells Genes/cells selection done: dropped [77] genes and [0] cells Working on [523] genes and [242] cells Dataset cleaning elapsed time: 0.476736783981323 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.849249124526978 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.166254045792573 | max: 224.924342782861 | % negative: 42.6386233269598 Model parameter estimation elapsed time: 1.29026007652283 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: 1.38076901435852 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00313997268676758 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0118570327758789 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.436384916305542 Total calculations elapsed time: 1.83215093612671 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.27225995063782 Dataset analysis elapsed time: 4.03925681114197 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0002' with 242 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0149619579315186 Calculate `GDI`: DONE Total calculations elapsed time: 1.35530495643616 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0116429328918457 Clean plots: DONE GDI plot Removed 2 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 242, is uniform Cluster 01_0002's shift to uniformity: -0.0473527936300249 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00764818355640535, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.34964720636998, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00764818355640535, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37472946305404, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38771313919655, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.43097703442027, isUniform = TRUE, clusterSize = 242 cluster 01_0002 is uniform * checking uniformity of cluster '3' of 4 clusters Asked to drop 0 genes and 812 cells COTAN dataset analysis: START Asked to drop 79 genes and 0 cells Genes/cells selection done: dropped [79] genes and [0] cells Working on [521] genes and [188] cells Dataset cleaning elapsed time: 0.4722740650177 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: 0.941170930862427 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735 Model parameter estimation elapsed time: 1.37332487106323 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: 1.38590407371521 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00318694114685059 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.010591983795166 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.421918153762817 Total calculations elapsed time: 1.82160115242004 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.23776912689209 Dataset analysis elapsed time: 4.08336806297302 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0003' with 188 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0139710903167725 Calculate `GDI`: DONE Total calculations elapsed time: 1.30137801170349 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0111510753631592 Clean plots: DONE GDI plot Removed 4 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0003, with size 188, is uniform Cluster 01_0003's shift to uniformity: -0.0672912272436468 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.32970877275635, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041519, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633951, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40148843025229, isUniform = TRUE, clusterSize = 188 cluster 01_0003 is uniform Found 4 uniform and 0 non-uniform clusters Stopping: too few cells left to cluster Unclustered cell left: 0 The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003 Differential Expression Analysis - START * DEA on cluster '1' with 313 cells * DEA on cluster '2' with 257 cells * DEA on cluster '3' with 242 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0164558887481689 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4 Total calculations elapsed time: 36.2901010513306 Creating cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4 Asked to drop 0 genes and 812 cells COTAN dataset analysis: START Asked to drop 79 genes and 0 cells Genes/cells selection done: dropped [79] genes and [0] cells Working on [521] genes and [188] cells Dataset cleaning elapsed time: 0.419148921966553 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: 0.865336894989014 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735 Model parameter estimation elapsed time: 1.29413104057312 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: 1.32063007354736 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00275707244873047 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0106639862060547 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.406401872634888 Total calculations elapsed time: 1.74045300483704 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.15477085113525 Dataset analysis elapsed time: 3.86805081367493 COTAN dataset analysis: DONE Checking uniformity for the cluster 'Cluster_4' with 188 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0133018493652344 Calculate `GDI`: DONE Total calculations elapsed time: 1.28817796707153 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0119888782501221 Clean plots: DONE GDI plot Removed 4 low GDI genes (such as the fully-expressed) in GDI plot Cluster Cluster_4, with size 188, is uniform Cluster Cluster_4's shift to uniformity: -0.0672912272436468 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.32970877275635, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041519, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633951, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40148843025229, isUniform = TRUE, clusterSize = 188 Differential Expression Analysis - START * DEA on cluster '-1' with 50 cells * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 280 cells * DEA on cluster '4' with 171 cells Total calculations elapsed time: 0.0131320953369141 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 4, 2 -> 3, 3 -> 2, 4 -> 1, -1 -> -1 Applied reordering to clusterization is: 1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4, -1 -> -1 Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters Asked to drop no genes or cells Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 600 genes using HVG_Seurat selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 1.69291591644287 Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1000 Number of edges: 67288 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.3650 Number of communities: 5 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 1.3 Total calculations elapsed time: 2.07701301574707 Creating new clusterization: DONE Using passed in clusterization Creating PDF UMAP in file: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpr4G5Sx/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 19:00:21 UMAP embedding parameters a = 0.9922 b = 1.112 19:00:21 Read 1000 rows and found 40 numeric columns 19:00:21 Using Annoy for neighbor search, n_neighbors = 30 19:00:21 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:00:21 Writing NN index file to temp file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpr4G5Sx/filea9b15b2fbafa 19:00:21 Searching Annoy index using 1 thread, search_k = 3000 19:00:21 Annoy recall = 100% 19:00:22 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 19:00:23 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1 19:00:23 Using 'irlba' for PCA 19:00:23 PCA: 2 components explained 36.15% variance 19:00:23 Scaling init to sdev = 1 19:00:23 Commencing optimization for 500 epochs, with 41630 positive edges 19:00:23 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:00:24 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 2.69286012649536 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 19:00:24 UMAP embedding parameters a = 0.9922 b = 1.112 19:00:24 Read 1000 rows and found 40 numeric columns 19:00:24 Using Annoy for neighbor search, n_neighbors = 30 19:00:24 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:00:24 Writing NN index file to temp file /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmpr4G5Sx/filea9b121463e83 19:00:24 Searching Annoy index using 1 thread, search_k = 3000 19:00:24 Annoy recall = 100% 19:00:25 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 19:00:26 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1 19:00:26 Using 'irlba' for PCA 19:00:26 PCA: 2 components explained 36.15% variance 19:00:26 Scaling init to sdev = 1 19:00:26 Commencing optimization for 500 epochs, with 41630 positive edges 19:00:26 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:00:27 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 2.85437393188477 UMAP plot: DONE * checking uniformity of cluster '1' of 2 clusters Asked to drop 0 genes and 500 cells COTAN dataset analysis: START Asked to drop 38 genes and 0 cells Genes/cells selection done: dropped [38] genes and [0] cells Working on [562] genes and [500] cells Dataset cleaning elapsed time: 0.446658849716187 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.912315845489502 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.108871643378045 | max: 295.971778839086 | % negative: 35.0533807829181 Model parameter estimation elapsed time: 1.33282899856567 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: 1.46181488037109 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00343608856201172 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0182619094848633 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.428941011428833 Total calculations elapsed time: 1.9124538898468 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.33749604225159 Dataset analysis elapsed time: 4.11698389053345 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0001' with 500 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0160529613494873 Calculate `GDI`: DONE Total calculations elapsed time: 1.26668810844421 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.011444091796875 Clean plots: DONE GDI plot Removed 2 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 500, is uniform Cluster 01_0001's shift to uniformity: -0.0417301990665557 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0124555160142349, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35526980093344, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00889679715302491, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.38536328181507, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.40346106115487, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42565794715046, isUniform = TRUE, clusterSize = 500 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 2 clusters Asked to drop 0 genes and 500 cells COTAN dataset analysis: START Asked to drop 44 genes and 0 cells Genes/cells selection done: dropped [44] genes and [0] cells Working on [556] genes and [500] cells Dataset cleaning elapsed time: 0.44337010383606 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.890130043029785 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0636486786621688 | max: 141.389145035675 | % negative: 36.1510791366906 Model parameter estimation elapsed time: 1.33678102493286 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: 1.49997305870056 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00305795669555664 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0174269676208496 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.438542127609253 Total calculations elapsed time: 1.95900011062622 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.41146087646484 Dataset analysis elapsed time: 4.19161200523376 COTAN dataset analysis: DONE Checking uniformity for the cluster '01_0002' with 500 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0162539482116699 Calculate `GDI`: DONE Total calculations elapsed time: 1.2981870174408 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0104539394378662 Clean plots: DONE GDI plot Removed 2 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 500, is uniform Cluster 01_0002's shift to uniformity: -0.0413872276843466 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00719424460431655, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35561277231565, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00359712230215827, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37204026755188, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38757136821582, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40876953414107, isUniform = TRUE, clusterSize = 500 cluster 01_0002 is uniform Found 2 uniform and 0 non-uniform clusters Stopping: too few cells left to cluster Unclustered cell left: 0 The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002 Differential Expression Analysis - START * DEA on cluster '1' with 500 cells * DEA on cluster '2' with 500 cells Total calculations elapsed time: 0.0120551586151123 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 22.1930470466614 Creating cells' uniform clustering: DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Total calculations elapsed time: 1.67400193214417 Log Fold Change Analysis - DONE Total calculations elapsed time: 1.67781710624695 findClustersMarkers - DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Total calculations elapsed time: 1.65104103088379 Log Fold Change Analysis - DONE Total calculations elapsed time: 1.6548011302948 findClustersMarkers - DONE findClustersMarkers - START Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0139839649200439 Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Total calculations elapsed time: 1.72500801086426 Log Fold Change Analysis - DONE Total calculations elapsed time: 1.74217200279236 findClustersMarkers - DONE [1] "Tested cluster: 1" Asked to drop 0 genes and 743 cells COTAN dataset analysis: START Asked to drop 51 genes and 0 cells Genes/cells selection done: dropped [51] genes and [0] cells Working on [549] genes and [257] cells Dataset cleaning elapsed time: 0.437412977218628 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 10 iterations Total calculations elapsed time: 0.887691020965576 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998 Model parameter estimation elapsed time: 1.3105149269104 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: 1.41103792190552 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0027461051940918 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0123579502105713 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.430463075637817 Total calculations elapsed time: 1.856605052948 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.3091151714325 Dataset analysis elapsed time: 4.05704307556152 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: 0.014970064163208 Calculate `GDI`: DONE Total calculations elapsed time: 1.2926070690155 Calculate GDI dataframe: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.898272037506104 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.440083980560303 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.908318996429443 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.31940293312073 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.440826177597046 Dataset analysis elapsed time: 2.20031309127808 COTAN dataset analysis: DONE Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000397, g-000525, g-000460, g-000458, g-000535, g-000217, g-000194, g-000497, g-000432, g-000383 g-000318, g-000486, g-000464, g-000588, g-000549, g-000368, g-000252, g-000151, g-000209, g-000538 g-000325, g-000514, g-000524, g-000244, g-000320, g-000201, g-000499, g-000309, g-000290, g-000483 Negative: g-000415, g-000506, g-000496, g-000579, g-000572, g-000421, g-000455, g-000328, g-000178, g-000567 g-000405, g-000296, g-000387, g-000501, g-000493, g-000481, g-000343, g-000528, g-000551, g-000414 g-000367, g-000594, g-000159, g-000517, g-000574, g-000229, g-000222, g-000533, g-000243, g-000306 PC_ 2 Positive: g-000141, g-000093, g-000089, g-000033, g-000123, g-000557, g-000330, g-000156, g-000142, g-000095 g-000061, g-000235, g-000032, g-000186, g-000056, g-000259, g-000027, g-000041, g-000333, g-000386 g-000009, g-000395, g-000048, g-000116, g-000340, g-000418, g-000035, g-000332, g-000086, g-000040 Negative: g-000088, g-000158, g-000255, g-000115, g-000054, g-000472, g-000554, g-000391, g-000253, g-000226 g-000051, g-000147, g-000541, g-000077, g-000224, g-000194, g-000290, g-000293, g-000313, g-000118 g-000121, g-000220, g-000467, g-000500, g-000341, g-000039, g-000091, g-000249, g-000426, g-000288 PC_ 3 Positive: g-000096, g-000575, g-000370, g-000337, g-000319, g-000364, g-000308, g-000293, g-000147, g-000307 g-000038, g-000492, g-000541, g-000185, g-000008, g-000482, g-000562, g-000097, g-000222, g-000084 g-000141, g-000377, g-000224, g-000223, g-000136, g-000434, g-000277, g-000426, g-000139, g-000093 Negative: g-000126, g-000083, g-000086, g-000117, g-000130, g-000010, g-000498, g-000333, g-000047, g-000179 g-000340, g-000035, g-000531, g-000140, g-000527, g-000049, g-000316, g-000031, g-000014, g-000073 g-000218, g-000445, g-000129, g-000175, g-000105, g-000581, g-000404, g-000025, g-000266, g-000354 PC_ 4 Positive: g-000006, g-000043, g-000462, g-000279, g-000180, g-000576, g-000087, g-000584, g-000498, g-000333 g-000189, g-000088, g-000451, g-000059, g-000135, g-000281, g-000106, g-000429, g-000316, g-000578 g-000303, g-000031, g-000581, g-000026, g-000122, g-000561, g-000546, g-000164, g-000353, g-000300 Negative: g-000072, g-000012, g-000129, g-000052, g-000097, g-000262, g-000080, g-000056, g-000025, g-000092 g-000354, g-000334, g-000423, g-000228, g-000002, g-000010, g-000086, g-000147, g-000185, g-000172 g-000124, g-000009, g-000077, g-000476, g-000126, g-000145, g-000065, g-000268, g-000152, g-000348 PC_ 5 Positive: g-000105, g-000037, g-000110, g-000054, g-000090, g-000389, g-000022, g-000578, g-000289, g-000147 g-000547, g-000011, g-000477, g-000433, g-000200, g-000348, g-000404, g-000003, g-000250, g-000109 g-000402, g-000241, g-000595, g-000341, g-000560, g-000385, g-000413, g-000352, g-000573, g-000265 Negative: g-000051, g-000150, g-000088, g-000476, g-000344, g-000116, g-000428, g-000012, g-000523, g-000394 g-000101, g-000127, g-000069, g-000214, g-000049, g-000357, g-000075, g-000081, g-000576, g-000342 g-000439, g-000018, g-000070, g-000079, g-000015, g-000550, g-000600, g-000247, g-000218, g-000331 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1000 Number of edges: 68208 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.6000 Number of communities: 3 Elapsed time: 0 seconds Clusterizations found: RNA_snn_res.0.8, seurat_clusters Conditions found: orig.ident COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.442989110946655 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.988198041915894 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.43917679786682 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.442566156387329 Dataset analysis elapsed time: 2.32473206520081 COTAN dataset analysis: DONE COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.421452045440674 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.967324018478394 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.45435190200806 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: 1.7710599899292 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00333309173583984 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0274720191955566 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.438317775726318 Total calculations elapsed time: 2.24018287658691 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.7227611541748 Dataset analysis elapsed time: 4.59856510162354 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: 0.00271701812744141 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: 0.00363588333129883 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 6 Number of rows (U set): 60 Total calculations elapsed time: 0.44904899597168 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: 0.00289392471313477 calculating PValues: DONE Number of selected secondary markers: 98 Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00347399711608887 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 98 Number of rows (U set): 60 Total calculations elapsed time: 0.452759981155396 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: 0.00400519371032715 calculating PValues: DONE Number of selected secondary markers: 98 Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0036768913269043 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 98 Number of rows (U set): 60 Total calculations elapsed time: 0.464877128601074 Calculating gene co-expression space - DONE Total calculations elapsed time: 0.489262819290161 Establishing gene clusters - DONE Initializing `COTAN` meta-data COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.461055040359497 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.00241899490356 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.46669578552246 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.469415187835693 Dataset analysis elapsed time: 2.39716601371765 COTAN dataset analysis: DONE Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0148589611053467 Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Total calculations elapsed time: 1.89932513237 Log Fold Change Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.10997640736885 Handling cluster '2' with mean UDE 1.00770245700749 Handling cluster '3' with mean UDE 0.95940682189354 Handling cluster '4' with mean UDE 0.907328369455933 clustersDeltaExpression - DONE In group G1 there are 3 detected over 3 genes In group G2 there are 2 detected over 3 genes In group G3 there are 5 detected over 5 genes Merging cells' uniform clustering: START The merge algorithm will use 2 passes Start merging nearest clusters - the main threshold is: 1.297 Start merging nearest clusters: iteration 1 Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0127639770507812 Differential Expression Analysis - DONE Updating check results for the 0 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("1", "2") *1_2-merge Asked to drop 0 genes and 501 cells COTAN dataset analysis: START Asked to drop 16 genes and 0 cells Genes/cells selection done: dropped [16] genes and [0] cells Working on [584] genes and [499] cells Dataset cleaning elapsed time: 0.451475858688354 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 10 iterations Total calculations elapsed time: 0.931008100509644 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644 Model parameter estimation elapsed time: 1.3804042339325 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: 1.53571391105652 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00299620628356934 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0171608924865723 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.471578121185303 Total calculations elapsed time: 2.02744913101196 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.51946592330933 Dataset analysis elapsed time: 4.35134601593018 COTAN dataset analysis: DONE Checking uniformity for the cluster '1_2-merge' with 499 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0220530033111572 Calculate `GDI`: DONE Total calculations elapsed time: 1.42868709564209 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0112118721008301 Clean plots: DONE GDI plot Removed 1 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge, with size 499, is not uniform Cluster 1_2-merge's shift to uniformity: 0.0566581136434186 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.178082191780822, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35365811364342, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.148972602739726, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37149326865972, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00513698630136986, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38256306292778, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 3, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42111642638126, isUniform = FALSE, clusterSize = 499 Clusters 1 and 2 cannot be merged Finished the first batch - no merges were executed Loop calculations elapsed time: 7.91440105438232 Start merging nearest clusters: iteration 2 Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.0122129917144775 Differential Expression Analysis - DONE Updating check results for the 1 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("3", "4") *3_4-merge Asked to drop 0 genes and 499 cells COTAN dataset analysis: START Asked to drop 37 genes and 0 cells Genes/cells selection done: dropped [37] genes and [0] cells Working on [563] genes and [501] cells Dataset cleaning elapsed time: 0.450811862945557 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 11 iterations Total calculations elapsed time: 0.939574003219604 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.107568326617881 | max: 698.639334552755 | % negative: 32.1492007104796 Model parameter estimation elapsed time: 1.36969304084778 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: 1.5427930355072 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00285100936889648 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0173358917236328 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.430116176605225 Total calculations elapsed time: 1.99309611320496 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.43426108360291 Dataset analysis elapsed time: 4.25476598739624 COTAN dataset analysis: DONE Checking uniformity for the cluster '3_4-merge' with 501 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0168838500976562 Calculate `GDI`: DONE Total calculations elapsed time: 1.38979387283325 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0115430355072021 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 3_4-merge, with size 501, is not uniform Cluster 3_4-merge's shift to uniformity: 0.0813107504724644 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.259325044404973, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37831075047246, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.216696269982238, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41473792188165, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0301953818827709, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43341610223173, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 17, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4617394878777, isUniform = FALSE, clusterSize = 501 Clusters 3 and 4 cannot be merged No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.297 out of 2 checks Start merging nearest clusters - the main threshold is: 1.397 Start merging nearest clusters: iteration 3 Differential Expression Analysis - START * DEA on cluster '1' with 257 cells * DEA on cluster '2' with 242 cells * DEA on cluster '3' with 313 cells * DEA on cluster '4' with 188 cells Total calculations elapsed time: 0.014441967010498 Differential Expression Analysis - DONE Updating check results for the 2 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("2", "4") *2_4-merge Asked to drop 0 genes and 570 cells COTAN dataset analysis: START Asked to drop 9 genes and 0 cells Genes/cells selection done: dropped [9] genes and [0] cells Working on [591] genes and [430] cells Dataset cleaning elapsed time: 0.426239013671875 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 0.941290855407715 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0739592351622374 | max: 400.051960722886 | % negative: 25.7191201353638 Model parameter estimation elapsed time: 1.44251203536987 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: 1.59552216529846 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0029609203338623 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0175449848175049 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.481971025466919 Total calculations elapsed time: 2.09799909591675 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.61511611938477 Dataset analysis elapsed time: 4.48386716842651 COTAN dataset analysis: DONE Checking uniformity for the cluster '2_4-merge' with 430 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0183930397033691 Calculate `GDI`: DONE Total calculations elapsed time: 1.38820719718933 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0116519927978516 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 2_4-merge, with size 430, is not uniform Cluster 2_4-merge's shift to uniformity: 3.07228472969514 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.583756345177665, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 3.7954982715656, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.576988155668359, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.08354952912925, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.524534686971235, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 4.42722016730736, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 310, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 4.57228472969514, isUniform = FALSE, clusterSize = 430 Clusters 2 and 4 cannot be merged Clusters 1 and 2 will be merged Clusters 4 and 3 will be merged Executed 2 merges Loop calculations elapsed time: 8.0389609336853 Start merging nearest clusters: iteration 4 Differential Expression Analysis - START * DEA on cluster '1_2-merge' with 499 cells * DEA on cluster '3_4-merge' with 501 cells Total calculations elapsed time: 0.0132617950439453 Differential Expression Analysis - DONE Updating check results for the 3 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("1_2-merge", "3_4-merge") *1_2-merge_3_4-merge-merge Asked to drop no genes or cells COTAN dataset analysis: START Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1000] cells Dataset cleaning elapsed time: 0.471195936203003 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 7 iterations Total calculations elapsed time: 1.02375602722168 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916524 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 1.52953910827637 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: 1.93629002571106 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00312685966491699 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0340061187744141 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.478273868560791 Total calculations elapsed time: 2.45169687271118 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.92330694198608 Dataset analysis elapsed time: 4.92404198646545 COTAN dataset analysis: DONE Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1000 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.0184361934661865 Calculate `GDI`: DONE Total calculations elapsed time: 1.48230600357056 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0121572017669678 Clean plots: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge_3_4-merge-merge, with size 1000, is not uniform Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 3.86988385120409 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.69, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 4.54596809454193, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.678333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.93144728766684, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.593333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 5.2532296852478, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 356, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 5.36988385120409, isUniform = FALSE, clusterSize = 1000 Clusters 1_2-merge and 3_4-merge cannot be merged No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.397 out of 4 checks The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge Differential Expression Analysis - START * DEA on cluster '1' with 499 cells * DEA on cluster '2' with 501 cells Total calculations elapsed time: 0.013477087020874 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 32.3104948997498 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: 0.911237001419067 Log Fold Change Analysis - DONE [1] "Tested cluster: 1" Asked to drop 0 genes and 501 cells COTAN dataset analysis: START Asked to drop 16 genes and 0 cells Genes/cells selection done: dropped [16] genes and [0] cells Working on [584] genes and [499] cells Dataset cleaning elapsed time: 0.45337986946106 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 10 iterations Total calculations elapsed time: 0.945123910903931 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644 Model parameter estimation elapsed time: 1.37972211837769 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: 1.53341794013977 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0031590461730957 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0192201137542725 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.444710969924927 Total calculations elapsed time: 2.00050806999207 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 2.4792468547821 Dataset analysis elapsed time: 4.31234884262085 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: 0.0171759128570557 Calculate `GDI`: DONE Total calculations elapsed time: 1.41059398651123 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 2 | WARN 3 | SKIP 0 | PASS 571 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-establishGenesClusters.R:70:5'): Establish genes clusters ──── abs(pcaClusters[, 1L:4L]) (`actual`) not equal to abs(pcaClustersExp[, 1L:4L]) (`expected`). actual vs expected PC3 PC4 - actual[1, ] 0.658895212 0.15883750 + expected[1, ] 0.658892533 0.15883934 - actual[2, ] 0.079564425 0.59203995 + expected[2, ] 0.079567203 0.59203753 - actual[3, ] 0.918532721 0.56313722 + expected[3, ] 0.918529216 0.56314516 - actual[4, ] 0.702531238 1.34693455 + expected[4, ] 0.702534262 1.34693118 - actual[5, ] 1.794575928 0.16243050 + expected[5, ] 1.794578322 0.16244473 - actual[6, ] 1.945309666 0.09807515 + expected[6, ] 1.945313360 0.09806812 - actual[7, ] 0.928430613 2.09901814 + expected[7, ] 0.928419834 2.09901875 - actual[8, ] 1.245356622 0.32562932 + expected[8, ] 1.245358368 0.32563594 - actual[9, ] 0.101983190 0.75673576 + expected[9, ] 0.101974678 0.75673771 - actual[10, ] 0.068781346 1.20531303 + expected[10, ] 0.068787701 1.20530874 and 50 more ... actual$PC3 | expected$PC3 [1] 0.6588952 - 0.6588925 [1] [2] 0.0795644 - 0.0795672 [2] [3] 0.9185327 - 0.9185292 [3] [4] 0.7025312 - 0.7025343 [4] [5] 1.7945759 - 1.7945783 [5] [6] 1.9453097 - 1.9453134 [6] [7] 0.9284306 - 0.9284198 [7] [8] 1.2453566 - 1.2453584 [8] [9] 0.1019832 - 0.1019747 [9] [10] 0.0687813 - 0.0687877 [10] ... ... ... and 50 more ... actual$PC4 | expected$PC4 [1] 0.1588375 - 0.1588393 [1] [2] 0.5920400 - 0.5920375 [2] [3] 0.5631372 - 0.5631452 [3] [4] 1.3469346 - 1.3469312 [4] [5] 0.1624305 - 0.1624447 [5] [6] 0.0980751 - 0.0980681 [6] [7] 2.0990181 - 2.0990188 [7] [8] 0.3256293 - 0.3256359 [8] [9] 0.7567358 - 0.7567377 [9] [10] 1.2053130 - 1.2053087 [10] ... ... ... and 50 more ... ── Failure ('test-mergeUniformCellsClusters.R:61:3'): Merge Uniform Cells Clusters ── pValDF[genes.names.test, ] (`actual`) not equal to `pValDF_exp` (`expected`). actual$1 | expected$1 [4] 0.0498493201708 | 0.0498493201708 [4] [5] 0.0300993067276 | 0.0300993067276 [5] [6] 0.0955934918513 | 0.0955934918513 [6] [7] 0.6014918777939 - 0.6014918778305 [7] [8] 0.0281551653290 | 0.0281551653290 [8] [9] 0.4183608572341 | 0.4183608572341 [9] [10] 0.0120860546555 | 0.0120860546555 [10] actual$2 | expected$2 [4] 0.2437891890693 | 0.2437891890693 [4] [5] 0.0193943343424 | 0.0193943343424 [5] [6] 0.0418391113514 | 0.0418391113514 [6] [7] 0.8631759805384 - 0.8631759805037 [7] [8] 0.0154679345550 | 0.0154679345550 [8] [9] 0.2868943611183 | 0.2868943611183 [9] [10] 0.9985072137642 | 0.9985072137642 [10] actual$3 | expected$3 [4] 0.8044041606620 | 0.8044041606620 [4] [5] 0.0892560406341 | 0.0892560406341 [5] [6] 0.5811105087841 | 0.5811105087841 [6] [7] 0.1745737870660 - 0.1745737870492 [7] [8] 0.0273787783267 | 0.0273787783267 [8] [9] 0.1663387509433 | 0.1663387509433 [9] [10] 0.0196095432116 | 0.0196095432116 [10] actual$3 | expected$3 [19] 0.0000000000000 | 0.0000000000000 [19] [20] 0.0259864410316 | 0.0259864410316 [20] [21] 0.0000000001334 | 0.0000000001334 [21] [22] 0.4866563107616 - 0.4866563107615 [22] [23] 0.0000000000000 | 0.0000000000000 [23] [24] 0.0070331857618 | 0.0070331857618 [24] [25] 0.0027353715256 | 0.0027353715256 [25] actual$4 | expected$4 [1] 0.5371388180944 | 0.5371388180944 [1] [2] 0.2738893632548 - 0.2738893632547 [2] [3] 0.2583567237534 | 0.2583567237534 [3] [4] 0.4893139226499 | 0.4893139226499 [4] [5] 0.0323031738549 | 0.0323031738549 [5] [6] 0.3139658627130 | 0.3139658627130 [6] [7] 0.2214564371627 - 0.2214564371736 [7] [8] 0.0778174753379 | 0.0778174753379 [8] [9] 0.1495024524018 | 0.1495024524018 [9] [10] 0.9395496327399 | 0.9395496327399 [10] [ FAIL 2 | WARN 3 | SKIP 0 | PASS 571 ] Error: Test failures Execution halted
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN_Legacy | 0.001 | 0.001 | 0.001 | |
COTAN_ObjectCreation | 5.070 | 0.079 | 5.265 | |
CalculatingCOEX | 24.453 | 0.371 | 25.000 | |
ClustersList | 0.003 | 0.000 | 0.003 | |
Conversions | 2.090 | 0.041 | 2.130 | |
GenesStatistics | 4.962 | 0.062 | 5.019 | |
HandleMetaData | 0.015 | 0.002 | 0.016 | |
HandlingClusterizations | 18.657 | 0.163 | 18.916 | |
HandlingConditions | 0.028 | 0.005 | 0.033 | |
HeatmapPlots | 14.200 | 0.406 | 14.618 | |
Installing_torch | 0 | 0 | 0 | |
LoggingFunctions | 0.000 | 0.000 | 0.001 | |
ParametersEstimations | 9.859 | 0.365 | 10.238 | |
RawDataCleaning | 1.767 | 0.041 | 1.794 | |
RawDataGetters | 0.014 | 0.002 | 0.017 | |
UniformClusters | 31.576 | 0.247 | 31.824 | |
getColorsVector | 0 | 0 | 0 | |