Yannis Schumann
| Snapshot Date: 2026-01-15 13:40 -0500 (Thu, 15 Jan 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 2026-01-16 11:11 -0500 (Fri, 16 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4849 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4628 |
| 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 168/2343 | 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 | | ||||||||
|
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: 2026-01-15 18:43:59 -0500 (Thu, 15 Jan 2026) |
| EndedAt: 2026-01-15 18:44:37 -0500 (Thu, 15 Jan 2026) |
| EllapsedTime: 37.6 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) (2025-11-04 r88984)
* 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 13.7.8
* 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 10.487 0.425 7.815
* 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) (2025-11-04 r88984) -- "Unsuffered Consequences"
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")
2026-01-15 18:44:27.52268 INFO::Formatting Data.
2026-01-15 18:44:27.525552 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:27.530785 INFO::Removing potential empty rows and columns
2026-01-15 18:44:27.643051 INFO::Found 0 missing values.
2026-01-15 18:44:27.644406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:27.64465 INFO::Done
2026-01-15 18:44:27.644839 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:27.653688 INFO::Starting hierarchical adjustment
2026-01-15 18:44:27.654114 INFO::Found 3 batches.
2026-01-15 18:44:27.654375 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:27.654907 INFO::Using default BPPARAM
2026-01-15 18:44:27.655156 INFO::Processing subtree level 1
2026-01-15 18:44:27.715845 INFO::Adjusting the last 1 batches sequentially
2026-01-15 18:44:27.717642 INFO::Done
2026-01-15 18:44:27.717877 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:27.719521 INFO::ASW Batch was -0.0262786255839067 prior to batch effect correction and is now -0.0262786255839067 .
2026-01-15 18:44:27.720048 INFO::Total function execution time is 0.197968006134033 s and adjustment time is 0.0636129379272461 s ( 32.13 )
2026-01-15 18:44:27.729633 INFO::Formatting Data.
2026-01-15 18:44:27.729977 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:27.730383 INFO::Removing potential empty rows and columns
2026-01-15 18:44:27.731017 INFO::Found 0 missing values.
2026-01-15 18:44:27.731568 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.
2026-01-15 18:44:27.737184 INFO::Formatting Data.
2026-01-15 18:44:27.737557 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:27.738171 INFO::Removing potential empty rows and columns
2026-01-15 18:44:27.738645 INFO::Found 0 missing values.
2026-01-15 18:44:27.739515 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.
2026-01-15 18:44:27.74808 INFO::Formatting Data.
2026-01-15 18:44:27.748447 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:27.748815 INFO::Removing potential empty rows and columns
2026-01-15 18:44:27.749297 INFO::Found 0 missing values.
2026-01-15 18:44:27.749678 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.
2026-01-15 18:44:27.758165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:27.758428 INFO::Done
2026-01-15 18:44:27.758675 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:27.759583 INFO::Starting hierarchical adjustment
2026-01-15 18:44:27.759859 INFO::Found 2 batches.
2026-01-15 18:44:27.760064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:27.760315 INFO::Using default BPPARAM
2026-01-15 18:44:27.760536 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:27.760827 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-15 18:44:27.779134 INFO::Done
2026-01-15 18:44:27.779635 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:27.780904 INFO::ASW Batch was 0.0225992486916594 prior to batch effect correction and is now -0.12630277143784 .
2026-01-15 18:44:27.781223 INFO::Total function execution time is 0.0332059860229492 s and adjustment time is 0.0192780494689941 s ( 58.06 )
2026-01-15 18:44:27.782625 INFO::Formatting Data.
2026-01-15 18:44:27.782882 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:27.786313 INFO::Formatting Data.
2026-01-15 18:44:27.786553 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:27.786853 INFO::Removing potential empty rows and columns
2026-01-15 18:44:27.787273 INFO::Found 0 missing values.
2026-01-15 18:44:27.7883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:27.788481 INFO::Done
2026-01-15 18:44:27.788644 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:27.789336 INFO::Starting hierarchical adjustment
2026-01-15 18:44:27.789558 INFO::Found 2 batches.
2026-01-15 18:44:27.789742 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:27.789944 INFO::Using default BPPARAM
2026-01-15 18:44:27.790096 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:27.790365 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-15 18:44:27.816077 INFO::Done
2026-01-15 18:44:27.81635 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:27.817103 INFO::ASW Batch was 0.023881230840154 prior to batch effect correction and is now -0.129619078642227 .
2026-01-15 18:44:27.817445 INFO::Total function execution time is 0.0311229228973389 s and adjustment time is 0.0265400409698486 s ( 85.27 )
2026-01-15 18:44:27.822346 INFO::Formatting Data.
2026-01-15 18:44:27.822597 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:27.822988 INFO::Removing potential empty rows and columns
2026-01-15 18:44:27.823354 INFO::Found 0 missing values.
2026-01-15 18:44:27.824532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:27.824762 INFO::Done
2026-01-15 18:44:27.824988 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:27.825868 INFO::Starting hierarchical adjustment
2026-01-15 18:44:27.826161 INFO::Found 2 batches.
2026-01-15 18:44:27.826368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:27.826609 INFO::Using default BPPARAM
2026-01-15 18:44:27.826808 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:27.827154 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-15 18:44:27.833758 INFO::Done
2026-01-15 18:44:27.834039 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:27.834916 INFO::ASW Batch was 0.023881230840154 prior to batch effect correction and is now -0.129619078642227 .
2026-01-15 18:44:27.835247 INFO::Total function execution time is 0.0129330158233643 s and adjustment time is 0.00765204429626465 s ( 59.17 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-15 18:44:29.112367 INFO::Formatting Data.
2026-01-15 18:44:29.112673 INFO::Recognized SummarizedExperiment
2026-01-15 18:44:29.112844 INFO::Typecasting input to dataframe.
2026-01-15 18:44:29.124126 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.124615 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.125916 INFO::Found 0 missing values.
2026-01-15 18:44:29.12821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.12839 INFO::Done
2026-01-15 18:44:29.128548 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.129745 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.129964 INFO::Found 2 batches.
2026-01-15 18:44:29.130117 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.130436 INFO::Using default BPPARAM
2026-01-15 18:44:29.130588 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.130869 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-15 18:44:29.155415 INFO::Done
2026-01-15 18:44:29.155686 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.156946 INFO::ASW Batch was 0.0268682422925833 prior to batch effect correction and is now -0.0892868198767819 .
2026-01-15 18:44:29.157243 INFO::Total function execution time is 0.0450010299682617 s and adjustment time is 0.0254771709442139 s ( 56.61 )
Warning: stack imbalance in '{', 73 then 75
2026-01-15 18:44:29.164791 INFO::Formatting Data.
2026-01-15 18:44:29.165041 INFO::Recognized SummarizedExperiment
2026-01-15 18:44:29.165207 INFO::Typecasting input to dataframe.
2026-01-15 18:44:29.168262 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.168626 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.169771 INFO::Found 0 missing values.
2026-01-15 18:44:29.171909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.172072 INFO::Done
2026-01-15 18:44:29.172221 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.173444 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.173655 INFO::Found 2 batches.
2026-01-15 18:44:29.173806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.173991 INFO::Using default BPPARAM
2026-01-15 18:44:29.174136 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.174421 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-15 18:44:29.182514 INFO::Done
2026-01-15 18:44:29.182755 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.184062 INFO::ASW Batch was -0.0177144590848827 prior to batch effect correction and is now -0.0177144590848827 .
2026-01-15 18:44:29.184397 INFO::Total function execution time is 0.0195989608764648 s and adjustment time is 0.0088951587677002 s ( 45.39 )
2026-01-15 18:44:29.194037 INFO::Formatting Data.
2026-01-15 18:44:29.194305 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.194599 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.19494 INFO::Found 0 missing values.
2026-01-15 18:44:29.19592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.196133 INFO::Done
2026-01-15 18:44:29.196332 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.19707 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.197326 INFO::Found 3 batches.
2026-01-15 18:44:29.197518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.197745 INFO::Using default BPPARAM
2026-01-15 18:44:29.197967 INFO::Processing subtree level 1
2026-01-15 18:44:29.269514 INFO::Adjusting the last 1 batches sequentially
2026-01-15 18:44:29.271728 INFO::Done
2026-01-15 18:44:29.27209 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.274243 INFO::ASW Batch was -0.0759710033426238 prior to batch effect correction and is now -0.164950908280896 .
2026-01-15 18:44:29.274918 INFO::Total function execution time is 0.0807490348815918 s and adjustment time is 0.0744509696960449 s ( 92.2 )
2026-01-15 18:44:29.282348 INFO::Skipping initial DF formatting
2026-01-15 18:44:29.282581 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.283952 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.284205 INFO::Found 5 batches.
2026-01-15 18:44:29.284383 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.284909 INFO::Using default BPPARAM
2026-01-15 18:44:29.285069 INFO::Processing subtree level 1
2026-01-15 18:44:29.410629 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.413831 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-15 18:44:29.428553 INFO::Done
2026-01-15 18:44:29.42918 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.467396 INFO::ASW Batch was 0.524483567031251 prior to batch effect correction and is now 0.524483567031251 .
2026-01-15 18:44:29.4677 INFO::ASW Label was 0.367303774183557 prior to batch effect correction and is now 0.367303774183557 .
2026-01-15 18:44:29.468086 INFO::Total function execution time is 0.185760974884033 s and adjustment time is 0.144382953643799 s ( 77.73 )
2026-01-15 18:44:29.479186 INFO::Formatting Data.
2026-01-15 18:44:29.479634 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.480101 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.480641 INFO::Found 0 missing values.
2026-01-15 18:44:29.482748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.483058 INFO::Done
2026-01-15 18:44:29.483301 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.484712 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.485168 INFO::Found 5 batches.
2026-01-15 18:44:29.485394 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.48573 INFO::Using default BPPARAM
2026-01-15 18:44:29.48596 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.
2026-01-15 18:44:29.569038 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.571559 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-15 18:44:29.584473 INFO::Done
2026-01-15 18:44:29.58491 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.587167 INFO::ASW Batch was 0.412436214818877 prior to batch effect correction and is now -0.0841189704254662 .
2026-01-15 18:44:29.587522 INFO::ASW Label was 0.245385336181221 prior to batch effect correction and is now 0.895669187783139 .
2026-01-15 18:44:29.588038 INFO::Total function execution time is 0.108824014663696 s and adjustment time is 0.0993640422821045 s ( 91.31 )
2026-01-15 18:44:29.588655 INFO::Formatting Data.
2026-01-15 18:44:29.588995 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.589689 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.590278 INFO::Found 0 missing values.
2026-01-15 18:44:29.592411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.592714 INFO::Done
2026-01-15 18:44:29.592966 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.594411 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.594763 INFO::Found 5 batches.
2026-01-15 18:44:29.595035 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.595363 INFO::Using default BPPARAM
2026-01-15 18:44:29.595745 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.
2026-01-15 18:44:29.671362 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.673865 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-15 18:44:29.684936 INFO::Done
2026-01-15 18:44:29.685484 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.687302 INFO::ASW Batch was 0.412436214818877 prior to batch effect correction and is now -0.0841189704254662 .
2026-01-15 18:44:29.687593 INFO::ASW Label was 0.245385336181221 prior to batch effect correction and is now 0.895669187783139 .
2026-01-15 18:44:29.688049 INFO::Total function execution time is 0.0993521213531494 s and adjustment time is 0.0902369022369385 s ( 90.83 )
2026-01-15 18:44:29.697647 INFO::Formatting Data.
2026-01-15 18:44:29.698123 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.69864 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.699156 INFO::Found 0 missing values.
2026-01-15 18:44:29.701074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.701294 INFO::Done
2026-01-15 18:44:29.701534 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.702781 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.703074 INFO::Found 5 batches.
2026-01-15 18:44:29.703265 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.703546 INFO::Using default BPPARAM
2026-01-15 18:44:29.70376 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.
2026-01-15 18:44:29.792961 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.797846 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-15 18:44:29.810877 INFO::Done
2026-01-15 18:44:29.811353 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.81319 INFO::ASW Batch was 0.314296753441752 prior to batch effect correction and is now -0.0909544683203391 .
2026-01-15 18:44:29.813457 INFO::ASW Label was 0.393558534704423 prior to batch effect correction and is now 0.887415756919958 .
2026-01-15 18:44:29.81497 INFO::Total function execution time is 0.117202997207642 s and adjustment time is 0.107836008071899 s ( 92.01 )
2026-01-15 18:44:29.81541 INFO::Formatting Data.
2026-01-15 18:44:29.815699 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.816297 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.816829 INFO::Found 0 missing values.
2026-01-15 18:44:29.818876 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.819204 INFO::Done
2026-01-15 18:44:29.819432 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.820769 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.821059 INFO::Found 5 batches.
2026-01-15 18:44:29.821264 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.821544 INFO::Using default BPPARAM
2026-01-15 18:44:29.821741 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.
2026-01-15 18:44:29.903671 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.906519 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-15 18:44:29.924254 INFO::Done
2026-01-15 18:44:29.924942 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.926892 INFO::ASW Batch was 0.314296753441752 prior to batch effect correction and is now -0.0909544683203391 .
2026-01-15 18:44:29.927134 INFO::ASW Label was 0.393558534704423 prior to batch effect correction and is now 0.887415756919958 .
2026-01-15 18:44:29.927635 INFO::Total function execution time is 0.112198829650879 s and adjustment time is 0.103176832199097 s ( 91.96 )
2026-01-15 18:44:29.935998 INFO::Formatting Data.
2026-01-15 18:44:29.936302 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.936671 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.937115 INFO::Found 0 missing values.
2026-01-15 18:44:29.938256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.938486 INFO::Done
2026-01-15 18:44:29.938684 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.939949 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.940247 INFO::Found 2 batches.
2026-01-15 18:44:29.940439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.940737 INFO::Using default BPPARAM
2026-01-15 18:44:29.94096 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.941306 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-15 18:44:29.947386 INFO::Done
2026-01-15 18:44:29.94763 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.948651 INFO::ASW Batch was 0.74120083862655 prior to batch effect correction and is now 0.0712323650658725 .
2026-01-15 18:44:29.9489 INFO::ASW Label was 0.348166774442653 prior to batch effect correction and is now 0.82627054670961 .
2026-01-15 18:44:29.949205 INFO::Total function execution time is 0.0132479667663574 s and adjustment time is 0.00719094276428223 s ( 54.28 )
2026-01-15 18:44:29.949452 INFO::Formatting Data.
2026-01-15 18:44:29.951233 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.951728 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.952172 INFO::Found 0 missing values.
2026-01-15 18:44:29.953188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.953389 INFO::Done
2026-01-15 18:44:29.953591 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.954706 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.954976 INFO::Found 2 batches.
2026-01-15 18:44:29.955168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.955391 INFO::Using default BPPARAM
2026-01-15 18:44:29.955545 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.955826 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-15 18:44:29.961706 INFO::Done
2026-01-15 18:44:29.961941 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.962919 INFO::ASW Batch was 0.74120083862655 prior to batch effect correction and is now 0.0712323650658725 .
2026-01-15 18:44:29.963121 INFO::ASW Label was 0.348166774442653 prior to batch effect correction and is now 0.82627054670961 .
2026-01-15 18:44:29.963374 INFO::Total function execution time is 0.0139169692993164 s and adjustment time is 0.00676894187927246 s ( 48.64 )
2026-01-15 18:44:29.967942 INFO::Formatting Data.
2026-01-15 18:44:29.968167 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.968437 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.968737 INFO::Found 0 missing values.
2026-01-15 18:44:29.969407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.969582 INFO::Done
2026-01-15 18:44:29.969733 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.970337 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.970558 INFO::Found 2 batches.
2026-01-15 18:44:29.97071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.970912 INFO::Using default BPPARAM
2026-01-15 18:44:29.971064 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.971384 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-15 18:44:29.984121 INFO::Done
2026-01-15 18:44:29.984345 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:29.98497 INFO::ASW Batch was -0.130614964829268 prior to batch effect correction and is now -0.159557121545303 .
2026-01-15 18:44:29.985272 INFO::Total function execution time is 0.0173449516296387 s and adjustment time is 0.0135939121246338 s ( 78.37 )
2026-01-15 18:44:29.990407 INFO::Formatting Data.
2026-01-15 18:44:29.990658 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:29.990967 INFO::Removing potential empty rows and columns
2026-01-15 18:44:29.991339 INFO::Found 0 missing values.
2026-01-15 18:44:29.991774 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.
2026-01-15 18:44:29.993326 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:29.993514 INFO::Done
2026-01-15 18:44:29.993695 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:29.994735 INFO::Starting hierarchical adjustment
2026-01-15 18:44:29.994977 INFO::Found 2 batches.
2026-01-15 18:44:29.995163 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:29.995366 INFO::Using default BPPARAM
2026-01-15 18:44:29.99553 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:29.99583 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-15 18:44:30.001211 INFO::Done
2026-01-15 18:44:30.001421 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:30.002291 INFO::ASW Batch was 0.804241078351893 prior to batch effect correction and is now 0.151277151757732 .
2026-01-15 18:44:30.002473 INFO::ASW Label was 0.245317951064883 prior to batch effect correction and is now 0.73312380027117 .
2026-01-15 18:44:30.002705 INFO::Total function execution time is 0.0123341083526611 s and adjustment time is 0.00627589225769043 s ( 50.88 )
2026-01-15 18:44:30.002929 INFO::Formatting Data.
2026-01-15 18:44:30.003094 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:30.003352 INFO::Removing potential empty rows and columns
2026-01-15 18:44:30.003636 INFO::Found 0 missing values.
2026-01-15 18:44:30.003877 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.
2026-01-15 18:44:30.005171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:30.005338 INFO::Done
2026-01-15 18:44:30.005489 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:30.006369 INFO::Starting hierarchical adjustment
2026-01-15 18:44:30.006605 INFO::Found 2 batches.
2026-01-15 18:44:30.006766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:30.006953 INFO::Using default BPPARAM
2026-01-15 18:44:30.010946 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:30.011292 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-15 18:44:30.01757 INFO::Done
2026-01-15 18:44:30.01778 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:30.018682 INFO::ASW Batch was 0.804241078351893 prior to batch effect correction and is now 0.151277151757732 .
2026-01-15 18:44:30.018903 INFO::ASW Label was 0.245317951064883 prior to batch effect correction and is now 0.73312380027117 .
2026-01-15 18:44:30.019173 INFO::Total function execution time is 0.0162379741668701 s and adjustment time is 0.010998010635376 s ( 67.73 )
2026-01-15 18:44:30.086934 INFO::Formatting Data.
2026-01-15 18:44:30.087205 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:30.087495 INFO::Removing potential empty rows and columns
2026-01-15 18:44:30.087813 INFO::Found 0 missing values.
2026-01-15 18:44:30.088688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:30.08885 INFO::Done
2026-01-15 18:44:30.089005 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:30.089645 INFO::Starting hierarchical adjustment
2026-01-15 18:44:30.089855 INFO::Found 3 batches.
2026-01-15 18:44:30.090003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:30.090184 INFO::Using default BPPARAM
2026-01-15 18:44:30.09033 INFO::Processing subtree level 1
2026-01-15 18:44:30.144788 INFO::Adjusting the last 1 batches sequentially
2026-01-15 18:44:30.149396 INFO::Done
2026-01-15 18:44:30.149747 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:30.151796 INFO::ASW Batch was 0.00573775384426573 prior to batch effect correction and is now 0.00573775384426573 .
2026-01-15 18:44:30.152683 INFO::Total function execution time is 0.0656349658966064 s and adjustment time is 0.059553861618042 s ( 90.73 )
2026-01-15 18:44:30.153037 INFO::Formatting Data.
2026-01-15 18:44:30.153236 INFO::Typecasting input to dataframe.
2026-01-15 18:44:30.153462 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:30.153759 INFO::Removing potential empty rows and columns
2026-01-15 18:44:30.154129 INFO::Found 0 missing values.
2026-01-15 18:44:30.155038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:30.155204 INFO::Done
2026-01-15 18:44:30.15537 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:30.156015 INFO::Starting hierarchical adjustment
2026-01-15 18:44:30.156531 INFO::Found 3 batches.
2026-01-15 18:44:30.1567 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:30.157243 INFO::Using default BPPARAM
2026-01-15 18:44:30.157409 INFO::Processing subtree level 1
2026-01-15 18:44:30.205674 INFO::Adjusting the last 1 batches sequentially
2026-01-15 18:44:30.208104 INFO::Done
2026-01-15 18:44:30.208544 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:30.210999 INFO::ASW Batch was 0.00573775384426573 prior to batch effect correction and is now 0.00573775384426573 .
2026-01-15 18:44:30.211694 INFO::Total function execution time is 0.0586168766021729 s and adjustment time is 0.0515949726104736 s ( 88.02 )
2026-01-15 18:44:30.219762 INFO::Formatting Data.
2026-01-15 18:44:30.22003 INFO::Typecasting input to dataframe.
2026-01-15 18:44:30.220329 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:30.220666 INFO::Removing potential empty rows and columns
2026-01-15 18:44:30.221106 INFO::Found 0 missing values.
2026-01-15 18:44:30.222001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:30.222179 INFO::Done
2026-01-15 18:44:30.222346 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:30.223029 INFO::Starting hierarchical adjustment
2026-01-15 18:44:30.223273 INFO::Found 3 batches.
2026-01-15 18:44:30.223439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:30.224104 INFO::Using default BPPARAM
2026-01-15 18:44:30.224265 INFO::Processing subtree level 1
2026-01-15 18:44:30.276014 INFO::Adjusting the last 1 batches sequentially
2026-01-15 18:44:30.278096 INFO::Done
2026-01-15 18:44:30.278686 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:30.280967 INFO::ASW Batch was -0.116358902232072 prior to batch effect correction and is now -0.116358902232072 .
2026-01-15 18:44:30.282014 INFO::Total function execution time is 0.0620839595794678 s and adjustment time is 0.0548520088195801 s ( 88.35 )
2026-01-15 18:44:30.359064 INFO::Formatting Data.
2026-01-15 18:44:30.359341 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:30.359747 INFO::Removing potential empty rows and columns
2026-01-15 18:44:30.360783 INFO::Found 1000 missing values.
2026-01-15 18:44:30.368943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:30.369295 INFO::Done
2026-01-15 18:44:30.369589 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:30.372286 INFO::Starting hierarchical adjustment
2026-01-15 18:44:30.372638 INFO::Found 10 batches.
2026-01-15 18:44:30.372872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:30.373178 INFO::Using default BPPARAM
2026-01-15 18:44:30.373366 INFO::Processing subtree level 1
2026-01-15 18:44:30.464176 INFO::Processing subtree level 2
2026-01-15 18:44:30.566213 INFO::Adjusting the last 1 batches sequentially
2026-01-15 18:44:30.574282 INFO::Done
2026-01-15 18:44:30.57453 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:30.577648 INFO::ASW Batch was 0.496806124193921 prior to batch effect correction and is now 0.496806124193921 .
2026-01-15 18:44:30.577925 INFO::ASW Label was 0.30895034556337 prior to batch effect correction and is now 0.30895034556337 .
2026-01-15 18:44:30.57836 INFO::Total function execution time is 0.219312906265259 s and adjustment time is 0.201688051223755 s ( 91.96 )
2026-01-15 18:44:30.57867 INFO::Formatting Data.
2026-01-15 18:44:30.578858 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:30.5793 INFO::Removing potential empty rows and columns
2026-01-15 18:44:30.580528 INFO::Found 1000 missing values.
2026-01-15 18:44:30.587034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:30.587456 INFO::Done
2026-01-15 18:44:30.587672 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:30.593463 INFO::Starting hierarchical adjustment
2026-01-15 18:44:30.593931 INFO::Found 10 batches.
2026-01-15 18:44:31.101467 INFO::Set up parallel execution backend with 2 workers
2026-01-15 18:44:31.101803 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-15 18:44:31.69638 INFO::Adjusting the last 2 batches sequentially
2026-01-15 18:44:31.697011 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-15 18:44:31.703541 INFO::Done
2026-01-15 18:44:31.70386 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:31.706257 INFO::ASW Batch was 0.496806124193921 prior to batch effect correction and is now 0.496806124193921 .
2026-01-15 18:44:31.706462 INFO::ASW Label was 0.30895034556337 prior to batch effect correction and is now 0.30895034556337 .
2026-01-15 18:44:31.706819 INFO::Total function execution time is 1.12812995910645 s and adjustment time is 1.10967683792114 s ( 98.36 )
2026-01-15 18:44:31.796504 INFO::Formatting Data.
2026-01-15 18:44:31.796846 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:31.797234 INFO::Removing potential empty rows and columns
2026-01-15 18:44:31.797739 INFO::Found 0 missing values.
2026-01-15 18:44:31.799061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:31.799243 INFO::Done
2026-01-15 18:44:31.799419 INFO::Acquiring quality metrics before batch effect correction.
2026-01-15 18:44:31.800403 INFO::Starting hierarchical adjustment
2026-01-15 18:44:31.800666 INFO::Found 3 batches.
2026-01-15 18:44:31.800854 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-15 18:44:31.801344 INFO::Using default BPPARAM
2026-01-15 18:44:31.801551 INFO::Processing subtree level 1
2026-01-15 18:44:31.868548 INFO::Adjusting the last 1 batches sequentially
2026-01-15 18:44:31.871718 INFO::Done
2026-01-15 18:44:31.872399 INFO::Acquiring quality metrics after batch effect correction.
2026-01-15 18:44:31.876118 INFO::ASW Batch was 0.116931501339359 prior to batch effect correction and is now -0.145928146528315 .
2026-01-15 18:44:31.876948 INFO::ASW Label was -0.182107576737876 prior to batch effect correction and is now -0.00166504697241748 .
2026-01-15 18:44:31.87756 INFO::Total function execution time is 0.0810630321502686 s and adjustment time is 0.0710759162902832 s ( 87.68 )
2026-01-15 18:44:31.941515 INFO::Formatting Data.
2026-01-15 18:44:31.941924 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:31.942361 INFO::Removing potential empty rows and columns
2026-01-15 18:44:31.942863 INFO::Found 2 missing values.
2026-01-15 18:44:31.944003 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:31.944215 INFO::Done
2026-01-15 18:44:31.964785 INFO::Found NA in Reference column
2026-01-15 18:44:31.971946 INFO::Require at least two references per batch.
2026-01-15 18:44:31.988498 INFO::Formatting Data.
2026-01-15 18:44:31.988863 INFO::Recognized SummarizedExperiment
2026-01-15 18:44:31.989059 INFO::Typecasting input to dataframe.
2026-01-15 18:44:31.993345 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:31.993786 INFO::Removing potential empty rows and columns
2026-01-15 18:44:31.995374 INFO::Found 0 missing values.
2026-01-15 18:44:31.998225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:31.998449 INFO::Done
2026-01-15 18:44:32.012952 INFO::Formatting Data.
2026-01-15 18:44:32.013265 INFO::Recognized SummarizedExperiment
2026-01-15 18:44:32.013448 INFO::Typecasting input to dataframe.
2026-01-15 18:44:32.020037 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:32.020458 INFO::Removing potential empty rows and columns
2026-01-15 18:44:32.021884 INFO::Found 0 missing values.
2026-01-15 18:44:32.025782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:32.025971 INFO::Done
2026-01-15 18:44:32.031397 INFO::Formatting Data.
2026-01-15 18:44:32.031625 INFO::Recognized SummarizedExperiment
2026-01-15 18:44:32.031788 INFO::Typecasting input to dataframe.
2026-01-15 18:44:32.03688 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:32.037221 INFO::Removing potential empty rows and columns
2026-01-15 18:44:32.037558 INFO::Found 0 missing values.
2026-01-15 18:44:32.037836 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.
2026-01-15 18:44:32.039185 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:32.039351 INFO::Done
2026-01-15 18:44:32.043646 INFO::Formatting Data.
2026-01-15 18:44:32.043871 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:32.044163 INFO::Removing potential empty rows and columns
2026-01-15 18:44:32.044461 INFO::Found 0 missing values.
2026-01-15 18:44:32.045319 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:32.045492 INFO::Done
2026-01-15 18:44:32.051041 INFO::Formatting Data.
2026-01-15 18:44:32.051359 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:32.05175 INFO::Removing potential empty rows and columns
2026-01-15 18:44:32.052123 INFO::Found 0 missing values.
2026-01-15 18:44:32.053181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:32.053378 INFO::Done
2026-01-15 18:44:32.066789 INFO::Formatting Data.
2026-01-15 18:44:32.0672 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:32.067751 INFO::Removing potential empty rows and columns
2026-01-15 18:44:32.068309 INFO::Found 1 missing values.
2026-01-15 18:44:32.069231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:32.069483 INFO::Done
2026-01-15 18:44:32.079241 INFO::Formatting Data.
2026-01-15 18:44:32.079531 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:32.079872 INFO::Removing potential empty rows and columns
2026-01-15 18:44:32.080205 INFO::Found 2 missing values.
2026-01-15 18:44:32.080537 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.
2026-01-15 18:44:32.081368 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:32.081583 INFO::Done
2026-01-15 18:44:32.085822 INFO::Formatting Data.
2026-01-15 18:44:32.086109 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:32.086429 INFO::Removing potential empty rows and columns
2026-01-15 18:44:32.086745 INFO::Found 2 missing values.
2026-01-15 18:44:32.087317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:32.087484 INFO::Done
2026-01-15 18:44:32.09214 INFO::Formatting Data.
2026-01-15 18:44:32.092385 INFO::Typecasting input to dataframe.
2026-01-15 18:44:32.092636 INFO::Replacing NaNs with NAs.
2026-01-15 18:44:32.092897 INFO::Removing potential empty rows and columns
2026-01-15 18:44:32.093218 INFO::Found 0 missing values.
2026-01-15 18:44:32.094096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-15 18:44:32.094255 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.389 1.909 9.897
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.487 | 0.425 | 7.815 | |
| compute_asw | 0.010 | 0.001 | 0.011 | |
| count_existing | 0.005 | 0.000 | 0.006 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.005 | 0.000 | 0.005 | |