Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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: 1.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz |
StartedAt: 2025-08-01 12:59:38 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 13:01:06 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 87.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BERT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BERT/DESCRIPTION’ ... OK * this is package ‘BERT’ version ‘1.4.0’ * 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 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 28.614 1.415 21.549 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.4.0’ ** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # 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") 2025-08-01 13:00:42.213188 INFO::Formatting Data. 2025-08-01 13:00:42.218271 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:42.233965 INFO::Removing potential empty rows and columns 2025-08-01 13:00:42.588396 INFO::Found 0 missing values. 2025-08-01 13:00:42.592458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:42.593261 INFO::Done 2025-08-01 13:00:42.593895 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:42.617653 INFO::Starting hierarchical adjustment 2025-08-01 13:00:42.618966 INFO::Found 3 batches. 2025-08-01 13:00:42.619783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:42.621508 INFO::Using default BPPARAM 2025-08-01 13:00:42.622285 INFO::Processing subtree level 1 2025-08-01 13:00:42.808594 INFO::Adjusting the last 1 batches sequentially 2025-08-01 13:00:42.814241 INFO::Done 2025-08-01 13:00:42.815124 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:42.820896 INFO::ASW Batch was 0.0525741312206555 prior to batch effect correction and is now 0.0525741312206555 . 2025-08-01 13:00:42.823346 INFO::Total function execution time is 0.61090898513794 s and adjustment time is 0.195528984069824 s ( 32.01 ) 2025-08-01 13:00:42.855047 INFO::Formatting Data. 2025-08-01 13:00:42.856976 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:42.858799 INFO::Removing potential empty rows and columns 2025-08-01 13:00:42.86083 INFO::Found 0 missing values. 2025-08-01 13:00:42.862873 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. 2025-08-01 13:00:42.87893 INFO::Formatting Data. 2025-08-01 13:00:42.879985 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:42.881279 INFO::Removing potential empty rows and columns 2025-08-01 13:00:42.882411 INFO::Found 0 missing values. 2025-08-01 13:00:42.883382 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. 2025-08-01 13:00:42.908004 INFO::Formatting Data. 2025-08-01 13:00:42.910974 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:42.912103 INFO::Removing potential empty rows and columns 2025-08-01 13:00:42.914858 INFO::Found 0 missing values. 2025-08-01 13:00:42.916683 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. 2025-08-01 13:00:42.924533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:42.925566 INFO::Done 2025-08-01 13:00:42.926186 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:42.928795 INFO::Starting hierarchical adjustment 2025-08-01 13:00:42.929573 INFO::Found 2 batches. 2025-08-01 13:00:42.930097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:42.930949 INFO::Using default BPPARAM 2025-08-01 13:00:42.931485 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:42.932454 INFO::Adjusting sequential tree level 1 with 2 batches 2025-08-01 13:00:42.981707 INFO::Done 2025-08-01 13:00:42.98269 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:42.989367 INFO::ASW Batch was 0.0788736072822083 prior to batch effect correction and is now -0.122814509024535 . 2025-08-01 13:00:42.990708 INFO::Total function execution time is 0.0831930637359619 s and adjustment time is 0.0521831512451172 s ( 62.73 ) 2025-08-01 13:00:42.994547 INFO::Formatting Data. 2025-08-01 13:00:42.995221 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:43.005236 INFO::Formatting Data. 2025-08-01 13:00:43.005979 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:43.069974 INFO::Removing potential empty rows and columns 2025-08-01 13:00:43.071403 INFO::Found 0 missing values. 2025-08-01 13:00:43.07451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:43.075328 INFO::Done 2025-08-01 13:00:43.075885 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:43.078112 INFO::Starting hierarchical adjustment 2025-08-01 13:00:43.078869 INFO::Found 2 batches. 2025-08-01 13:00:43.079395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:43.079958 INFO::Using default BPPARAM 2025-08-01 13:00:43.080403 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:43.081181 INFO::Adjusting sequential tree level 1 with 2 batches design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:43.096417 INFO::Done 2025-08-01 13:00:43.097963 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:43.100957 INFO::ASW Batch was -0.0180244391307817 prior to batch effect correction and is now -0.112250062760211 . 2025-08-01 13:00:43.10195 INFO::Total function execution time is 0.0967020988464355 s and adjustment time is 0.0176680088043213 s ( 18.27 ) 2025-08-01 13:00:43.103015 INFO::Formatting Data. 2025-08-01 13:00:43.103571 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:43.104386 INFO::Removing potential empty rows and columns 2025-08-01 13:00:43.105377 INFO::Found 0 missing values. 2025-08-01 13:00:43.108175 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:43.108725 INFO::Done 2025-08-01 13:00:43.109206 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:43.111022 INFO::Starting hierarchical adjustment 2025-08-01 13:00:43.111719 INFO::Found 2 batches. 2025-08-01 13:00:43.11225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:43.112842 INFO::Using default BPPARAM 2025-08-01 13:00:43.113309 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:43.114128 INFO::Adjusting sequential tree level 1 with 2 batches design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:43.129848 INFO::Done 2025-08-01 13:00:43.130553 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:43.132732 INFO::ASW Batch was -0.0180244391307817 prior to batch effect correction and is now -0.112250062760211 . 2025-08-01 13:00:43.133609 INFO::Total function execution time is 0.0305840969085693 s and adjustment time is 0.0182309150695801 s ( 59.61 ) 2025-08-01 13:00:46.773382 INFO::Formatting Data. 2025-08-01 13:00:46.774225 INFO::Recognized SummarizedExperiment 2025-08-01 13:00:46.775276 INFO::Typecasting input to dataframe. 2025-08-01 13:00:46.81437 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:46.815872 INFO::Removing potential empty rows and columns 2025-08-01 13:00:46.819719 INFO::Found 0 missing values. 2025-08-01 13:00:46.826723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:46.827476 INFO::Done 2025-08-01 13:00:46.82799 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:46.832003 INFO::Starting hierarchical adjustment 2025-08-01 13:00:46.832751 INFO::Found 2 batches. 2025-08-01 13:00:46.833239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:46.834428 INFO::Using default BPPARAM 2025-08-01 13:00:46.834905 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:46.835899 INFO::Adjusting sequential tree level 1 with 2 batches 2025-08-01 13:00:46.909973 INFO::Done 2025-08-01 13:00:46.910813 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:46.915909 INFO::ASW Batch was 0.0106442095518023 prior to batch effect correction and is now -0.0921612659435057 . 2025-08-01 13:00:46.917418 INFO::Total function execution time is 0.144280910491943 s and adjustment time is 0.0772881507873535 s ( 53.57 ) 2025-08-01 13:00:46.94041 INFO::Formatting Data. 2025-08-01 13:00:46.941345 INFO::Recognized SummarizedExperiment 2025-08-01 13:00:46.941862 INFO::Typecasting input to dataframe. 2025-08-01 13:00:46.951524 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:46.952705 INFO::Removing potential empty rows and columns 2025-08-01 13:00:46.956218 INFO::Found 0 missing values. 2025-08-01 13:00:46.962791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:46.963422 INFO::Done 2025-08-01 13:00:46.963956 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:46.967862 INFO::Starting hierarchical adjustment 2025-08-01 13:00:46.968651 INFO::Found 2 batches. 2025-08-01 13:00:46.96914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:46.969705 INFO::Using default BPPARAM 2025-08-01 13:00:46.970197 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:46.971161 INFO::Adjusting sequential tree level 1 with 2 batches 2025-08-01 13:00:46.999725 INFO::Done 2025-08-01 13:00:47.001528 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:47.005731 INFO::ASW Batch was -0.00108481348071974 prior to batch effect correction and is now -0.00108481348071974 . 2025-08-01 13:00:47.006891 INFO::Total function execution time is 0.0663280487060547 s and adjustment time is 0.0309591293334961 s ( 46.68 ) 2025-08-01 13:00:47.028762 INFO::Formatting Data. 2025-08-01 13:00:47.029655 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:47.030589 INFO::Removing potential empty rows and columns 2025-08-01 13:00:47.031606 INFO::Found 0 missing values. 2025-08-01 13:00:47.034341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:47.034967 INFO::Done 2025-08-01 13:00:47.035474 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:47.037594 INFO::Starting hierarchical adjustment 2025-08-01 13:00:47.038326 INFO::Found 3 batches. 2025-08-01 13:00:47.038812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:47.03938 INFO::Using default BPPARAM 2025-08-01 13:00:47.039836 INFO::Processing subtree level 1 2025-08-01 13:00:47.502003 INFO::Adjusting the last 1 batches sequentially 2025-08-01 13:00:47.508621 INFO::Done 2025-08-01 13:00:47.510374 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:47.515851 INFO::ASW Batch was -0.113150088015841 prior to batch effect correction and is now -0.186014452966773 . 2025-08-01 13:00:47.517809 INFO::Total function execution time is 0.489025115966797 s and adjustment time is 0.47036600112915 s ( 96.18 ) 2025-08-01 13:00:47.671281 INFO::Skipping initial DF formatting 2025-08-01 13:00:47.67231 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:47.676929 INFO::Starting hierarchical adjustment 2025-08-01 13:00:47.67788 INFO::Found 5 batches. 2025-08-01 13:00:47.678583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:47.679381 INFO::Using default BPPARAM 2025-08-01 13:00:47.679855 INFO::Processing subtree level 1 2025-08-01 13:00:47.956721 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:47.965735 INFO::Adjusting sequential tree level 1 with 2 batches 2025-08-01 13:00:48.012809 INFO::Done 2025-08-01 13:00:48.013924 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:48.027303 INFO::ASW Batch was 0.511444672399942 prior to batch effect correction and is now 0.511444672399942 . 2025-08-01 13:00:48.030116 INFO::ASW Label was 0.405831846247961 prior to batch effect correction and is now 0.405831846247961 . 2025-08-01 13:00:48.031685 INFO::Total function execution time is 0.360388994216919 s and adjustment time is 0.3350830078125 s ( 92.98 ) 2025-08-01 13:00:48.085323 INFO::Formatting Data. 2025-08-01 13:00:48.086648 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:48.089003 INFO::Removing potential empty rows and columns 2025-08-01 13:00:48.092958 INFO::Found 0 missing values. 2025-08-01 13:00:48.10138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:48.102625 INFO::Done 2025-08-01 13:00:48.103462 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:48.10834 INFO::Starting hierarchical adjustment 2025-08-01 13:00:48.109499 INFO::Found 5 batches. 2025-08-01 13:00:48.110246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:48.111034 INFO::Using default BPPARAM 2025-08-01 13:00:48.111676 INFO::Processing subtree level 1 design matrix of interest not specified. Assuming a one-group experiment. design matrix of interest not specified. Assuming a one-group experiment. design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:48.380433 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:48.387849 INFO::Adjusting sequential tree level 1 with 2 batches design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:48.427209 INFO::Done 2025-08-01 13:00:48.428169 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:48.435651 INFO::ASW Batch was 0.524534060904593 prior to batch effect correction and is now -0.0291005573773538 . 2025-08-01 13:00:48.437056 INFO::ASW Label was 0.217401156111185 prior to batch effect correction and is now 0.667044489130173 . 2025-08-01 13:00:48.439799 INFO::Total function execution time is 0.354451894760132 s and adjustment time is 0.317870140075684 s ( 89.68 ) 2025-08-01 13:00:48.440952 INFO::Formatting Data. 2025-08-01 13:00:48.441841 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:48.444831 INFO::Removing potential empty rows and columns 2025-08-01 13:00:48.446463 INFO::Found 0 missing values. 2025-08-01 13:00:48.45336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:48.454449 INFO::Done 2025-08-01 13:00:48.485336 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:48.491559 INFO::Starting hierarchical adjustment 2025-08-01 13:00:48.492531 INFO::Found 5 batches. 2025-08-01 13:00:48.493134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:48.494624 INFO::Using default BPPARAM 2025-08-01 13:00:48.495341 INFO::Processing subtree level 1 design matrix of interest not specified. Assuming a one-group experiment. design matrix of interest not specified. Assuming a one-group experiment. design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:48.73385 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:48.739104 INFO::Adjusting sequential tree level 1 with 2 batches design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:48.772476 INFO::Done 2025-08-01 13:00:48.773531 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:48.778844 INFO::ASW Batch was 0.524534060904593 prior to batch effect correction and is now -0.0291005573773538 . 2025-08-01 13:00:48.779625 INFO::ASW Label was 0.217401156111185 prior to batch effect correction and is now 0.667044489130173 . 2025-08-01 13:00:48.780698 INFO::Total function execution time is 0.339721918106079 s and adjustment time is 0.280073165893555 s ( 82.44 ) 2025-08-01 13:00:48.805003 INFO::Formatting Data. 2025-08-01 13:00:48.80618 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:48.807523 INFO::Removing potential empty rows and columns 2025-08-01 13:00:48.808831 INFO::Found 0 missing values. 2025-08-01 13:00:48.814076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:48.814915 INFO::Done 2025-08-01 13:00:48.815589 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:48.820847 INFO::Starting hierarchical adjustment 2025-08-01 13:00:48.821978 INFO::Found 5 batches. 2025-08-01 13:00:48.822581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:48.823374 INFO::Using default BPPARAM 2025-08-01 13:00:48.825218 INFO::Processing subtree level 1 design matrix of interest not specified. Assuming a one-group experiment. design matrix of interest not specified. Assuming a one-group experiment. design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:49.022426 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:49.028256 INFO::Adjusting sequential tree level 1 with 2 batches design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:49.065229 INFO::Done 2025-08-01 13:00:49.069037 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:49.077007 INFO::ASW Batch was 0.470714734901068 prior to batch effect correction and is now -0.0455391700452347 . 2025-08-01 13:00:49.078241 INFO::ASW Label was 0.27363809314325 prior to batch effect correction and is now 0.811447715574333 . 2025-08-01 13:00:49.079407 INFO::Total function execution time is 0.274467945098877 s and adjustment time is 0.243373155593872 s ( 88.67 ) 2025-08-01 13:00:49.080522 INFO::Formatting Data. 2025-08-01 13:00:49.081351 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:49.082591 INFO::Removing potential empty rows and columns 2025-08-01 13:00:49.083936 INFO::Found 0 missing values. 2025-08-01 13:00:49.088579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:49.08937 INFO::Done 2025-08-01 13:00:49.090018 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:49.09367 INFO::Starting hierarchical adjustment 2025-08-01 13:00:49.094665 INFO::Found 5 batches. 2025-08-01 13:00:49.095287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:49.0961 INFO::Using default BPPARAM 2025-08-01 13:00:49.097165 INFO::Processing subtree level 1 design matrix of interest not specified. Assuming a one-group experiment. design matrix of interest not specified. Assuming a one-group experiment. design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:49.304185 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:49.310777 INFO::Adjusting sequential tree level 1 with 2 batches design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:49.352309 INFO::Done 2025-08-01 13:00:49.353375 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:49.358835 INFO::ASW Batch was 0.470714734901068 prior to batch effect correction and is now -0.0455391700452347 . 2025-08-01 13:00:49.359695 INFO::ASW Label was 0.27363809314325 prior to batch effect correction and is now 0.811447715574333 . 2025-08-01 13:00:49.360844 INFO::Total function execution time is 0.280176877975464 s and adjustment time is 0.257788896560669 s ( 92.01 ) 2025-08-01 13:00:49.387406 INFO::Formatting Data. 2025-08-01 13:00:49.388454 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:49.389653 INFO::Removing potential empty rows and columns 2025-08-01 13:00:49.39095 INFO::Found 0 missing values. 2025-08-01 13:00:49.395076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:49.395752 INFO::Done 2025-08-01 13:00:49.396339 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:49.40003 INFO::Starting hierarchical adjustment 2025-08-01 13:00:49.401961 INFO::Found 2 batches. 2025-08-01 13:00:49.404043 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:49.404985 INFO::Using default BPPARAM 2025-08-01 13:00:49.405583 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:49.406644 INFO::Adjusting sequential tree level 1 with 2 batches design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:49.428109 INFO::Done 2025-08-01 13:00:49.429066 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:49.433133 INFO::ASW Batch was 0.63255476365755 prior to batch effect correction and is now 0.0811567144733356 . 2025-08-01 13:00:49.434089 INFO::ASW Label was 0.369060535063936 prior to batch effect correction and is now 0.846691055169851 . 2025-08-01 13:00:49.435155 INFO::Total function execution time is 0.0479528903961182 s and adjustment time is 0.0272760391235352 s ( 56.88 ) 2025-08-01 13:00:49.436081 INFO::Formatting Data. 2025-08-01 13:00:49.436772 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:49.437977 INFO::Removing potential empty rows and columns 2025-08-01 13:00:49.439087 INFO::Found 0 missing values. 2025-08-01 13:00:49.442069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:49.4427 INFO::Done 2025-08-01 13:00:49.443248 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:49.446555 INFO::Starting hierarchical adjustment 2025-08-01 13:00:49.44749 INFO::Found 2 batches. 2025-08-01 13:00:49.44805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:49.448698 INFO::Using default BPPARAM 2025-08-01 13:00:49.449251 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:49.450288 INFO::Adjusting sequential tree level 1 with 2 batches design matrix of interest not specified. Assuming a one-group experiment. 2025-08-01 13:00:49.46873 INFO::Done 2025-08-01 13:00:49.469658 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:49.473415 INFO::ASW Batch was 0.63255476365755 prior to batch effect correction and is now 0.0811567144733356 . 2025-08-01 13:00:49.475411 INFO::ASW Label was 0.369060535063936 prior to batch effect correction and is now 0.846691055169851 . 2025-08-01 13:00:49.47703 INFO::Total function execution time is 0.040895938873291 s and adjustment time is 0.0213570594787598 s ( 52.22 ) 2025-08-01 13:00:49.521162 INFO::Formatting Data. 2025-08-01 13:00:49.522431 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:49.523809 INFO::Removing potential empty rows and columns 2025-08-01 13:00:49.525371 INFO::Found 0 missing values. 2025-08-01 13:00:49.528795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:49.529848 INFO::Done 2025-08-01 13:00:49.530483 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:49.533145 INFO::Starting hierarchical adjustment 2025-08-01 13:00:49.534161 INFO::Found 2 batches. 2025-08-01 13:00:49.534818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:49.535576 INFO::Using default BPPARAM 2025-08-01 13:00:49.536128 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:49.537212 INFO::Adjusting sequential tree level 1 with 2 batches 2025-08-01 13:00:49.576246 INFO::Done 2025-08-01 13:00:49.577184 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:49.579705 INFO::ASW Batch was -0.0615969925728752 prior to batch effect correction and is now -0.125396141538137 . 2025-08-01 13:00:49.580739 INFO::Total function execution time is 0.0602560043334961 s and adjustment time is 0.042248010635376 s ( 70.11 ) 2025-08-01 13:00:49.59618 INFO::Formatting Data. 2025-08-01 13:00:49.59713 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:49.598045 INFO::Removing potential empty rows and columns 2025-08-01 13:00:49.599095 INFO::Found 0 missing values. 2025-08-01 13:00:49.600537 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. 2025-08-01 13:00:49.605166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:49.605859 INFO::Done 2025-08-01 13:00:49.606405 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:49.609623 INFO::Starting hierarchical adjustment 2025-08-01 13:00:49.610443 INFO::Found 2 batches. 2025-08-01 13:00:49.610981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:49.611566 INFO::Using default BPPARAM 2025-08-01 13:00:49.612067 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:49.612966 INFO::Adjusting sequential tree level 1 with 2 batches 2025-08-01 13:00:49.630695 INFO::Done 2025-08-01 13:00:49.631624 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:49.635543 INFO::ASW Batch was 0.662156445855856 prior to batch effect correction and is now -0.0218735744478527 . 2025-08-01 13:00:49.636439 INFO::ASW Label was 0.401187716478134 prior to batch effect correction and is now 0.895946987183127 . 2025-08-01 13:00:49.63748 INFO::Total function execution time is 0.0413970947265625 s and adjustment time is 0.0203211307525635 s ( 49.09 ) 2025-08-01 13:00:49.638474 INFO::Formatting Data. 2025-08-01 13:00:49.639266 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:49.640474 INFO::Removing potential empty rows and columns 2025-08-01 13:00:49.641816 INFO::Found 0 missing values. 2025-08-01 13:00:49.643067 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. 2025-08-01 13:00:49.649334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:49.652841 INFO::Done 2025-08-01 13:00:49.654141 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:49.65921 INFO::Starting hierarchical adjustment 2025-08-01 13:00:49.660441 INFO::Found 2 batches. 2025-08-01 13:00:49.661108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:49.661787 INFO::Using default BPPARAM 2025-08-01 13:00:49.662302 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:49.663808 INFO::Adjusting sequential tree level 1 with 2 batches 2025-08-01 13:00:49.686238 INFO::Done 2025-08-01 13:00:49.687147 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:49.690469 INFO::ASW Batch was 0.662156445855856 prior to batch effect correction and is now -0.0218735744478527 . 2025-08-01 13:00:49.691158 INFO::ASW Label was 0.401187716478134 prior to batch effect correction and is now 0.895946987183127 . 2025-08-01 13:00:49.691991 INFO::Total function execution time is 0.0535488128662109 s and adjustment time is 0.0259959697723389 s ( 48.55 ) 2025-08-01 13:00:49.916092 INFO::Formatting Data. 2025-08-01 13:00:49.916944 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:49.91783 INFO::Removing potential empty rows and columns 2025-08-01 13:00:49.918865 INFO::Found 0 missing values. 2025-08-01 13:00:49.921624 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:49.922332 INFO::Done 2025-08-01 13:00:49.922839 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:49.925031 INFO::Starting hierarchical adjustment 2025-08-01 13:00:49.925954 INFO::Found 3 batches. 2025-08-01 13:00:49.92647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:49.927981 INFO::Using default BPPARAM 2025-08-01 13:00:49.928784 INFO::Processing subtree level 1 2025-08-01 13:00:50.055603 INFO::Adjusting the last 1 batches sequentially 2025-08-01 13:00:50.059555 INFO::Done 2025-08-01 13:00:50.060975 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:50.06654 INFO::ASW Batch was -0.0608313498274232 prior to batch effect correction and is now -0.0608313498274232 . 2025-08-01 13:00:50.06836 INFO::Total function execution time is 0.152233839035034 s and adjustment time is 0.133713006973267 s ( 87.83 ) 2025-08-01 13:00:50.06966 INFO::Formatting Data. 2025-08-01 13:00:50.070281 INFO::Typecasting input to dataframe. 2025-08-01 13:00:50.071026 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:50.072006 INFO::Removing potential empty rows and columns 2025-08-01 13:00:50.073286 INFO::Found 0 missing values. 2025-08-01 13:00:50.076966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:50.077598 INFO::Done 2025-08-01 13:00:50.078106 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:50.080241 INFO::Starting hierarchical adjustment 2025-08-01 13:00:50.080968 INFO::Found 3 batches. 2025-08-01 13:00:50.081821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:50.082911 INFO::Using default BPPARAM 2025-08-01 13:00:50.083429 INFO::Processing subtree level 1 2025-08-01 13:00:50.223344 INFO::Adjusting the last 1 batches sequentially 2025-08-01 13:00:50.228373 INFO::Done 2025-08-01 13:00:50.228837 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:50.234264 INFO::ASW Batch was -0.0608313498274232 prior to batch effect correction and is now -0.0608313498274232 . 2025-08-01 13:00:50.236967 INFO::Total function execution time is 0.167236089706421 s and adjustment time is 0.147561073303223 s ( 88.24 ) 2025-08-01 13:00:50.259905 INFO::Formatting Data. 2025-08-01 13:00:50.261105 INFO::Typecasting input to dataframe. 2025-08-01 13:00:50.262192 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:50.26325 INFO::Removing potential empty rows and columns 2025-08-01 13:00:50.265474 INFO::Found 0 missing values. 2025-08-01 13:00:50.273578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:50.274897 INFO::Done 2025-08-01 13:00:50.276444 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:50.279638 INFO::Starting hierarchical adjustment 2025-08-01 13:00:50.280578 INFO::Found 3 batches. 2025-08-01 13:00:50.28126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:50.282119 INFO::Using default BPPARAM 2025-08-01 13:00:50.282705 INFO::Processing subtree level 1 2025-08-01 13:00:50.416873 INFO::Adjusting the last 1 batches sequentially 2025-08-01 13:00:50.443008 INFO::Done 2025-08-01 13:00:50.444983 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:50.454224 INFO::ASW Batch was 0.0283355913934227 prior to batch effect correction and is now 0.0283355913934227 . 2025-08-01 13:00:50.45626 INFO::Total function execution time is 0.196591854095459 s and adjustment time is 0.161116123199463 s ( 81.95 ) 2025-08-01 13:00:50.709705 INFO::Formatting Data. 2025-08-01 13:00:50.710954 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:50.712854 INFO::Removing potential empty rows and columns 2025-08-01 13:00:50.716603 INFO::Found 1000 missing values. 2025-08-01 13:00:50.734948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:50.735977 INFO::Done 2025-08-01 13:00:50.736605 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:50.743221 INFO::Starting hierarchical adjustment 2025-08-01 13:00:50.744829 INFO::Found 10 batches. 2025-08-01 13:00:50.745393 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:50.746143 INFO::Using default BPPARAM 2025-08-01 13:00:50.746681 INFO::Processing subtree level 1 2025-08-01 13:00:50.93567 INFO::Processing subtree level 2 2025-08-01 13:00:51.169851 INFO::Adjusting the last 1 batches sequentially 2025-08-01 13:00:51.177919 INFO::Done 2025-08-01 13:00:51.17887 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:51.187422 INFO::ASW Batch was 0.504687897633452 prior to batch effect correction and is now 0.504687897633452 . 2025-08-01 13:00:51.188335 INFO::ASW Label was 0.299709738161134 prior to batch effect correction and is now 0.299709738161134 . 2025-08-01 13:00:51.190824 INFO::Total function execution time is 0.480398893356323 s and adjustment time is 0.433260202407837 s ( 90.19 ) 2025-08-01 13:00:51.191964 INFO::Formatting Data. 2025-08-01 13:00:51.192682 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:51.194906 INFO::Removing potential empty rows and columns 2025-08-01 13:00:51.201117 INFO::Found 1000 missing values. 2025-08-01 13:00:51.230443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:51.231732 INFO::Done 2025-08-01 13:00:51.232332 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:51.240595 INFO::Starting hierarchical adjustment 2025-08-01 13:00:51.241564 INFO::Found 10 batches. 2025-08-01 13:00:52.917357 INFO::Set up parallel execution backend with 2 workers 2025-08-01 13:00:52.918327 INFO::Processing subtree level 1 with 10 batches using 2 cores. 2025-08-01 13:00:54.653548 INFO::Adjusting the last 2 batches sequentially 2025-08-01 13:00:54.655282 INFO::Adjusting sequential tree level 1 with 2 batches 2025-08-01 13:00:54.672495 INFO::Done 2025-08-01 13:00:54.673265 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:54.678914 INFO::ASW Batch was 0.504687897633452 prior to batch effect correction and is now 0.504687897633452 . 2025-08-01 13:00:54.679558 INFO::ASW Label was 0.299709738161134 prior to batch effect correction and is now 0.299709738161134 . 2025-08-01 13:00:54.682114 INFO::Total function execution time is 3.49008202552795 s and adjustment time is 3.43105292320251 s ( 98.31 ) 2025-08-01 13:00:54.885847 INFO::Formatting Data. 2025-08-01 13:00:54.887302 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:54.888801 INFO::Removing potential empty rows and columns 2025-08-01 13:00:54.890325 INFO::Found 0 missing values. 2025-08-01 13:00:54.894493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:54.895248 INFO::Done 2025-08-01 13:00:54.895905 INFO::Acquiring quality metrics before batch effect correction. 2025-08-01 13:00:54.899433 INFO::Starting hierarchical adjustment 2025-08-01 13:00:54.900367 INFO::Found 3 batches. 2025-08-01 13:00:54.901452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2025-08-01 13:00:54.90222 INFO::Using default BPPARAM 2025-08-01 13:00:54.902775 INFO::Processing subtree level 1 2025-08-01 13:00:55.062616 INFO::Adjusting the last 1 batches sequentially 2025-08-01 13:00:55.067281 INFO::Done 2025-08-01 13:00:55.067815 INFO::Acquiring quality metrics after batch effect correction. 2025-08-01 13:00:55.074023 INFO::ASW Batch was 0.0795576494318088 prior to batch effect correction and is now -0.144456595593604 . 2025-08-01 13:00:55.07481 INFO::ASW Label was -0.163351995562323 prior to batch effect correction and is now 0.0636768472540417 . 2025-08-01 13:00:55.078579 INFO::Total function execution time is 0.192512989044189 s and adjustment time is 0.167114019393921 s ( 86.81 ) 2025-08-01 13:00:55.283438 INFO::Formatting Data. 2025-08-01 13:00:55.284135 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.284727 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.285451 INFO::Found 2 missing values. 2025-08-01 13:00:55.28727 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.28761 INFO::Done 2025-08-01 13:00:55.324516 INFO::Found NA in Reference column 2025-08-01 13:00:55.337037 INFO::Require at least two references per batch. 2025-08-01 13:00:55.366022 INFO::Formatting Data. 2025-08-01 13:00:55.367844 INFO::Recognized SummarizedExperiment 2025-08-01 13:00:55.368622 INFO::Typecasting input to dataframe. 2025-08-01 13:00:55.37736 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.380181 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.385006 INFO::Found 0 missing values. 2025-08-01 13:00:55.393929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.394533 INFO::Done 2025-08-01 13:00:55.413503 INFO::Formatting Data. 2025-08-01 13:00:55.414596 INFO::Recognized SummarizedExperiment 2025-08-01 13:00:55.415209 INFO::Typecasting input to dataframe. 2025-08-01 13:00:55.434638 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.436455 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.441138 INFO::Found 0 missing values. 2025-08-01 13:00:55.454994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.455962 INFO::Done 2025-08-01 13:00:55.474505 INFO::Formatting Data. 2025-08-01 13:00:55.475373 INFO::Recognized SummarizedExperiment 2025-08-01 13:00:55.475643 INFO::Typecasting input to dataframe. 2025-08-01 13:00:55.487038 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.487553 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.488007 INFO::Found 0 missing values. 2025-08-01 13:00:55.488428 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. 2025-08-01 13:00:55.494612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.494916 INFO::Done 2025-08-01 13:00:55.503425 INFO::Formatting Data. 2025-08-01 13:00:55.503855 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.504255 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.504695 INFO::Found 0 missing values. 2025-08-01 13:00:55.505984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.506292 INFO::Done 2025-08-01 13:00:55.518843 INFO::Formatting Data. 2025-08-01 13:00:55.519647 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.520512 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.521487 INFO::Found 0 missing values. 2025-08-01 13:00:55.524398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.524958 INFO::Done 2025-08-01 13:00:55.559144 INFO::Formatting Data. 2025-08-01 13:00:55.559718 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.560459 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.56186 INFO::Found 1 missing values. 2025-08-01 13:00:55.565965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.566628 INFO::Done 2025-08-01 13:00:55.590657 INFO::Formatting Data. 2025-08-01 13:00:55.592453 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.593273 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.594154 INFO::Found 2 missing values. 2025-08-01 13:00:55.595023 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. 2025-08-01 13:00:55.598307 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.599227 INFO::Done 2025-08-01 13:00:55.609433 INFO::Formatting Data. 2025-08-01 13:00:55.610218 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.610991 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.611917 INFO::Found 2 missing values. 2025-08-01 13:00:55.613447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.614037 INFO::Done 2025-08-01 13:00:55.627034 INFO::Formatting Data. 2025-08-01 13:00:55.62929 INFO::Typecasting input to dataframe. 2025-08-01 13:00:55.630358 INFO::Replacing NaNs with NAs. 2025-08-01 13:00:55.631392 INFO::Removing potential empty rows and columns 2025-08-01 13:00:55.632532 INFO::Found 0 missing values. 2025-08-01 13:00:55.63752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2025-08-01 13:00:55.638269 INFO::Done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ] > > proc.time() user system elapsed 20.402 5.759 28.016
BERT.Rcheck/BERT-Ex.timings
name | user | system | elapsed | |
BERT | 28.614 | 1.415 | 21.549 | |
compute_asw | 0.031 | 0.002 | 0.032 | |
count_existing | 0.016 | 0.001 | 0.017 | |
generate_data_covariables | 0.015 | 0.002 | 0.018 | |
generate_dataset | 0.014 | 0.002 | 0.017 | |