Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:36:18 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.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: BERT |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz |
StartedAt: 2024-05-03 21:00:43 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 21:02:13 -0400 (Fri, 03 May 2024) |
EllapsedTime: 89.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BERT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘BERT/DESCRIPTION’ ... OK * this is package ‘BERT’ version ‘1.0.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘BERT’ 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BERT 24.675 1.169 17.739 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** 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 (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(BERT) > > test_check("BERT") 2024-05-03 21:01:36.51177 INFO::Formatting Data. 2024-05-03 21:01:36.51345 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:36.524218 INFO::Removing potential empty rows and columns 2024-05-03 21:01:36.774114 INFO::Found 0 missing values. 2024-05-03 21:01:36.777612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:36.778317 INFO::Done 2024-05-03 21:01:36.778893 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:36.791134 INFO::Starting hierarchical adjustment 2024-05-03 21:01:36.792047 INFO::Found 3 batches. 2024-05-03 21:01:36.792586 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:36.793711 INFO::Using default BPPARAM 2024-05-03 21:01:36.794281 INFO::Processing subtree level 1 2024-05-03 21:01:36.883623 INFO::Adjusting the last 1 batches sequentially 2024-05-03 21:01:36.885414 INFO::Done 2024-05-03 21:01:36.886075 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:36.888566 INFO::ASW Batch was 0.0416507221885453 prior to batch effect correction and is now 0.0416507221885453 . 2024-05-03 21:01:36.889635 INFO::Total function execution time is 0.37879467010498 s and adjustment time is 0.0935544967651367 s ( 24.7 ) 2024-05-03 21:01:36.903276 INFO::Formatting Data. 2024-05-03 21:01:36.904074 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:36.905051 INFO::Removing potential empty rows and columns 2024-05-03 21:01:36.90617 INFO::Found 0 missing values. 2024-05-03 21:01:36.907216 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique. 2024-05-03 21:01:36.918507 INFO::Formatting Data. 2024-05-03 21:01:36.919277 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:36.920195 INFO::Removing potential empty rows and columns 2024-05-03 21:01:36.921332 INFO::Found 0 missing values. 2024-05-03 21:01:36.922283 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique. 2024-05-03 21:01:36.938421 INFO::Formatting Data. 2024-05-03 21:01:36.939193 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:36.940074 INFO::Removing potential empty rows and columns 2024-05-03 21:01:36.941079 INFO::Found 0 missing values. 2024-05-03 21:01:36.941961 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique. 2024-05-03 21:01:36.946182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:36.946699 INFO::Done 2024-05-03 21:01:36.94719 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:36.949119 INFO::Starting hierarchical adjustment 2024-05-03 21:01:36.949791 INFO::Found 2 batches. 2024-05-03 21:01:36.950288 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:36.950896 INFO::Using default BPPARAM 2024-05-03 21:01:36.95139 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:36.952265 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:36.974039 INFO::Done 2024-05-03 21:01:36.974736 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:36.976762 INFO::ASW Batch was 0.0126994706326246 prior to batch effect correction and is now -0.102476377073645 . 2024-05-03 21:01:36.977576 INFO::Total function execution time is 0.0392165184020996 s and adjustment time is 0.0243501663208008 s ( 62.09 ) 2024-05-03 21:01:36.980292 INFO::Formatting Data. 2024-05-03 21:01:36.980927 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:36.989209 INFO::Formatting Data. 2024-05-03 21:01:36.989863 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:36.990694 INFO::Removing potential empty rows and columns 2024-05-03 21:01:36.991647 INFO::Found 0 missing values. 2024-05-03 21:01:36.994329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:36.994829 INFO::Done 2024-05-03 21:01:36.995307 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:36.997185 INFO::Starting hierarchical adjustment 2024-05-03 21:01:36.99784 INFO::Found 2 batches. 2024-05-03 21:01:36.998327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:36.998918 INFO::Using default BPPARAM 2024-05-03 21:01:36.99941 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:37.000253 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:37.014472 INFO::Done 2024-05-03 21:01:37.015116 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:37.017006 INFO::ASW Batch was -0.0152346396355173 prior to batch effect correction and is now -0.11699521440991 . 2024-05-03 21:01:37.017745 INFO::Total function execution time is 0.0285739898681641 s and adjustment time is 0.0167446136474609 s ( 58.6 ) 2024-05-03 21:01:37.0188 INFO::Formatting Data. 2024-05-03 21:01:37.019367 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:37.020182 INFO::Removing potential empty rows and columns 2024-05-03 21:01:37.021189 INFO::Found 0 missing values. 2024-05-03 21:01:37.023872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:37.024373 INFO::Done 2024-05-03 21:01:37.02487 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:37.026755 INFO::Starting hierarchical adjustment 2024-05-03 21:01:37.027408 INFO::Found 2 batches. 2024-05-03 21:01:37.02791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:37.028472 INFO::Using default BPPARAM 2024-05-03 21:01:37.028979 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:37.029833 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:37.044367 INFO::Done 2024-05-03 21:01:37.045069 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:37.047034 INFO::ASW Batch was -0.0152346396355173 prior to batch effect correction and is now -0.11699521440991 . 2024-05-03 21:01:37.047788 INFO::Total function execution time is 0.0289950370788574 s and adjustment time is 0.0170600414276123 s ( 58.84 ) 2024-05-03 21:01:39.242175 INFO::Formatting Data. 2024-05-03 21:01:39.243253 INFO::Recognized SummarizedExperiment 2024-05-03 21:01:39.243869 INFO::Typecasting input to dataframe. 2024-05-03 21:01:39.278306 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:39.279734 INFO::Removing potential empty rows and columns 2024-05-03 21:01:39.283863 INFO::Found 0 missing values. 2024-05-03 21:01:39.291424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:39.292042 INFO::Done 2024-05-03 21:01:39.292564 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:39.296309 INFO::Starting hierarchical adjustment 2024-05-03 21:01:39.297048 INFO::Found 2 batches. 2024-05-03 21:01:39.297553 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:39.298656 INFO::Using default BPPARAM 2024-05-03 21:01:39.299175 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:39.300191 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:39.395106 INFO::Done 2024-05-03 21:01:39.395924 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:39.399353 INFO::ASW Batch was -0.0236126661945875 prior to batch effect correction and is now -0.0894659594454457 . 2024-05-03 21:01:39.40016 INFO::Total function execution time is 0.158441781997681 s and adjustment time is 0.0981988906860352 s ( 61.98 ) 2024-05-03 21:01:39.422696 INFO::Formatting Data. 2024-05-03 21:01:39.423418 INFO::Recognized SummarizedExperiment 2024-05-03 21:01:39.423914 INFO::Typecasting input to dataframe. 2024-05-03 21:01:39.433831 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:39.435 INFO::Removing potential empty rows and columns 2024-05-03 21:01:39.438416 INFO::Found 0 missing values. 2024-05-03 21:01:39.444986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:39.445491 INFO::Done 2024-05-03 21:01:39.445951 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:39.449005 INFO::Starting hierarchical adjustment 2024-05-03 21:01:39.449681 INFO::Found 2 batches. 2024-05-03 21:01:39.450165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:39.450709 INFO::Using default BPPARAM 2024-05-03 21:01:39.451176 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:39.452113 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:39.474076 INFO::Done 2024-05-03 21:01:39.474716 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:39.478004 INFO::ASW Batch was -0.0100878085470991 prior to batch effect correction and is now -0.0100878085470991 . 2024-05-03 21:01:39.478781 INFO::Total function execution time is 0.0560698509216309 s and adjustment time is 0.0245182514190674 s ( 43.73 ) 2024-05-03 21:01:39.494973 INFO::Formatting Data. 2024-05-03 21:01:39.495665 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:39.496479 INFO::Removing potential empty rows and columns 2024-05-03 21:01:39.497411 INFO::Found 0 missing values. 2024-05-03 21:01:39.50006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:39.500549 INFO::Done 2024-05-03 21:01:39.501038 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:39.502848 INFO::Starting hierarchical adjustment 2024-05-03 21:01:39.503454 INFO::Found 3 batches. 2024-05-03 21:01:39.503919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:39.504451 INFO::Using default BPPARAM 2024-05-03 21:01:39.504963 INFO::Processing subtree level 1 2024-05-03 21:01:39.675635 INFO::Adjusting the last 1 batches sequentially 2024-05-03 21:01:39.67837 INFO::Done 2024-05-03 21:01:39.679372 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:39.682679 INFO::ASW Batch was -0.100858085789061 prior to batch effect correction and is now -0.152736693156514 . 2024-05-03 21:01:39.683901 INFO::Total function execution time is 0.188865661621094 s and adjustment time is 0.174886226654053 s ( 92.6 ) 2024-05-03 21:01:39.703156 INFO::Skipping initial DF formatting 2024-05-03 21:01:39.70407 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:39.709129 INFO::Starting hierarchical adjustment 2024-05-03 21:01:39.709965 INFO::Found 5 batches. 2024-05-03 21:01:39.710527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:39.711195 INFO::Using default BPPARAM 2024-05-03 21:01:39.711747 INFO::Processing subtree level 1 2024-05-03 21:01:39.880181 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:39.882939 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:39.921344 INFO::Done 2024-05-03 21:01:39.922718 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:39.927641 INFO::ASW Batch was 0.557136344295379 prior to batch effect correction and is now 0.557136344295379 . 2024-05-03 21:01:39.928406 INFO::ASW Label was 0.365340081783398 prior to batch effect correction and is now 0.365340081783398 . 2024-05-03 21:01:39.929447 INFO::Total function execution time is 0.226390600204468 s and adjustment time is 0.211401224136353 s ( 93.38 ) 2024-05-03 21:01:39.948698 INFO::Formatting Data. 2024-05-03 21:01:39.949606 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:39.950619 INFO::Removing potential empty rows and columns 2024-05-03 21:01:39.951745 INFO::Found 0 missing values. 2024-05-03 21:01:39.956006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:39.956566 INFO::Done 2024-05-03 21:01:39.957117 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:39.960212 INFO::Starting hierarchical adjustment 2024-05-03 21:01:39.96097 INFO::Found 5 batches. 2024-05-03 21:01:39.961539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:39.962185 INFO::Using default BPPARAM 2024-05-03 21:01:39.962753 INFO::Processing subtree level 1 2024-05-03 21:01:40.086984 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.088871 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.106656 INFO::Done 2024-05-03 21:01:40.107555 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.111756 INFO::ASW Batch was 0.188153524950227 prior to batch effect correction and is now -0.0302228903670908 . 2024-05-03 21:01:40.112679 INFO::ASW Label was 0.574517119884809 prior to batch effect correction and is now 0.829708010922304 . 2024-05-03 21:01:40.113698 INFO::Total function execution time is 0.165111303329468 s and adjustment time is 0.145810127258301 s ( 88.31 ) 2024-05-03 21:01:40.114653 INFO::Formatting Data. 2024-05-03 21:01:40.11533 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:40.116355 INFO::Removing potential empty rows and columns 2024-05-03 21:01:40.117523 INFO::Found 0 missing values. 2024-05-03 21:01:40.12186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:40.122478 INFO::Done 2024-05-03 21:01:40.123034 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:40.126115 INFO::Starting hierarchical adjustment 2024-05-03 21:01:40.126842 INFO::Found 5 batches. 2024-05-03 21:01:40.127392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:40.128079 INFO::Using default BPPARAM 2024-05-03 21:01:40.128645 INFO::Processing subtree level 1 2024-05-03 21:01:40.241558 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.24333 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.259803 INFO::Done 2024-05-03 21:01:40.260551 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.26398 INFO::ASW Batch was 0.188153524950227 prior to batch effect correction and is now -0.0302228903670908 . 2024-05-03 21:01:40.264623 INFO::ASW Label was 0.574517119884809 prior to batch effect correction and is now 0.829708010922304 . 2024-05-03 21:01:40.265472 INFO::Total function execution time is 0.150847434997559 s and adjustment time is 0.133078575134277 s ( 88.22 ) 2024-05-03 21:01:40.281847 INFO::Formatting Data. 2024-05-03 21:01:40.282862 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:40.283903 INFO::Removing potential empty rows and columns 2024-05-03 21:01:40.284983 INFO::Found 0 missing values. 2024-05-03 21:01:40.289286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:40.289845 INFO::Done 2024-05-03 21:01:40.290385 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:40.293858 INFO::Starting hierarchical adjustment 2024-05-03 21:01:40.294585 INFO::Found 5 batches. 2024-05-03 21:01:40.29511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:40.295797 INFO::Using default BPPARAM 2024-05-03 21:01:40.296337 INFO::Processing subtree level 1 2024-05-03 21:01:40.410139 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.411746 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.428697 INFO::Done 2024-05-03 21:01:40.429488 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.433058 INFO::ASW Batch was 0.409732203847541 prior to batch effect correction and is now -0.0905681208609874 . 2024-05-03 21:01:40.433758 INFO::ASW Label was 0.211514479372491 prior to batch effect correction and is now 0.877159952635034 . 2024-05-03 21:01:40.434653 INFO::Total function execution time is 0.153115510940552 s and adjustment time is 0.134225368499756 s ( 87.66 ) 2024-05-03 21:01:40.435534 INFO::Formatting Data. 2024-05-03 21:01:40.43619 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:40.437195 INFO::Removing potential empty rows and columns 2024-05-03 21:01:40.438181 INFO::Found 0 missing values. 2024-05-03 21:01:40.442198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:40.44275 INFO::Done 2024-05-03 21:01:40.443288 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:40.44629 INFO::Starting hierarchical adjustment 2024-05-03 21:01:40.447001 INFO::Found 5 batches. 2024-05-03 21:01:40.447515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:40.448123 INFO::Using default BPPARAM 2024-05-03 21:01:40.448661 INFO::Processing subtree level 1 2024-05-03 21:01:40.568606 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.570375 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.586914 INFO::Done 2024-05-03 21:01:40.587742 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.591025 INFO::ASW Batch was 0.409732203847541 prior to batch effect correction and is now -0.0905681208609874 . 2024-05-03 21:01:40.591732 INFO::ASW Label was 0.211514479372491 prior to batch effect correction and is now 0.877159952635034 . 2024-05-03 21:01:40.592648 INFO::Total function execution time is 0.157106161117554 s and adjustment time is 0.140029668807983 s ( 89.13 ) 2024-05-03 21:01:40.608149 INFO::Formatting Data. 2024-05-03 21:01:40.609036 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:40.610034 INFO::Removing potential empty rows and columns 2024-05-03 21:01:40.611128 INFO::Found 0 missing values. 2024-05-03 21:01:40.614111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:40.614667 INFO::Done 2024-05-03 21:01:40.6152 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:40.618437 INFO::Starting hierarchical adjustment 2024-05-03 21:01:40.619165 INFO::Found 2 batches. 2024-05-03 21:01:40.619731 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:40.620379 INFO::Using default BPPARAM 2024-05-03 21:01:40.620979 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.621949 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.636595 INFO::Done 2024-05-03 21:01:40.637255 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.640379 INFO::ASW Batch was 0.591465938343518 prior to batch effect correction and is now -0.0276049858063221 . 2024-05-03 21:01:40.641046 INFO::ASW Label was 0.437678817906159 prior to batch effect correction and is now 0.898871718956448 . 2024-05-03 21:01:40.641958 INFO::Total function execution time is 0.0339019298553467 s and adjustment time is 0.0175983905792236 s ( 51.91 ) 2024-05-03 21:01:40.642904 INFO::Formatting Data. 2024-05-03 21:01:40.643583 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:40.644488 INFO::Removing potential empty rows and columns 2024-05-03 21:01:40.645522 INFO::Found 0 missing values. 2024-05-03 21:01:40.648356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:40.648943 INFO::Done 2024-05-03 21:01:40.649486 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:40.652494 INFO::Starting hierarchical adjustment 2024-05-03 21:01:40.653374 INFO::Found 2 batches. 2024-05-03 21:01:40.653934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:40.654591 INFO::Using default BPPARAM 2024-05-03 21:01:40.655125 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.656107 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.672151 INFO::Done 2024-05-03 21:01:40.672836 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.675829 INFO::ASW Batch was 0.591465938343518 prior to batch effect correction and is now -0.0276049858063221 . 2024-05-03 21:01:40.676399 INFO::ASW Label was 0.437678817906159 prior to batch effect correction and is now 0.898871718956448 . 2024-05-03 21:01:40.677229 INFO::Total function execution time is 0.0343723297119141 s and adjustment time is 0.01896071434021 s ( 55.16 ) 2024-05-03 21:01:40.688688 INFO::Formatting Data. 2024-05-03 21:01:40.689418 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:40.690262 INFO::Removing potential empty rows and columns 2024-05-03 21:01:40.691155 INFO::Found 0 missing values. 2024-05-03 21:01:40.693222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:40.693785 INFO::Done 2024-05-03 21:01:40.694298 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:40.696243 INFO::Starting hierarchical adjustment 2024-05-03 21:01:40.696962 INFO::Found 2 batches. 2024-05-03 21:01:40.69749 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:40.698113 INFO::Using default BPPARAM 2024-05-03 21:01:40.698648 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.699556 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.730963 INFO::Done 2024-05-03 21:01:40.731667 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.733611 INFO::ASW Batch was 0.0515172193272295 prior to batch effect correction and is now -0.130863339301644 . 2024-05-03 21:01:40.734393 INFO::Total function execution time is 0.0457620620727539 s and adjustment time is 0.0341596603393555 s ( 74.65 ) 2024-05-03 21:01:40.745792 INFO::Formatting Data. 2024-05-03 21:01:40.746578 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:40.747444 INFO::Removing potential empty rows and columns 2024-05-03 21:01:40.748436 INFO::Found 0 missing values. 2024-05-03 21:01:40.74966 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique. 2024-05-03 21:01:40.754202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:40.754764 INFO::Done 2024-05-03 21:01:40.789719 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:40.793049 INFO::Starting hierarchical adjustment 2024-05-03 21:01:40.793801 INFO::Found 2 batches. 2024-05-03 21:01:40.794344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:40.794972 INFO::Using default BPPARAM 2024-05-03 21:01:40.795515 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.796532 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.815356 INFO::Done 2024-05-03 21:01:40.816093 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.819215 INFO::ASW Batch was 0.459377002937553 prior to batch effect correction and is now 0.080290987688744 . 2024-05-03 21:01:40.819807 INFO::ASW Label was 0.554945586692493 prior to batch effect correction and is now 0.869938268507952 . 2024-05-03 21:01:40.820648 INFO::Total function execution time is 0.074864387512207 s and adjustment time is 0.0217103958129883 s ( 29 ) 2024-05-03 21:01:40.821506 INFO::Formatting Data. 2024-05-03 21:01:40.822111 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:40.823049 INFO::Removing potential empty rows and columns 2024-05-03 21:01:40.824077 INFO::Found 0 missing values. 2024-05-03 21:01:40.825028 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique. 2024-05-03 21:01:40.829983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:40.830665 INFO::Done 2024-05-03 21:01:40.831182 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:40.834291 INFO::Starting hierarchical adjustment 2024-05-03 21:01:40.835031 INFO::Found 2 batches. 2024-05-03 21:01:40.835574 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:40.836211 INFO::Using default BPPARAM 2024-05-03 21:01:40.836762 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:40.837823 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:40.856668 INFO::Done 2024-05-03 21:01:40.85737 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:40.860418 INFO::ASW Batch was 0.459377002937553 prior to batch effect correction and is now 0.080290987688744 . 2024-05-03 21:01:40.861059 INFO::ASW Label was 0.554945586692493 prior to batch effect correction and is now 0.869938268507952 . 2024-05-03 21:01:40.861906 INFO::Total function execution time is 0.0404114723205566 s and adjustment time is 0.0217993259429932 s ( 53.94 ) 2024-05-03 21:01:41.073564 INFO::Formatting Data. 2024-05-03 21:01:41.074408 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:41.075328 INFO::Removing potential empty rows and columns 2024-05-03 21:01:41.076346 INFO::Found 0 missing values. 2024-05-03 21:01:41.079364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:41.079891 INFO::Done 2024-05-03 21:01:41.080396 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:41.082427 INFO::Starting hierarchical adjustment 2024-05-03 21:01:41.083107 INFO::Found 3 batches. 2024-05-03 21:01:41.083618 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:41.084194 INFO::Using default BPPARAM 2024-05-03 21:01:41.084726 INFO::Processing subtree level 1 2024-05-03 21:01:41.18254 INFO::Adjusting the last 1 batches sequentially 2024-05-03 21:01:41.184222 INFO::Done 2024-05-03 21:01:41.184832 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:41.187191 INFO::ASW Batch was -0.141783480813346 prior to batch effect correction and is now -0.141783480813346 . 2024-05-03 21:01:41.188114 INFO::Total function execution time is 0.114622116088867 s and adjustment time is 0.101240396499634 s ( 88.33 ) 2024-05-03 21:01:41.189232 INFO::Formatting Data. 2024-05-03 21:01:41.189878 INFO::Typecasting input to dataframe. 2024-05-03 21:01:41.190625 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:41.19151 INFO::Removing potential empty rows and columns 2024-05-03 21:01:41.192559 INFO::Found 0 missing values. 2024-05-03 21:01:41.195498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:41.196027 INFO::Done 2024-05-03 21:01:41.196581 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:41.198689 INFO::Starting hierarchical adjustment 2024-05-03 21:01:41.199407 INFO::Found 3 batches. 2024-05-03 21:01:41.199953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:41.200604 INFO::Using default BPPARAM 2024-05-03 21:01:41.201156 INFO::Processing subtree level 1 2024-05-03 21:01:41.292065 INFO::Adjusting the last 1 batches sequentially 2024-05-03 21:01:41.293777 INFO::Done 2024-05-03 21:01:41.294394 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:41.296671 INFO::ASW Batch was -0.141783480813346 prior to batch effect correction and is now -0.141783480813346 . 2024-05-03 21:01:41.297617 INFO::Total function execution time is 0.108356237411499 s and adjustment time is 0.094496488571167 s ( 87.21 ) 2024-05-03 21:01:41.310361 INFO::Formatting Data. 2024-05-03 21:01:41.311242 INFO::Typecasting input to dataframe. 2024-05-03 21:01:41.312121 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:41.313049 INFO::Removing potential empty rows and columns 2024-05-03 21:01:41.314081 INFO::Found 0 missing values. 2024-05-03 21:01:41.316915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:41.317426 INFO::Done 2024-05-03 21:01:41.317922 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:41.319845 INFO::Starting hierarchical adjustment 2024-05-03 21:01:41.320559 INFO::Found 3 batches. 2024-05-03 21:01:41.321093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:41.32169 INFO::Using default BPPARAM 2024-05-03 21:01:41.3222 INFO::Processing subtree level 1 2024-05-03 21:01:41.412299 INFO::Adjusting the last 1 batches sequentially 2024-05-03 21:01:41.414147 INFO::Done 2024-05-03 21:01:41.414807 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:41.417367 INFO::ASW Batch was -0.143055910296877 prior to batch effect correction and is now -0.143055910296877 . 2024-05-03 21:01:41.418312 INFO::Total function execution time is 0.108072519302368 s and adjustment time is 0.0936951637268066 s ( 86.7 ) 2024-05-03 21:01:41.563628 INFO::Formatting Data. 2024-05-03 21:01:41.564448 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:41.565506 INFO::Removing potential empty rows and columns 2024-05-03 21:01:41.568031 INFO::Found 1000 missing values. 2024-05-03 21:01:41.586338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:41.587069 INFO::Done 2024-05-03 21:01:41.587631 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:41.593255 INFO::Starting hierarchical adjustment 2024-05-03 21:01:41.594104 INFO::Found 10 batches. 2024-05-03 21:01:41.594696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:41.595355 INFO::Using default BPPARAM 2024-05-03 21:01:41.595881 INFO::Processing subtree level 1 2024-05-03 21:01:41.726197 INFO::Processing subtree level 2 2024-05-03 21:01:41.92109 INFO::Adjusting the last 1 batches sequentially 2024-05-03 21:01:41.923272 INFO::Done 2024-05-03 21:01:41.924047 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:41.930713 INFO::ASW Batch was 0.519440250726608 prior to batch effect correction and is now 0.519440250726608 . 2024-05-03 21:01:41.931462 INFO::ASW Label was 0.355118787529197 prior to batch effect correction and is now 0.355118787529197 . 2024-05-03 21:01:41.932544 INFO::Total function execution time is 0.368951082229614 s and adjustment time is 0.329316377639771 s ( 89.26 ) 2024-05-03 21:01:41.933555 INFO::Formatting Data. 2024-05-03 21:01:41.934341 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:41.935754 INFO::Removing potential empty rows and columns 2024-05-03 21:01:41.939189 INFO::Found 1000 missing values. 2024-05-03 21:01:41.961642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:41.962492 INFO::Done 2024-05-03 21:01:41.963153 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:41.969815 INFO::Starting hierarchical adjustment 2024-05-03 21:01:41.970651 INFO::Found 10 batches. 2024-05-03 21:01:43.060709 INFO::Set up parallel execution backend with 2 workers 2024-05-03 21:01:43.065778 INFO::Processing subtree level 1 with 10 batches using 2 cores. 2024-05-03 21:01:44.218302 INFO::Adjusting the last 2 batches sequentially 2024-05-03 21:01:44.219757 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 21:01:44.235395 INFO::Done 2024-05-03 21:01:44.236035 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:44.240664 INFO::ASW Batch was 0.519440250726608 prior to batch effect correction and is now 0.519440250726608 . 2024-05-03 21:01:44.24123 INFO::ASW Label was 0.355118787529197 prior to batch effect correction and is now 0.355118787529197 . 2024-05-03 21:01:44.241954 INFO::Total function execution time is 2.30846619606018 s and adjustment time is 2.26490163803101 s ( 98.11 ) 2024-05-03 21:01:44.382231 INFO::Formatting Data. 2024-05-03 21:01:44.38308 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.38405 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.385186 INFO::Found 0 missing values. 2024-05-03 21:01:44.388957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.389534 INFO::Done 2024-05-03 21:01:44.39007 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 21:01:44.392924 INFO::Starting hierarchical adjustment 2024-05-03 21:01:44.393644 INFO::Found 3 batches. 2024-05-03 21:01:44.394183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 21:01:44.394829 INFO::Using default BPPARAM 2024-05-03 21:01:44.395368 INFO::Processing subtree level 1 2024-05-03 21:01:44.495676 INFO::Adjusting the last 1 batches sequentially 2024-05-03 21:01:44.497362 INFO::Done 2024-05-03 21:01:44.497991 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 21:01:44.501004 INFO::ASW Batch was 0.192275704686832 prior to batch effect correction and is now -0.146735573231181 . 2024-05-03 21:01:44.501592 INFO::ASW Label was -0.175314653509889 prior to batch effect correction and is now -0.0110504755138043 . 2024-05-03 21:01:44.502458 INFO::Total function execution time is 0.120273590087891 s and adjustment time is 0.103844165802002 s ( 86.34 ) 2024-05-03 21:01:44.612465 INFO::Formatting Data. 2024-05-03 21:01:44.61346 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.614541 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.615584 INFO::Found 2 missing values. 2024-05-03 21:01:44.618361 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.61888 INFO::Done 2024-05-03 21:01:44.645293 INFO::Found NA in Reference column 2024-05-03 21:01:44.654026 INFO::Require at least two references per batch. 2024-05-03 21:01:44.672597 INFO::Formatting Data. 2024-05-03 21:01:44.67353 INFO::Recognized SummarizedExperiment 2024-05-03 21:01:44.674273 INFO::Typecasting input to dataframe. 2024-05-03 21:01:44.688919 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.690831 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.69658 INFO::Found 0 missing values. 2024-05-03 21:01:44.70757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.708605 INFO::Done 2024-05-03 21:01:44.733194 INFO::Formatting Data. 2024-05-03 21:01:44.734307 INFO::Recognized SummarizedExperiment 2024-05-03 21:01:44.735128 INFO::Typecasting input to dataframe. 2024-05-03 21:01:44.763047 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.764923 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.770654 INFO::Found 0 missing values. 2024-05-03 21:01:44.788531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.789676 INFO::Done 2024-05-03 21:01:44.806869 INFO::Formatting Data. 2024-05-03 21:01:44.807746 INFO::Recognized SummarizedExperiment 2024-05-03 21:01:44.808284 INFO::Typecasting input to dataframe. 2024-05-03 21:01:44.824677 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.825778 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.826939 INFO::Found 0 missing values. 2024-05-03 21:01:44.827903 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique. 2024-05-03 21:01:44.832321 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.83296 INFO::Done 2024-05-03 21:01:44.842951 INFO::Formatting Data. 2024-05-03 21:01:44.843739 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.844648 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.845708 INFO::Found 0 missing values. 2024-05-03 21:01:44.848485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.849018 INFO::Done 2024-05-03 21:01:44.859527 INFO::Formatting Data. 2024-05-03 21:01:44.86031 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.861183 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.862122 INFO::Found 0 missing values. 2024-05-03 21:01:44.864903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.865441 INFO::Done 2024-05-03 21:01:44.893426 INFO::Formatting Data. 2024-05-03 21:01:44.894248 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.895263 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.896338 INFO::Found 1 missing values. 2024-05-03 21:01:44.898804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.899304 INFO::Done 2024-05-03 21:01:44.91783 INFO::Formatting Data. 2024-05-03 21:01:44.918712 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.919661 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.920684 INFO::Found 2 missing values. 2024-05-03 21:01:44.921609 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique. 2024-05-03 21:01:44.923803 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.924334 INFO::Done 2024-05-03 21:01:44.933863 INFO::Formatting Data. 2024-05-03 21:01:44.934633 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.935486 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.936372 INFO::Found 2 missing values. 2024-05-03 21:01:44.93791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.938408 INFO::Done 2024-05-03 21:01:44.948623 INFO::Formatting Data. 2024-05-03 21:01:44.949523 INFO::Typecasting input to dataframe. 2024-05-03 21:01:44.950317 INFO::Replacing NaNs with NAs. 2024-05-03 21:01:44.95118 INFO::Removing potential empty rows and columns 2024-05-03 21:01:44.952125 INFO::Found 0 missing values. 2024-05-03 21:01:44.954938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 21:01:44.955481 INFO::Done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ] > > proc.time() user system elapsed 17.506 3.385 20.613
BERT.Rcheck/BERT-Ex.timings
name | user | system | elapsed | |
BERT | 24.675 | 1.169 | 17.739 | |
compute_asw | 0.020 | 0.008 | 0.028 | |
count_existing | 0.006 | 0.012 | 0.018 | |
generate_data_covariables | 0.011 | 0.004 | 0.015 | |
generate_dataset | 0.011 | 0.004 | 0.015 | |