Yannis Schumann
| Snapshot Date: 2026-03-04 13:40 -0500 (Wed, 04 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-05 11:35 -0500 (Thu, 05 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4891 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4583 |
| 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 169/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2026-03-04 18:40:11 -0500 (Wed, 04 Mar 2026) |
| EndedAt: 2026-03-04 18:40:48 -0500 (Wed, 04 Mar 2026) |
| EllapsedTime: 36.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 10.319 0.442 7.722
* 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/4.6-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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")
2026-03-04 18:40:38.575267 INFO::Formatting Data.
2026-03-04 18:40:38.576695 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:38.581588 INFO::Removing potential empty rows and columns
2026-03-04 18:40:38.700279 INFO::Found 0 missing values.
2026-03-04 18:40:38.701503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:38.70172 INFO::Done
2026-03-04 18:40:38.701899 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:38.708936 INFO::Starting hierarchical adjustment
2026-03-04 18:40:38.70928 INFO::Found 3 batches.
2026-03-04 18:40:38.709574 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:38.709973 INFO::Using default BPPARAM
2026-03-04 18:40:38.710146 INFO::Processing subtree level 1
2026-03-04 18:40:38.796802 INFO::Adjusting the last 1 batches sequentially
2026-03-04 18:40:38.798064 INFO::Done
2026-03-04 18:40:38.798393 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:38.799691 INFO::ASW Batch was -0.0552176715178276 prior to batch effect correction and is now -0.0552176715178276 .
2026-03-04 18:40:38.80024 INFO::Total function execution time is 0.225238084793091 s and adjustment time is 0.0888350009918213 s ( 39.44 )
2026-03-04 18:40:38.809587 INFO::Formatting Data.
2026-03-04 18:40:38.809961 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:38.8104 INFO::Removing potential empty rows and columns
2026-03-04 18:40:38.811098 INFO::Found 0 missing values.
2026-03-04 18:40:38.811553 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.
2026-03-04 18:40:38.816724 INFO::Formatting Data.
2026-03-04 18:40:38.817097 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:38.817408 INFO::Removing potential empty rows and columns
2026-03-04 18:40:38.817814 INFO::Found 0 missing values.
2026-03-04 18:40:38.818151 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.
2026-03-04 18:40:38.82536 INFO::Formatting Data.
2026-03-04 18:40:38.825686 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:38.826075 INFO::Removing potential empty rows and columns
2026-03-04 18:40:38.826609 INFO::Found 0 missing values.
2026-03-04 18:40:38.826987 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.
2026-03-04 18:40:38.829092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:38.829349 INFO::Done
2026-03-04 18:40:38.829584 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:38.830393 INFO::Starting hierarchical adjustment
2026-03-04 18:40:38.830656 INFO::Found 2 batches.
2026-03-04 18:40:38.830884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:38.831155 INFO::Using default BPPARAM
2026-03-04 18:40:38.831357 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:38.83167 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 18:40:38.841159 INFO::Done
2026-03-04 18:40:38.841416 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:38.842265 INFO::ASW Batch was -0.021163211491243 prior to batch effect correction and is now -0.105061342037085 .
2026-03-04 18:40:38.842615 INFO::Total function execution time is 0.017280101776123 s and adjustment time is 0.0105559825897217 s ( 61.09 )
2026-03-04 18:40:38.843878 INFO::Formatting Data.
2026-03-04 18:40:38.844104 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:38.847429 INFO::Formatting Data.
2026-03-04 18:40:38.847676 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:38.847977 INFO::Removing potential empty rows and columns
2026-03-04 18:40:38.848362 INFO::Found 0 missing values.
2026-03-04 18:40:38.849396 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:38.849593 INFO::Done
2026-03-04 18:40:38.849772 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:38.850457 INFO::Starting hierarchical adjustment
2026-03-04 18:40:38.850693 INFO::Found 2 batches.
2026-03-04 18:40:38.850859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:38.851067 INFO::Using default BPPARAM
2026-03-04 18:40:38.864939 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:38.865959 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 18:40:38.870737 INFO::Done
2026-03-04 18:40:38.870938 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:38.871532 INFO::ASW Batch was -0.00549922823990278 prior to batch effect correction and is now -0.123477696502356 .
2026-03-04 18:40:38.871762 INFO::Total function execution time is 0.0243351459503174 s and adjustment time is 0.0200860500335693 s ( 82.54 )
2026-03-04 18:40:38.872049 INFO::Formatting Data.
2026-03-04 18:40:38.872212 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:38.872439 INFO::Removing potential empty rows and columns
2026-03-04 18:40:38.87272 INFO::Found 0 missing values.
2026-03-04 18:40:38.87352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:38.873679 INFO::Done
2026-03-04 18:40:38.873831 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:38.87438 INFO::Starting hierarchical adjustment
2026-03-04 18:40:38.874584 INFO::Found 2 batches.
2026-03-04 18:40:38.874739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:38.874908 INFO::Using default BPPARAM
2026-03-04 18:40:38.875051 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:38.875285 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 18:40:38.879694 INFO::Done
2026-03-04 18:40:38.879893 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:38.880453 INFO::ASW Batch was -0.00549922823990278 prior to batch effect correction and is now -0.123477696502356 .
2026-03-04 18:40:38.880682 INFO::Total function execution time is 0.00862002372741699 s and adjustment time is 0.00514388084411621 s ( 59.67 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-04 18:40:40.189261 INFO::Formatting Data.
2026-03-04 18:40:40.189613 INFO::Recognized SummarizedExperiment
2026-03-04 18:40:40.189815 INFO::Typecasting input to dataframe.
2026-03-04 18:40:40.202046 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:40.202502 INFO::Removing potential empty rows and columns
2026-03-04 18:40:40.203707 INFO::Found 0 missing values.
2026-03-04 18:40:40.205966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:40.20614 INFO::Done
2026-03-04 18:40:40.206293 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:40.207508 INFO::Starting hierarchical adjustment
2026-03-04 18:40:40.207734 INFO::Found 2 batches.
2026-03-04 18:40:40.207889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:40.208219 INFO::Using default BPPARAM
2026-03-04 18:40:40.208394 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:40.208687 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 18:40:40.226988 INFO::Done
2026-03-04 18:40:40.227249 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:40.228513 INFO::ASW Batch was 0.0185878614064805 prior to batch effect correction and is now -0.0929004775442082 .
2026-03-04 18:40:40.228786 INFO::Total function execution time is 0.0405762195587158 s and adjustment time is 0.0192811489105225 s ( 47.52 )
Warning: stack imbalance in '{', 73 then 75
2026-03-04 18:40:40.236341 INFO::Formatting Data.
2026-03-04 18:40:40.236603 INFO::Recognized SummarizedExperiment
2026-03-04 18:40:40.236774 INFO::Typecasting input to dataframe.
2026-03-04 18:40:40.240173 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:40.2406 INFO::Removing potential empty rows and columns
2026-03-04 18:40:40.241782 INFO::Found 0 missing values.
2026-03-04 18:40:40.244109 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:40.244292 INFO::Done
2026-03-04 18:40:40.244451 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:40.245748 INFO::Starting hierarchical adjustment
2026-03-04 18:40:40.245974 INFO::Found 2 batches.
2026-03-04 18:40:40.246131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:40.246324 INFO::Using default BPPARAM
2026-03-04 18:40:40.246475 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:40.246775 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 18:40:40.256609 INFO::Done
2026-03-04 18:40:40.256883 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:40.258356 INFO::ASW Batch was 0.00455055995250099 prior to batch effect correction and is now 0.00455055995250099 .
2026-03-04 18:40:40.258696 INFO::Total function execution time is 0.022352933883667 s and adjustment time is 0.0106699466705322 s ( 47.73 )
2026-03-04 18:40:40.267842 INFO::Formatting Data.
2026-03-04 18:40:40.268123 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:40.26847 INFO::Removing potential empty rows and columns
2026-03-04 18:40:40.268835 INFO::Found 0 missing values.
2026-03-04 18:40:40.269799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:40.269986 INFO::Done
2026-03-04 18:40:40.270154 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:40.270834 INFO::Starting hierarchical adjustment
2026-03-04 18:40:40.271068 INFO::Found 3 batches.
2026-03-04 18:40:40.271229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:40.271439 INFO::Using default BPPARAM
2026-03-04 18:40:40.271594 INFO::Processing subtree level 1
2026-03-04 18:40:40.39857 INFO::Adjusting the last 1 batches sequentially
2026-03-04 18:40:40.399968 INFO::Done
2026-03-04 18:40:40.400292 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:40.401576 INFO::ASW Batch was -0.14533165487023 prior to batch effect correction and is now -0.188203383247601 .
2026-03-04 18:40:40.402041 INFO::Total function execution time is 0.134181976318359 s and adjustment time is 0.128926038742065 s ( 96.08 )
2026-03-04 18:40:40.41212 INFO::Skipping initial DF formatting
2026-03-04 18:40:40.41244 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:40.415556 INFO::Starting hierarchical adjustment
2026-03-04 18:40:40.415906 INFO::Found 5 batches.
2026-03-04 18:40:40.416126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:40.416406 INFO::Using default BPPARAM
2026-03-04 18:40:40.416606 INFO::Processing subtree level 1
2026-03-04 18:40:40.63612 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:40.637558 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 18:40:40.646327 INFO::Done
2026-03-04 18:40:40.646629 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:40.697966 INFO::ASW Batch was 0.502614961730051 prior to batch effect correction and is now 0.502614961730051 .
2026-03-04 18:40:40.698386 INFO::ASW Label was 0.363888398080717 prior to batch effect correction and is now 0.363888398080717 .
2026-03-04 18:40:40.698874 INFO::Total function execution time is 0.286777973175049 s and adjustment time is 0.230481147766113 s ( 80.37 )
2026-03-04 18:40:40.708979 INFO::Formatting Data.
2026-03-04 18:40:40.709262 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:40.709628 INFO::Removing potential empty rows and columns
2026-03-04 18:40:40.710063 INFO::Found 0 missing values.
2026-03-04 18:40:40.71185 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:40.712187 INFO::Done
2026-03-04 18:40:40.712458 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:40.713763 INFO::Starting hierarchical adjustment
2026-03-04 18:40:40.714029 INFO::Found 5 batches.
2026-03-04 18:40:40.714252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:40.714595 INFO::Using default BPPARAM
2026-03-04 18:40:40.714822 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.
2026-03-04 18:40:40.837393 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:40.838827 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 18:40:40.84981 INFO::Done
2026-03-04 18:40:40.850168 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:40.851992 INFO::ASW Batch was 0.213106230745285 prior to batch effect correction and is now -0.0327606237035652 .
2026-03-04 18:40:40.85228 INFO::ASW Label was 0.505864804268498 prior to batch effect correction and is now 0.872125192275316 .
2026-03-04 18:40:40.852736 INFO::Total function execution time is 0.143752098083496 s and adjustment time is 0.135807991027832 s ( 94.47 )
2026-03-04 18:40:40.8532 INFO::Formatting Data.
2026-03-04 18:40:40.853459 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:40.853877 INFO::Removing potential empty rows and columns
2026-03-04 18:40:40.854385 INFO::Found 0 missing values.
2026-03-04 18:40:40.856196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:40.856452 INFO::Done
2026-03-04 18:40:40.856697 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:40.857974 INFO::Starting hierarchical adjustment
2026-03-04 18:40:40.858298 INFO::Found 5 batches.
2026-03-04 18:40:40.858523 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:40.858822 INFO::Using default BPPARAM
2026-03-04 18:40:40.859038 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.
2026-03-04 18:40:40.958075 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:40.960509 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 18:40:40.971916 INFO::Done
2026-03-04 18:40:40.972369 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:40.974474 INFO::ASW Batch was 0.213106230745285 prior to batch effect correction and is now -0.0327606237035652 .
2026-03-04 18:40:40.974819 INFO::ASW Label was 0.505864804268498 prior to batch effect correction and is now 0.872125192275316 .
2026-03-04 18:40:40.97532 INFO::Total function execution time is 0.12205696105957 s and adjustment time is 0.113677024841309 s ( 93.13 )
2026-03-04 18:40:40.984226 INFO::Formatting Data.
2026-03-04 18:40:40.984522 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:40.984905 INFO::Removing potential empty rows and columns
2026-03-04 18:40:40.985365 INFO::Found 0 missing values.
2026-03-04 18:40:40.987051 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:40.987276 INFO::Done
2026-03-04 18:40:40.987455 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:40.988693 INFO::Starting hierarchical adjustment
2026-03-04 18:40:40.989055 INFO::Found 5 batches.
2026-03-04 18:40:40.989266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:40.989562 INFO::Using default BPPARAM
2026-03-04 18:40:40.989823 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.
2026-03-04 18:40:41.086326 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:41.088209 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 18:40:41.097317 INFO::Done
2026-03-04 18:40:41.09764 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.099266 INFO::ASW Batch was 0.244589372559781 prior to batch effect correction and is now -0.0949248114265436 .
2026-03-04 18:40:41.099498 INFO::ASW Label was 0.46068646317399 prior to batch effect correction and is now 0.889705810204561 .
2026-03-04 18:40:41.099829 INFO::Total function execution time is 0.115608930587769 s and adjustment time is 0.108319997787476 s ( 93.7 )
2026-03-04 18:40:41.100155 INFO::Formatting Data.
2026-03-04 18:40:41.100348 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.100681 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.101096 INFO::Found 0 missing values.
2026-03-04 18:40:41.102792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.103033 INFO::Done
2026-03-04 18:40:41.103362 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.104649 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.104996 INFO::Found 5 batches.
2026-03-04 18:40:41.105196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.105491 INFO::Using default BPPARAM
2026-03-04 18:40:41.105701 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.
2026-03-04 18:40:41.200892 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:41.201926 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 18:40:41.212131 INFO::Done
2026-03-04 18:40:41.212419 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.213936 INFO::ASW Batch was 0.244589372559781 prior to batch effect correction and is now -0.0949248114265436 .
2026-03-04 18:40:41.214239 INFO::ASW Label was 0.46068646317399 prior to batch effect correction and is now 0.889705810204561 .
2026-03-04 18:40:41.214999 INFO::Total function execution time is 0.114809989929199 s and adjustment time is 0.10723614692688 s ( 93.4 )
2026-03-04 18:40:41.223728 INFO::Formatting Data.
2026-03-04 18:40:41.224084 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.224484 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.224895 INFO::Found 0 missing values.
2026-03-04 18:40:41.225827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.226009 INFO::Done
2026-03-04 18:40:41.226191 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.227217 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.227462 INFO::Found 2 batches.
2026-03-04 18:40:41.22764 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.227864 INFO::Using default BPPARAM
2026-03-04 18:40:41.228031 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:41.228323 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 18:40:41.233612 INFO::Done
2026-03-04 18:40:41.233817 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.234774 INFO::ASW Batch was 0.490469084317582 prior to batch effect correction and is now -0.0368369218037247 .
2026-03-04 18:40:41.234971 INFO::ASW Label was 0.588749812109756 prior to batch effect correction and is now 0.936971048966706 .
2026-03-04 18:40:41.2352 INFO::Total function execution time is 0.011538028717041 s and adjustment time is 0.00619602203369141 s ( 53.7 )
2026-03-04 18:40:41.23542 INFO::Formatting Data.
2026-03-04 18:40:41.2356 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.235862 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.236171 INFO::Found 0 missing values.
2026-03-04 18:40:41.237006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.237173 INFO::Done
2026-03-04 18:40:41.237343 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.238168 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.238384 INFO::Found 2 batches.
2026-03-04 18:40:41.238546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.238726 INFO::Using default BPPARAM
2026-03-04 18:40:41.238883 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:41.239145 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-04 18:40:41.244058 INFO::Done
2026-03-04 18:40:41.244264 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.245227 INFO::ASW Batch was 0.490469084317582 prior to batch effect correction and is now -0.0368369218037247 .
2026-03-04 18:40:41.245432 INFO::ASW Label was 0.588749812109756 prior to batch effect correction and is now 0.936971048966706 .
2026-03-04 18:40:41.245689 INFO::Total function execution time is 0.0102541446685791 s and adjustment time is 0.00570487976074219 s ( 55.63 )
2026-03-04 18:40:41.252245 INFO::Formatting Data.
2026-03-04 18:40:41.252536 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.252854 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.253174 INFO::Found 0 missing values.
2026-03-04 18:40:41.253854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.254027 INFO::Done
2026-03-04 18:40:41.254202 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.254829 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.255044 INFO::Found 2 batches.
2026-03-04 18:40:41.255212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.255411 INFO::Using default BPPARAM
2026-03-04 18:40:41.255572 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:41.255836 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 18:40:41.267963 INFO::Done
2026-03-04 18:40:41.268281 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.269104 INFO::ASW Batch was 0.0835351252261822 prior to batch effect correction and is now -0.14478663873797 .
2026-03-04 18:40:41.269411 INFO::Total function execution time is 0.017186164855957 s and adjustment time is 0.0129318237304688 s ( 75.25 )
2026-03-04 18:40:41.28022 INFO::Formatting Data.
2026-03-04 18:40:41.280535 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.280882 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.281315 INFO::Found 0 missing values.
2026-03-04 18:40:41.281812 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.
2026-03-04 18:40:41.283419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.283623 INFO::Done
2026-03-04 18:40:41.28381 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.284866 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.285109 INFO::Found 2 batches.
2026-03-04 18:40:41.285277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.285476 INFO::Using default BPPARAM
2026-03-04 18:40:41.285645 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:41.285938 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 18:40:41.292264 INFO::Done
2026-03-04 18:40:41.292521 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.293681 INFO::ASW Batch was 0.634585894499409 prior to batch effect correction and is now 0.155873335529345 .
2026-03-04 18:40:41.293923 INFO::ASW Label was 0.502608695528589 prior to batch effect correction and is now 0.819506400371482 .
2026-03-04 18:40:41.29424 INFO::Total function execution time is 0.0140769481658936 s and adjustment time is 0.00719714164733887 s ( 51.13 )
2026-03-04 18:40:41.294549 INFO::Formatting Data.
2026-03-04 18:40:41.294782 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.295107 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.295494 INFO::Found 0 missing values.
2026-03-04 18:40:41.295841 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.
2026-03-04 18:40:41.297556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.297782 INFO::Done
2026-03-04 18:40:41.297993 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.299111 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.2994 INFO::Found 2 batches.
2026-03-04 18:40:41.299606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.299856 INFO::Using default BPPARAM
2026-03-04 18:40:41.300039 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:41.300387 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 18:40:41.307388 INFO::Done
2026-03-04 18:40:41.307664 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.308869 INFO::ASW Batch was 0.634585894499409 prior to batch effect correction and is now 0.155873335529345 .
2026-03-04 18:40:41.30912 INFO::ASW Label was 0.502608695528589 prior to batch effect correction and is now 0.819506400371482 .
2026-03-04 18:40:41.309426 INFO::Total function execution time is 0.0148921012878418 s and adjustment time is 0.00802397727966309 s ( 53.88 )
2026-03-04 18:40:41.380129 INFO::Formatting Data.
2026-03-04 18:40:41.380495 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.380867 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.38128 INFO::Found 0 missing values.
2026-03-04 18:40:41.382352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.382527 INFO::Done
2026-03-04 18:40:41.382702 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.383476 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.383712 INFO::Found 3 batches.
2026-03-04 18:40:41.383867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.384077 INFO::Using default BPPARAM
2026-03-04 18:40:41.384224 INFO::Processing subtree level 1
2026-03-04 18:40:41.463808 INFO::Adjusting the last 1 batches sequentially
2026-03-04 18:40:41.464905 INFO::Done
2026-03-04 18:40:41.465161 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.466379 INFO::ASW Batch was 0.0171828707076009 prior to batch effect correction and is now 0.0171828707076009 .
2026-03-04 18:40:41.466869 INFO::Total function execution time is 0.0867719650268555 s and adjustment time is 0.081226110458374 s ( 93.61 )
2026-03-04 18:40:41.467281 INFO::Formatting Data.
2026-03-04 18:40:41.467756 INFO::Typecasting input to dataframe.
2026-03-04 18:40:41.468179 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.468651 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.469201 INFO::Found 0 missing values.
2026-03-04 18:40:41.470365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.470548 INFO::Done
2026-03-04 18:40:41.47074 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.47175 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.472082 INFO::Found 3 batches.
2026-03-04 18:40:41.472315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.472622 INFO::Using default BPPARAM
2026-03-04 18:40:41.472826 INFO::Processing subtree level 1
2026-03-04 18:40:41.542281 INFO::Adjusting the last 1 batches sequentially
2026-03-04 18:40:41.543491 INFO::Done
2026-03-04 18:40:41.543766 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.544876 INFO::ASW Batch was 0.0171828707076009 prior to batch effect correction and is now 0.0171828707076009 .
2026-03-04 18:40:41.545309 INFO::Total function execution time is 0.0780220031738281 s and adjustment time is 0.0714740753173828 s ( 91.61 )
2026-03-04 18:40:41.552031 INFO::Formatting Data.
2026-03-04 18:40:41.552324 INFO::Typecasting input to dataframe.
2026-03-04 18:40:41.552659 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.55302 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.553516 INFO::Found 0 missing values.
2026-03-04 18:40:41.554654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.554902 INFO::Done
2026-03-04 18:40:41.555101 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.555825 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.556057 INFO::Found 3 batches.
2026-03-04 18:40:41.556274 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.556631 INFO::Using default BPPARAM
2026-03-04 18:40:41.556901 INFO::Processing subtree level 1
2026-03-04 18:40:41.636248 INFO::Adjusting the last 1 batches sequentially
2026-03-04 18:40:41.637277 INFO::Done
2026-03-04 18:40:41.637527 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.638578 INFO::ASW Batch was -0.105658829158699 prior to batch effect correction and is now -0.105658829158699 .
2026-03-04 18:40:41.638952 INFO::Total function execution time is 0.0869340896606445 s and adjustment time is 0.0812489986419678 s ( 93.46 )
2026-03-04 18:40:41.728676 INFO::Formatting Data.
2026-03-04 18:40:41.728931 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.729308 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.730238 INFO::Found 1000 missing values.
2026-03-04 18:40:41.737034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.737333 INFO::Done
2026-03-04 18:40:41.737528 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.739651 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.739925 INFO::Found 10 batches.
2026-03-04 18:40:41.740103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:41.740334 INFO::Using default BPPARAM
2026-03-04 18:40:41.740492 INFO::Processing subtree level 1
2026-03-04 18:40:41.843191 INFO::Processing subtree level 2
2026-03-04 18:40:41.929688 INFO::Adjusting the last 1 batches sequentially
2026-03-04 18:40:41.931055 INFO::Done
2026-03-04 18:40:41.931343 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:41.93449 INFO::ASW Batch was 0.519515987704628 prior to batch effect correction and is now 0.519515987704628 .
2026-03-04 18:40:41.934781 INFO::ASW Label was 0.327519004979153 prior to batch effect correction and is now 0.327519004979153 .
2026-03-04 18:40:41.935338 INFO::Total function execution time is 0.206629991531372 s and adjustment time is 0.191174983978271 s ( 92.52 )
2026-03-04 18:40:41.935714 INFO::Formatting Data.
2026-03-04 18:40:41.935963 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:41.936479 INFO::Removing potential empty rows and columns
2026-03-04 18:40:41.937571 INFO::Found 1000 missing values.
2026-03-04 18:40:41.944431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:41.944725 INFO::Done
2026-03-04 18:40:41.944927 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:41.947309 INFO::Starting hierarchical adjustment
2026-03-04 18:40:41.947622 INFO::Found 10 batches.
2026-03-04 18:40:42.480267 INFO::Set up parallel execution backend with 2 workers
2026-03-04 18:40:42.480584 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-04 18:40:43.118013 INFO::Adjusting the last 2 batches sequentially
2026-03-04 18:40:43.118544 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-04 18:40:43.12417 INFO::Done
2026-03-04 18:40:43.124371 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:43.126498 INFO::ASW Batch was 0.519515987704628 prior to batch effect correction and is now 0.519515987704628 .
2026-03-04 18:40:43.126675 INFO::ASW Label was 0.327519004979153 prior to batch effect correction and is now 0.327519004979153 .
2026-03-04 18:40:43.126908 INFO::Total function execution time is 1.19121789932251 s and adjustment time is 1.17661213874817 s ( 98.77 )
2026-03-04 18:40:43.277324 INFO::Formatting Data.
2026-03-04 18:40:43.277654 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.278049 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.278547 INFO::Found 0 missing values.
2026-03-04 18:40:43.279937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.280129 INFO::Done
2026-03-04 18:40:43.280305 INFO::Acquiring quality metrics before batch effect correction.
2026-03-04 18:40:43.2813 INFO::Starting hierarchical adjustment
2026-03-04 18:40:43.281537 INFO::Found 3 batches.
2026-03-04 18:40:43.281711 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-04 18:40:43.28196 INFO::Using default BPPARAM
2026-03-04 18:40:43.282177 INFO::Processing subtree level 1
2026-03-04 18:40:43.370518 INFO::Adjusting the last 1 batches sequentially
2026-03-04 18:40:43.372053 INFO::Done
2026-03-04 18:40:43.372319 INFO::Acquiring quality metrics after batch effect correction.
2026-03-04 18:40:43.373839 INFO::ASW Batch was 0.0981469019081232 prior to batch effect correction and is now -0.148818852175336 .
2026-03-04 18:40:43.374068 INFO::ASW Label was -0.185733192176766 prior to batch effect correction and is now -0.0686006854299043 .
2026-03-04 18:40:43.374478 INFO::Total function execution time is 0.0971858501434326 s and adjustment time is 0.0905520915985107 s ( 93.17 )
2026-03-04 18:40:43.429838 INFO::Formatting Data.
2026-03-04 18:40:43.430205 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.430563 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.430992 INFO::Found 2 missing values.
2026-03-04 18:40:43.432341 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.432585 INFO::Done
2026-03-04 18:40:43.446796 INFO::Found NA in Reference column
2026-03-04 18:40:43.450992 INFO::Require at least two references per batch.
2026-03-04 18:40:43.459387 INFO::Formatting Data.
2026-03-04 18:40:43.459656 INFO::Recognized SummarizedExperiment
2026-03-04 18:40:43.459872 INFO::Typecasting input to dataframe.
2026-03-04 18:40:43.464137 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.464599 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.46601 INFO::Found 0 missing values.
2026-03-04 18:40:43.468618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.46884 INFO::Done
2026-03-04 18:40:43.475853 INFO::Formatting Data.
2026-03-04 18:40:43.476191 INFO::Recognized SummarizedExperiment
2026-03-04 18:40:43.476388 INFO::Typecasting input to dataframe.
2026-03-04 18:40:43.482678 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.483142 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.484566 INFO::Found 0 missing values.
2026-03-04 18:40:43.488844 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.489061 INFO::Done
2026-03-04 18:40:43.495098 INFO::Formatting Data.
2026-03-04 18:40:43.495366 INFO::Recognized SummarizedExperiment
2026-03-04 18:40:43.495559 INFO::Typecasting input to dataframe.
2026-03-04 18:40:43.501772 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.502169 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.502571 INFO::Found 0 missing values.
2026-03-04 18:40:43.502868 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.
2026-03-04 18:40:43.504299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.504473 INFO::Done
2026-03-04 18:40:43.508704 INFO::Formatting Data.
2026-03-04 18:40:43.508959 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.50925 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.509572 INFO::Found 0 missing values.
2026-03-04 18:40:43.510602 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.510786 INFO::Done
2026-03-04 18:40:43.523246 INFO::Formatting Data.
2026-03-04 18:40:43.523714 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.524176 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.524687 INFO::Found 0 missing values.
2026-03-04 18:40:43.525987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.526212 INFO::Done
2026-03-04 18:40:43.545154 INFO::Formatting Data.
2026-03-04 18:40:43.545681 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.546115 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.546614 INFO::Found 1 missing values.
2026-03-04 18:40:43.54755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.547741 INFO::Done
2026-03-04 18:40:43.556133 INFO::Formatting Data.
2026-03-04 18:40:43.556428 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.556739 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.557094 INFO::Found 2 missing values.
2026-03-04 18:40:43.557399 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.
2026-03-04 18:40:43.558224 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.55865 INFO::Done
2026-03-04 18:40:43.564501 INFO::Formatting Data.
2026-03-04 18:40:43.564815 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.565114 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.565462 INFO::Found 2 missing values.
2026-03-04 18:40:43.566277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.566448 INFO::Done
2026-03-04 18:40:43.573493 INFO::Formatting Data.
2026-03-04 18:40:43.573835 INFO::Typecasting input to dataframe.
2026-03-04 18:40:43.574149 INFO::Replacing NaNs with NAs.
2026-03-04 18:40:43.574476 INFO::Removing potential empty rows and columns
2026-03-04 18:40:43.574867 INFO::Found 0 missing values.
2026-03-04 18:40:43.575925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-04 18:40:43.576122 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.427 2.418 10.197
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.319 | 0.442 | 7.722 | |
| compute_asw | 0.010 | 0.000 | 0.012 | |
| count_existing | 0.006 | 0.000 | 0.006 | |
| generate_data_covariables | 0.004 | 0.001 | 0.005 | |
| generate_dataset | 0.005 | 0.001 | 0.005 | |