Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-13 12:03 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings COTAN_2.9.7.tar.gz |
StartedAt: 2025-10-12 22:32:57 -0400 (Sun, 12 Oct 2025) |
EndedAt: 2025-10-12 23:09:38 -0400 (Sun, 12 Oct 2025) |
EllapsedTime: 2200.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: COTAN.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings COTAN_2.9.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.9.7’ * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed UniformClusters 1360.980 2.523 122.217 CalculatingCOEX 1281.849 1.631 101.648 HeatmapPlots 927.956 0.857 65.934 HandlingClusterizations 404.291 2.090 61.124 COTAN_ObjectCreation 360.755 0.957 23.250 GenesStatistics 341.594 0.248 23.216 ParametersEstimations 28.883 0.712 28.435 RawDataCleaning 6.103 0.020 6.265 Conversions 4.953 0.128 5.200 * 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: [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 ... [ FAIL 1 | WARN 3 | SKIP 0 | PASS 572 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > > 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 0.200 0.035 0.259
COTAN.Rcheck/tests/spelling.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace("spelling", quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) All Done! > > proc.time() user system elapsed 0.221 0.038 0.287
COTAN.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > 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: 2.2037091255188 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: 3.23611164093018 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000825166702270508 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00924396514892578 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.850473165512085 Total calculations elapsed time: 4.09665393829346 Calculate genes' COEX (legacy): DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 5 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 4 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 5.41007828712463 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: 0.893769025802612 Estimate `nu`: DONE `nu` change (abs) | max: 1.75595238095238 | median: 1.07156808035714 | mean: 1.07156808035714 Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.83934903144836 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: 0.894364356994629 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: 1.91969156265259 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: 0.94269847869873 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: 1.86533737182617 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: 0.889820098876953 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: 1.87411499023438 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: 0.858798980712891 Estimate `nu`: DONE `nu` change (abs) | max: 0.05539667181205 | median: 0.0321044921874999 | mean: 0.0321044921874999 `nu` mean: 0.97670782037545 Marginal errors | max: 0.095347789718808 | median 0.0796003827042702 | mean: 0.0725509735761708 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.70631694793701 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: 0.867950916290283 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 0.0273479725376324 | mean: 0.025029675152131 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: 2.25298166275024 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: 0.977941274642944 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 0.00972280144873849 | mean: 0.00889105008777538 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: 2.2462739944458 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: 1.20480799674988 Estimate `nu`: DONE `nu` change (abs) | max: 0.00251004753849005 | median: 0.00146484374999994 | mean: 0.00146484374999994 `nu` mean: 1.00104520378849 Marginal errors | max: 0.00430755646112857 | median 0.00358203399504298 | mean: 0.00327684342604062 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 2.00635981559753 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: 0.953233957290649 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: 1.74563670158386 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: 0.933024883270264 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: 0.00054590699507937 Total calculations elapsed time: 51.5173087120056 Estimate `dispersion`/`nu`: DONE Estimate `dispersion`/`nu`: START Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.94984602928162 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: 3.15041542053223 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.00069880485534668 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00321483612060547 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.969901323318481 Total calculations elapsed time: 4.12423038482666 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: 3.19943141937256 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00065922737121582 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00214195251464844 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.953985452651978 Total calculations elapsed time: 4.1562180519104 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: 0.0106441974639893 Calculate `GDI`: DONE Total calculations elapsed time: 2.9124698638916 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: 0.00300240516662598 Calculate `GDI`: DONE Total calculations elapsed time: 2.91678142547607 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: 2.0185694694519 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Total calculations elapsed time: 1.95298957824707 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: 2.03118062019348 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: 3.07166147232056 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 2.83408236503601 Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Total calculations elapsed time: 2.68589353561401 Elaborating Reduced dimensionality Data Matrix - DONE Initializing `COTAN` meta-data Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.76117658615112 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: 0.923034191131592 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 1.37997441333659 | mean: 1.32181397451301 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.85040760040283 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: 0.939979553222656 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: 1.78166580200195 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: 1.00327277183533 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: 1.89571928977966 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: 0.95396089553833 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: 0.0697673030094085 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.92204809188843 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: 0.897531270980835 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: 1.82473945617676 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: 0.902328252792358 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 0.00912386940474796 | mean: 0.00834350038184244 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.92539811134338 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: 0.923991680145264 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: 0.00286709489297579 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 1.85765957832336 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: 0.997650384902954 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: 1.95670795440674 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: 0.255046800817986 | max: 3.9150866760965 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Total calculations elapsed time: 1.03524017333984 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: 0.00054589991652243 Total calculations elapsed time: 50.775918006897 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: 3.16791844367981 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00075840950012207 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00191617012023926 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.902483701705933 Total calculations elapsed time: 4.0730767250061 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: 3.16522455215454 Calculating cells' COEX normalization factor Calculate cells' normalization factor elapsed time: 0.000834941864013672 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00226163864135742 Estimating cells' COEX Calculate cells' COEX elapsed time: 1.04809880256653 Total calculations elapsed time: 4.21641993522644 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: 0.00458836555480957 Calculate `GDI`: DONE Total calculations elapsed time: 2.71519255638123 Calculate GDI dataframe: DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.325 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Total calculations elapsed time: 7.81483268737793 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: 8.12520790100098 Calculate cells' partial COEX: DONE Asked to drop 2 genes and 0 cells Asked to drop 0 genes and 4 cells Asked to drop 2 genes and 2 cells Attaching package: 'rlang' The following objects are masked from 'package:testthat': is_false, is_null, is_true Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating YN..NY..NN..t().. done Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.78948926925659 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: 3.21218967437744 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000797033309936523 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00161027908325195 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.35855793952942 Total calculations elapsed time: 4.57315492630005 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: 4.1967453956604 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000622034072875977 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00158190727233887 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.04423689842224 Total calculations elapsed time: 5.24318623542786 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: 8.2471342086792 Calculate genes' partial COEX: DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.4 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Total calculations elapsed time: 7.88297939300537 Calculate genes' partial COEX: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating NY..YN..NN..t().. done Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.95794367790222 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: 0.897523403167725 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 0.080731376500534 | mean: 0.101968565509112 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: 4.70951151847839 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: 0.861288547515869 Estimate `nu`: DONE `nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 `nu` mean: 1.69735147626627 Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964 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: 4.26385569572449 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: 1.22371435165405 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: 25.4940361976624 Estimate `dispersion`/`nu`: DONE calculating NN.. done calculating NN.. done calculating YN..NY..YY..t().. done Calculate cells' COEX (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 3.60204124450684 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00104236602783203 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00209307670593262 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.932638883590698 Total calculations elapsed time: 4.5378155708313 Calculate cells' COEX (legacy): DONE Calculate cells' partial COEX: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial COEX Total calculations elapsed time: 7.87535715103149 Calculate cells' partial COEX: DONE Calculate cells' partial COEX: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial COEX Total calculations elapsed time: 7.83412003517151 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: 4.83712959289551 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: 1.06386208534241 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 0.080731376500534 | mean: 0.101968565509112 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: 4.07145857810974 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: 0.898319244384766 Estimate `nu`: DONE `nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 `nu` mean: 1.69735147626627 Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Parallel dispersion Newton-Raphson: used up to 5 iterations Total calculations elapsed time: 3.7846040725708 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: 0.880115270614624 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: 24.336564540863 Estimate `dispersion`/`nu`: DONE Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.04963827133179 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00059819221496582 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00159168243408203 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.921944379806519 Total calculations elapsed time: 3.97377252578735 Calculate genes' COEX (legacy): DONE Calculating S: START Calculating S: DONE Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Total calculations elapsed time: 6.96775698661804 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: 0.00229144096374512 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: 7.64965295791626 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: 7.65130233764648 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: 0.00482773780822754 Calculate `GDI`: DONE Total calculations elapsed time: 2.98997688293457 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: 7.44213342666626 Calculating G: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00379610061645508 Calculate `GDI`: DONE Total calculations elapsed time: 10.2272243499756 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: 0.00709176063537598 Calculate `GDI`: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Total calculations elapsed time: 0.00559735298156738 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: 0.923923492431641 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: 2.02974820137024 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.96680164337158 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: 14.6460013389587 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0157861709594727 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.127403497695923 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.24430680274963 Total calculations elapsed time: 16.0334978103638 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 17.3203902244568 Dataset analysis elapsed time: 21.21111536026 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: 1.01398348808289 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: 2.54535865783691 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 3.64551162719727 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: 15.4929902553558 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00770998001098633 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0881106853485107 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.00815582275391 Total calculations elapsed time: 16.5969667434692 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 17.6542074680328 Dataset analysis elapsed time: 22.313702583313 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: 0.0407464504241943 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: 0.0375440120697021 Calculate `GDI`: DONE Total calculations elapsed time: 3.59775519371033 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: 1.08752512931824 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: 2.70849132537842 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 4.04062986373901 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: 16.0073022842407 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0121326446533203 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.095128059387207 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.15926289558411 Total calculations elapsed time: 17.2738258838654 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 18.2364716529846 Dataset analysis elapsed time: 23.3646266460419 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: 0.0224676132202148 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: 0.036968469619751 Calculate `GDI`: DONE Total calculations elapsed time: 3.19064211845398 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: 0.981706857681274 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: 2.28360319137573 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 3.15228152275085 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: 14.6836466789246 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00668048858642578 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0622737407684326 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.895078659057617 Total calculations elapsed time: 15.647679567337 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 16.5106816291809 Dataset analysis elapsed time: 20.644670009613 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: 0.00784635543823242 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: 0.0330061912536621 Calculate `GDI`: DONE Total calculations elapsed time: 3.01022791862488 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: 0.884346961975098 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: 1.74525117874146 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.267567793681876 | max: 101.923257389521 | % negative: 52.6112185686654 Model parameter estimation elapsed time: 2.71096801757812 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.907442808151245 Dataset analysis elapsed time: 4.50275778770447 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: 8.29061937332153 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00612473487854004 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0151197910308838 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.15616536140442 Total calculations elapsed time: 9.46802926063538 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: 7.92530179023743 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00546503067016602 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0141448974609375 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.918715238571167 Total calculations elapsed time: 8.8636269569397 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: 8.49558138847351 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00568079948425293 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0144259929656982 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.986333131790161 Total calculations elapsed time: 9.50202131271362 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: 0.00624990463256836 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: 2.40449810028076 Clean plots: DONE Dataset cleaning elapsed time: 4.9860565662384 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: 2.5080201625824 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 3.54841470718384 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: 9.36710214614868 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00828933715820312 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0696063041687012 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.37592577934265 Total calculations elapsed time: 10.8209235668182 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 12.0683445930481 Dataset analysis elapsed time: 20.6028158664703 COTAN dataset analysis: DONE Saving elaborated data locally at: /tmp/Rtmp7sbJbr/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: 4.02641201019287 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: 5.15100622177124 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: 3.65872883796692 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: 4.5330286026001 Creating new clusterization: DONE Creating PDF UMAP in file: /tmp/Rtmp7sbJbr/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 22:55:31 UMAP embedding parameters a = 0.9922 b = 1.112 22:55:31 Read 1000 rows and found 65 numeric columns 22:55:31 Using Annoy for neighbor search, n_neighbors = 30 22:55:31 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:55:32 Writing NN index file to temp file /tmp/Rtmp7sbJbr/file28d1001249b15c 22:55:32 Searching Annoy index using 1 thread, search_k = 3000 22:55:32 Annoy recall = 100% 22:55:33 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 22:55:36 Initializing from normalized Laplacian + noise (using RSpectra) 22:55:36 Commencing optimization for 500 epochs, with 39044 positive edges 22:55:36 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:55:38 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 6.79003667831421 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 22:55:38 UMAP embedding parameters a = 0.9922 b = 1.112 22:55:38 Read 1000 rows and found 65 numeric columns 22:55:38 Using Annoy for neighbor search, n_neighbors = 30 22:55:38 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:55:39 Writing NN index file to temp file /tmp/Rtmp7sbJbr/file28d10059e559d4 22:55:39 Searching Annoy index using 1 thread, search_k = 3000 22:55:39 Annoy recall = 100% 22:55:40 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 22:55:42 Initializing from normalized Laplacian + noise (using RSpectra) 22:55:42 Commencing optimization for 500 epochs, with 39044 positive edges 22:55:42 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:55:44 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 5.97390818595886 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: 0.975281238555908 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: 2.21292901039124 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.126565269702225 | max: 788.372048308528 | % negative: 38.5996409335727 Model parameter estimation elapsed time: 3.48701977729797 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: 8.53246712684631 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00703310966491699 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0318074226379395 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.89381742477417 Total calculations elapsed time: 9.46512508392334 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.356495141983 Dataset analysis elapsed time: 14.8187961578369 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: 0.0281846523284912 Calculate `GDI`: DONE Total calculations elapsed time: 2.7443630695343 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0363962650299072 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: -0.0175178017151365 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 = 1.37948219828486, 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 = 1.43089123341141, 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 = 1.44383613651627, 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: 1.06337881088257 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: 1.99988150596619 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998 Model parameter estimation elapsed time: 2.88017988204956 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: 8.12171244621277 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00506591796875 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0279693603515625 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.11664867401123 Total calculations elapsed time: 9.27139639854431 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.4078197479248 Dataset analysis elapsed time: 14.3513784408569 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: 0.0294859409332275 Calculate `GDI`: DONE Total calculations elapsed time: 3.3170166015625 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0377557277679443 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: -0.0466523594846431 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 = 1.35034764051536, 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 = 1.37278730407697, 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 = 1.38664163146849, 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: 1.04269218444824 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: 2.11789917945862 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.166254045792573 | max: 224.924342782861 | % negative: 42.6386233269598 Model parameter estimation elapsed time: 3.14894723892212 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: 8.09630703926086 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00540900230407715 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0271415710449219 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.885377883911133 Total calculations elapsed time: 9.014235496521 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 9.89264345169067 Dataset analysis elapsed time: 14.084282875061 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: 0.0268094539642334 Calculate `GDI`: DONE Total calculations elapsed time: 2.82739019393921 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0366919040679932 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: -0.0473527936300242 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 = 1.38771313919654, 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: 0.940701484680176 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: 2.04143095016479 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735 Model parameter estimation elapsed time: 3.00346112251282 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: 8.05945372581482 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00551319122314453 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0242774486541748 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.05713152885437 Total calculations elapsed time: 9.14637589454651 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.1055090427399 Dataset analysis elapsed time: 14.0496716499329 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: 0.0255618095397949 Calculate `GDI`: DONE Total calculations elapsed time: 3.15266466140747 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.037355899810791 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: -0.0672912272435866 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 = 1.32970877275641, 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 = 1.35752445041521, 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 = 1.37495297633956, 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 = 1.4014884302523, 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: 0.0774369239807129 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4 Total calculations elapsed time: 103.789066553116 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: 1.1142430305481 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: 2.15327763557434 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735 Model parameter estimation elapsed time: 3.28745269775391 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: 8.9639880657196 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00658178329467773 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0254812240600586 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.13281631469727 Total calculations elapsed time: 10.1288673877716 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 11.3947167396545 Dataset analysis elapsed time: 15.7964124679565 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: 0.0273392200469971 Calculate `GDI`: DONE Total calculations elapsed time: 3.23522806167603 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0412089824676514 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: -0.0672912272435866 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 = 1.32970877275641, 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 = 1.35752445041521, 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 = 1.37495297633956, 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 = 1.4014884302523, 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: 0.0962579250335693 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: 3.96342515945435 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: 4.87581753730774 Creating new clusterization: DONE Using passed in clusterization Creating PDF UMAP in file: /tmp/Rtmp7sbJbr/test/reclustering/pdf_umap_1.pdf UMAP plot: START Calculating UMAP: START 22:57:39 UMAP embedding parameters a = 0.9922 b = 1.112 22:57:39 Read 1000 rows and found 40 numeric columns 22:57:39 Using Annoy for neighbor search, n_neighbors = 30 22:57:39 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:57:39 Writing NN index file to temp file /tmp/Rtmp7sbJbr/file28d1007d27c64 22:57:39 Searching Annoy index using 1 thread, search_k = 3000 22:57:39 Annoy recall = 100% 22:57:40 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 22:57:42 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1 22:57:42 Using 'irlba' for PCA 22:57:42 PCA: 2 components explained 36.15% variance 22:57:42 Scaling init to sdev = 1 22:57:42 Commencing optimization for 500 epochs, with 41630 positive edges 22:57:42 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:57:45 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 5.95457410812378 UMAP plot: DONE UMAP plot: START Calculating UMAP: START 22:57:45 UMAP embedding parameters a = 0.9922 b = 1.112 22:57:45 Read 1000 rows and found 40 numeric columns 22:57:45 Using Annoy for neighbor search, n_neighbors = 30 22:57:45 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:57:45 Writing NN index file to temp file /tmp/Rtmp7sbJbr/file28d10054d734ea 22:57:45 Searching Annoy index using 1 thread, search_k = 3000 22:57:45 Annoy recall = 100% 22:57:47 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 22:57:49 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1 22:57:49 Using 'irlba' for PCA 22:57:49 PCA: 2 components explained 36.15% variance 22:57:49 Scaling init to sdev = 1 22:57:49 Commencing optimization for 500 epochs, with 41630 positive edges 22:57:49 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:57:51 Optimization finished Calculating UMAP: DONE Total calculations elapsed time: 6.03701877593994 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: 0.977043628692627 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: 2.18863487243652 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.108871643378045 | max: 295.971778839086 | % negative: 35.0533807829181 Model parameter estimation elapsed time: 3.17764544487 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: 8.59216833114624 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00585746765136719 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0392720699310303 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.951826333999634 Total calculations elapsed time: 9.58912420272827 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.5169365406036 Dataset analysis elapsed time: 14.6716256141663 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: 0.0310781002044678 Calculate `GDI`: DONE Total calculations elapsed time: 3.12781381607056 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0385050773620605 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: -0.041730199066494 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 = 1.35526980093351, 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 = 1.38536328181495, 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 = 1.40346106115492, 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 = 1.42565794715045, 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: 0.987294912338257 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: 1.92340350151062 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0636486786621688 | max: 141.389145035675 | % negative: 36.1510791366906 Model parameter estimation elapsed time: 2.95234060287476 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: 8.56003379821777 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00774073600769043 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0395095348358154 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.89194917678833 Total calculations elapsed time: 9.49923324584961 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.3520684242249 Dataset analysis elapsed time: 14.2917039394379 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: 0.0278844833374023 Calculate `GDI`: DONE Total calculations elapsed time: 2.8717668056488 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0357499122619629 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: -0.0413872276843505 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 = 1.38757136821537, 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 = 1.40876953414106, 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: 0.0577497482299805 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 61.2277677059174 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: 3.79420137405396 Log Fold Change Analysis - DONE Total calculations elapsed time: 3.80549836158752 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: 4.19127130508423 Log Fold Change Analysis - DONE Total calculations elapsed time: 4.20229959487915 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: 0.0662038326263428 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: 3.79517698287964 Log Fold Change Analysis - DONE Total calculations elapsed time: 3.87118911743164 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: 0.939069271087646 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: 1.90054130554199 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998 Model parameter estimation elapsed time: 2.9160521030426 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: 8.322918176651 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00609517097473145 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0296306610107422 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.926876068115234 Total calculations elapsed time: 9.28552007675171 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.2270793914795 Dataset analysis elapsed time: 14.0822007656097 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: 0.0272672176361084 Calculate `GDI`: DONE Total calculations elapsed time: 3.00236248970032 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: 2.20815539360046 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | 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: 0.95585560798645 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: 2.16018557548523 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 3.10450983047485 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 1.03368258476257 Dataset analysis elapsed time: 5.09404802322388 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-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 Negative: 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 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: 68107 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5999 Number of communities: 2 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: 0.949445724487305 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: 2.01011300086975 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.82681369781494 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.872999906539917 Dataset analysis elapsed time: 4.64925932884216 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: 0.881399631500244 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: 2.10804176330566 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 3.09709501266479 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: 8.72442102432251 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0059351921081543 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.064974308013916 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.965062141418457 Total calculations elapsed time: 9.76039266586304 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.7492446899414 Dataset analysis elapsed time: 14.7277393341064 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: 0.00452160835266113 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: 0.00797367095947266 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 6 Number of rows (U set): 60 Total calculations elapsed time: 0.988675832748413 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: 0.00633335113525391 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: 0.00775408744812012 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 98 Number of rows (U set): 60 Total calculations elapsed time: 1.00931572914124 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: 0.00645875930786133 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: 0.00783586502075195 Calculate `GDI`: DONE Number of columns (V set - secondary markers): 98 Number of rows (U set): 60 Total calculations elapsed time: 1.00176811218262 Calculating gene co-expression space - DONE Total calculations elapsed time: 1.06489777565002 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: 0.935380935668945 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: 2.03638243675232 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 2.97089695930481 COTAN genes' COEX estimation not requested Only genes' COEX elapsed time: 0.886125087738037 Dataset analysis elapsed time: 4.79240298271179 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: 0.0599377155303955 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: 3.51618719100952 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: 0.0829911231994629 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: 0.911775588989258 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: 1.92658996582031 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644 Model parameter estimation elapsed time: 2.94361519813538 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: 8.58580040931702 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00584840774536133 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0413327217102051 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.03966283798218 Total calculations elapsed time: 9.67264437675476 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.6132209300995 Dataset analysis elapsed time: 14.4686117172241 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: 0.0312340259552002 Calculate `GDI`: DONE Total calculations elapsed time: 3.14371919631958 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0393261909484863 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: 0.0566581136434114 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 = 1.35365811364341, 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 = 1.38256306292787, 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 = 1.42111642638124, isUniform = FALSE, clusterSize = 499 Clusters 1 and 2 cannot be merged Finished the first batch - no merges were executed Loop calculations elapsed time: 22.4481837749481 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: 0.0675849914550781 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: 0.936667203903198 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: 1.94659638404846 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.107568326617881 | max: 698.639334552754 | % negative: 32.1492007104796 Model parameter estimation elapsed time: 2.79134202003479 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: 8.43952679634094 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00671148300170898 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0400826930999756 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.962003707885742 Total calculations elapsed time: 9.44832468032837 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 10.350976228714 Dataset analysis elapsed time: 14.078985452652 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: 0.0305190086364746 Calculate `GDI`: DONE Total calculations elapsed time: 2.94098162651062 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0370807647705078 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: 0.0813107504723223 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 = 1.37831075047232, 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 = 1.41473792188166, 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 = 1.43341610223243, 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 = 1.46173948790285, 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: 0.073915958404541 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: 0.946242094039917 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: 2.13304471969604 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0739592351622374 | max: 400.051960722894 | % negative: 25.7191201353638 Model parameter estimation elapsed time: 3.24566292762756 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: 9.41685009002686 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00790286064147949 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0436205863952637 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.21886920928955 Total calculations elapsed time: 10.6872427463531 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 11.9821124076843 Dataset analysis elapsed time: 16.1740174293518 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: 0.0346100330352783 Calculate `GDI`: DONE Total calculations elapsed time: 3.5907735824585 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.038541316986084 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: 25.4732306003571 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: 0.0589611530303955 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: 1.26595616340637 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: 2.21069431304932 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333 Model parameter estimation elapsed time: 3.1465470790863 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: 9.5771005153656 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00901484489440918 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0656404495239258 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.16710019111633 Total calculations elapsed time: 10.8188560009003 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 12.042290687561 Dataset analysis elapsed time: 16.4547939300537 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: 0.0355396270751953 Calculate `GDI`: DONE Total calculations elapsed time: 3.72575402259827 Calculate GDI dataframe: DONE Clean plots: START Total calculations elapsed time: 0.0398149490356445 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: 0.0557014942169189 Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Total calculations elapsed time: 96.0053701400757 Merging cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Total calculations elapsed time: 2.14882135391235 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: 1.04288339614868 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: 2.05779957771301 Estimate `dispersion`: DONE Estimate `dispersion`: DONE `dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644 Model parameter estimation elapsed time: 3.00948309898376 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: 9.69299745559692 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0072333812713623 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0408699512481689 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.02052450180054 Total calculations elapsed time: 10.761625289917 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 12.2473754882812 Dataset analysis elapsed time: 16.2997419834137 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: 0.0374112129211426 Calculate `GDI`: DONE Total calculations elapsed time: 3.39733481407166 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 1 | WARN 3 | SKIP 0 | PASS 572 ] ══ 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 ... [ FAIL 1 | WARN 3 | SKIP 0 | PASS 572 ] Error: Test failures Execution halted
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN_Legacy | 0.003 | 0.000 | 0.002 | |
COTAN_ObjectCreation | 360.755 | 0.957 | 23.250 | |
CalculatingCOEX | 1281.849 | 1.631 | 101.648 | |
ClustersList | 0.009 | 0.000 | 0.010 | |
Conversions | 4.953 | 0.128 | 5.200 | |
GenesStatistics | 341.594 | 0.248 | 23.216 | |
HandleMetaData | 0.059 | 0.000 | 0.059 | |
HandlingClusterizations | 404.291 | 2.090 | 61.124 | |
HandlingConditions | 0.071 | 0.001 | 0.072 | |
HeatmapPlots | 927.956 | 0.857 | 65.934 | |
Installing_torch | 0.001 | 0.000 | 0.001 | |
LoggingFunctions | 0.002 | 0.000 | 0.003 | |
ParametersEstimations | 28.883 | 0.712 | 28.435 | |
RawDataCleaning | 6.103 | 0.020 | 6.265 | |
RawDataGetters | 0.059 | 0.001 | 0.060 | |
UniformClusters | 1360.980 | 2.523 | 122.217 | |
getColorsVector | 0.001 | 0.000 | 0.001 | |