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This page was generated on 2026-03-26 11:57 -0400 (Thu, 26 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4893
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Package 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-03-25 13:45 -0400 (Wed, 25 Mar 2026)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_22
git_last_commit: 49dbe48
git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
See other builds for BERT in R Universe.

CHECK results for BERT on nebbiolo2

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.

raw results


Summary

Package: BERT
Version: 1.6.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
StartedAt: 2026-03-25 21:26:23 -0400 (Wed, 25 Mar 2026)
EndedAt: 2026-03-25 21:27:52 -0400 (Wed, 25 Mar 2026)
EllapsedTime: 89.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 23.976  1.323  17.322
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.6.0’
** 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)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # 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")
2026-03-25 21:27:14.928922 INFO::Formatting Data.
2026-03-25 21:27:14.930224 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:14.94108 INFO::Removing potential empty rows and columns
2026-03-25 21:27:15.174656 INFO::Found  0  missing values.
2026-03-25 21:27:15.17778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:15.178383 INFO::Done
2026-03-25 21:27:15.178892 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:15.189446 INFO::Starting hierarchical adjustment
2026-03-25 21:27:15.190294 INFO::Found  3  batches.
2026-03-25 21:27:15.190829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:15.191915 INFO::Using default BPPARAM
2026-03-25 21:27:15.192463 INFO::Processing subtree level 1
2026-03-25 21:27:15.286438 INFO::Adjusting the last 1 batches sequentially
2026-03-25 21:27:15.288095 INFO::Done
2026-03-25 21:27:15.288733 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:15.291146 INFO::ASW Batch was -0.113564097843151 prior to batch effect correction and is now -0.113564097843151 .
2026-03-25 21:27:15.292148 INFO::Total function execution time is  0.363879203796387  s and adjustment time is  0.0979726314544678 s ( 26.92 )
2026-03-25 21:27:15.305201 INFO::Formatting Data.
2026-03-25 21:27:15.305972 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:15.306958 INFO::Removing potential empty rows and columns
2026-03-25 21:27:15.308083 INFO::Found  0  missing values.
2026-03-25 21:27:15.309003 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.
2026-03-25 21:27:15.319467 INFO::Formatting Data.
2026-03-25 21:27:15.320194 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:15.321084 INFO::Removing potential empty rows and columns
2026-03-25 21:27:15.322133 INFO::Found  0  missing values.
2026-03-25 21:27:15.323065 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.
2026-03-25 21:27:15.338709 INFO::Formatting Data.
2026-03-25 21:27:15.339568 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:15.340539 INFO::Removing potential empty rows and columns
2026-03-25 21:27:15.341624 INFO::Found  0  missing values.
2026-03-25 21:27:15.342556 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.
2026-03-25 21:27:15.346969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:15.347559 INFO::Done
2026-03-25 21:27:15.348075 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:15.350012 INFO::Starting hierarchical adjustment
2026-03-25 21:27:15.350706 INFO::Found  2  batches.
2026-03-25 21:27:15.351212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:15.351837 INFO::Using default BPPARAM
2026-03-25 21:27:15.352354 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:15.353233 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-25 21:27:15.374081 INFO::Done
2026-03-25 21:27:15.374838 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:15.377065 INFO::ASW Batch was -0.037947982731896 prior to batch effect correction and is now -0.102469958436086 .
2026-03-25 21:27:15.378001 INFO::Total function execution time is  0.0393667221069336  s and adjustment time is  0.0234644412994385 s ( 59.6 )
2026-03-25 21:27:15.380972 INFO::Formatting Data.
2026-03-25 21:27:15.381645 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:15.39062 INFO::Formatting Data.
2026-03-25 21:27:15.391402 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:15.392315 INFO::Removing potential empty rows and columns
2026-03-25 21:27:15.393375 INFO::Found  0  missing values.
2026-03-25 21:27:15.396313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:15.396846 INFO::Done
2026-03-25 21:27:15.397381 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:15.420282 INFO::Starting hierarchical adjustment
2026-03-25 21:27:15.421492 INFO::Found  2  batches.
2026-03-25 21:27:15.422004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:15.422552 INFO::Using default BPPARAM
2026-03-25 21:27:15.423031 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:15.423859 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-25 21:27:15.437488 INFO::Done
2026-03-25 21:27:15.43813 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:15.440021 INFO::ASW Batch was 0.0670726976360395 prior to batch effect correction and is now -0.0579519450788674 .
2026-03-25 21:27:15.440746 INFO::Total function execution time is  0.0502030849456787  s and adjustment time is  0.0161423683166504 s ( 32.15 )
2026-03-25 21:27:15.441726 INFO::Formatting Data.
2026-03-25 21:27:15.442292 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:15.443078 INFO::Removing potential empty rows and columns
2026-03-25 21:27:15.444001 INFO::Found  0  missing values.
2026-03-25 21:27:15.446536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:15.447037 INFO::Done
2026-03-25 21:27:15.447522 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:15.449364 INFO::Starting hierarchical adjustment
2026-03-25 21:27:15.450005 INFO::Found  2  batches.
2026-03-25 21:27:15.45049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:15.451032 INFO::Using default BPPARAM
2026-03-25 21:27:15.451521 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:15.452347 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-25 21:27:15.465896 INFO::Done
2026-03-25 21:27:15.466561 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:15.468447 INFO::ASW Batch was 0.0670726976360395 prior to batch effect correction and is now -0.0579519450788674 .
2026-03-25 21:27:15.469191 INFO::Total function execution time is  0.0274536609649658  s and adjustment time is  0.0159842967987061 s ( 58.22 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-25 21:27:18.390206 INFO::Formatting Data.
2026-03-25 21:27:18.390973 INFO::Recognized SummarizedExperiment
2026-03-25 21:27:18.39151 INFO::Typecasting input to dataframe.
2026-03-25 21:27:18.421476 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:18.42273 INFO::Removing potential empty rows and columns
2026-03-25 21:27:18.426784 INFO::Found  0  missing values.
2026-03-25 21:27:18.433996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:18.434686 INFO::Done
2026-03-25 21:27:18.435219 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:18.438953 INFO::Starting hierarchical adjustment
2026-03-25 21:27:18.43971 INFO::Found  2  batches.
2026-03-25 21:27:18.440239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:18.44135 INFO::Using default BPPARAM
2026-03-25 21:27:18.441889 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:18.442871 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-25 21:27:18.500437 INFO::Done
2026-03-25 21:27:18.501182 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:18.504827 INFO::ASW Batch was -0.00887751013012381 prior to batch effect correction and is now -0.0965367908168156 .
2026-03-25 21:27:18.505745 INFO::Total function execution time is  0.115839242935181  s and adjustment time is  0.0608570575714111 s ( 52.54 )
Warning: stack imbalance in '{', 73 then 75
2026-03-25 21:27:18.525058 INFO::Formatting Data.
2026-03-25 21:27:18.525888 INFO::Recognized SummarizedExperiment
2026-03-25 21:27:18.526454 INFO::Typecasting input to dataframe.
2026-03-25 21:27:18.536387 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:18.537674 INFO::Removing potential empty rows and columns
2026-03-25 21:27:18.541406 INFO::Found  0  missing values.
2026-03-25 21:27:18.548641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:18.549363 INFO::Done
2026-03-25 21:27:18.549911 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:18.553755 INFO::Starting hierarchical adjustment
2026-03-25 21:27:18.554562 INFO::Found  2  batches.
2026-03-25 21:27:18.555094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:18.555699 INFO::Using default BPPARAM
2026-03-25 21:27:18.556214 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:18.557194 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-25 21:27:18.58253 INFO::Done
2026-03-25 21:27:18.583337 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:18.58707 INFO::ASW Batch was -0.010782087740358 prior to batch effect correction and is now -0.010782087740358 .
2026-03-25 21:27:18.587998 INFO::Total function execution time is  0.0629327297210693  s and adjustment time is  0.0280702114105225 s ( 44.6 )
2026-03-25 21:27:18.607749 INFO::Formatting Data.
2026-03-25 21:27:18.608597 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:18.609535 INFO::Removing potential empty rows and columns
2026-03-25 21:27:18.610592 INFO::Found  0  missing values.
2026-03-25 21:27:18.613582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:18.614133 INFO::Done
2026-03-25 21:27:18.61466 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:18.616736 INFO::Starting hierarchical adjustment
2026-03-25 21:27:18.617441 INFO::Found  3  batches.
2026-03-25 21:27:18.617963 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:18.618572 INFO::Using default BPPARAM
2026-03-25 21:27:18.619079 INFO::Processing subtree level 1
2026-03-25 21:27:18.75125 INFO::Adjusting the last 1 batches sequentially
2026-03-25 21:27:18.753034 INFO::Done
2026-03-25 21:27:18.753692 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:18.75636 INFO::ASW Batch was -0.0633325281855142 prior to batch effect correction and is now -0.167958454187476 .
2026-03-25 21:27:18.757287 INFO::Total function execution time is  0.149889945983887  s and adjustment time is  0.135725021362305 s ( 90.55 )
2026-03-25 21:27:18.771693 INFO::Skipping initial DF formatting
2026-03-25 21:27:18.772414 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:18.776435 INFO::Starting hierarchical adjustment
2026-03-25 21:27:18.777228 INFO::Found  5  batches.
2026-03-25 21:27:18.777779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:18.778395 INFO::Using default BPPARAM
2026-03-25 21:27:18.778933 INFO::Processing subtree level 1
2026-03-25 21:27:19.0283 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:19.030354 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-25 21:27:19.051474 INFO::Done
2026-03-25 21:27:19.052341 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:19.057133 INFO::ASW Batch was 0.507388776869142 prior to batch effect correction and is now 0.507388776869142 .
2026-03-25 21:27:19.057859 INFO::ASW Label was 0.394686661268207 prior to batch effect correction and is now 0.394686661268207 .
2026-03-25 21:27:19.058835 INFO::Total function execution time is  0.287175416946411  s and adjustment time is  0.27434778213501 s ( 95.53 )
2026-03-25 21:27:19.18199 INFO::Formatting Data.
2026-03-25 21:27:19.183189 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:19.184311 INFO::Removing potential empty rows and columns
2026-03-25 21:27:19.185515 INFO::Found  0  missing values.
2026-03-25 21:27:19.189974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:19.190596 INFO::Done
2026-03-25 21:27:19.191143 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:19.194482 INFO::Starting hierarchical adjustment
2026-03-25 21:27:19.195297 INFO::Found  5  batches.
2026-03-25 21:27:19.195845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:19.196504 INFO::Using default BPPARAM
2026-03-25 21:27:19.197042 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.

2026-03-25 21:27:19.35007 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:19.352048 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-25 21:27:19.370234 INFO::Done
2026-03-25 21:27:19.371021 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:19.374744 INFO::ASW Batch was 0.484204855272931 prior to batch effect correction and is now -0.0674068539091455 .
2026-03-25 21:27:19.375438 INFO::ASW Label was 0.211939486845964 prior to batch effect correction and is now 0.845971857477116 .
2026-03-25 21:27:19.376317 INFO::Total function execution time is  0.194467544555664  s and adjustment time is  0.175083160400391 s ( 90.03 )
2026-03-25 21:27:19.377258 INFO::Formatting Data.
2026-03-25 21:27:19.377907 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:19.378952 INFO::Removing potential empty rows and columns
2026-03-25 21:27:19.380048 INFO::Found  0  missing values.
2026-03-25 21:27:19.384559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:19.385178 INFO::Done
2026-03-25 21:27:19.385739 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:19.388972 INFO::Starting hierarchical adjustment
2026-03-25 21:27:19.389753 INFO::Found  5  batches.
2026-03-25 21:27:19.390285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:19.39093 INFO::Using default BPPARAM
2026-03-25 21:27:19.39152 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.

2026-03-25 21:27:19.522801 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:19.524621 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-25 21:27:19.54341 INFO::Done
2026-03-25 21:27:19.544228 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:19.547932 INFO::ASW Batch was 0.484204855272931 prior to batch effect correction and is now -0.0674068539091455 .
2026-03-25 21:27:19.548631 INFO::ASW Label was 0.211939486845964 prior to batch effect correction and is now 0.845971857477116 .
2026-03-25 21:27:19.549596 INFO::Total function execution time is  0.172325611114502  s and adjustment time is  0.153773307800293 s ( 89.23 )
2026-03-25 21:27:19.565303 INFO::Formatting Data.
2026-03-25 21:27:19.566128 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:19.567113 INFO::Removing potential empty rows and columns
2026-03-25 21:27:19.56819 INFO::Found  0  missing values.
2026-03-25 21:27:19.572451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:19.573068 INFO::Done
2026-03-25 21:27:19.573655 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:19.57694 INFO::Starting hierarchical adjustment
2026-03-25 21:27:19.577812 INFO::Found  5  batches.
2026-03-25 21:27:19.578447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:19.579181 INFO::Using default BPPARAM
2026-03-25 21:27:19.579734 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.

2026-03-25 21:27:19.711094 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:19.712888 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-25 21:27:19.730093 INFO::Done
2026-03-25 21:27:19.730955 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:19.734674 INFO::ASW Batch was 0.370716227642519 prior to batch effect correction and is now -0.0897174692581621 .
2026-03-25 21:27:19.735362 INFO::ASW Label was 0.336792840452985 prior to batch effect correction and is now 0.888530461254082 .
2026-03-25 21:27:19.736258 INFO::Total function execution time is  0.171037435531616  s and adjustment time is  0.15240216255188 s ( 89.1 )
2026-03-25 21:27:19.737158 INFO::Formatting Data.
2026-03-25 21:27:19.737835 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:19.738781 INFO::Removing potential empty rows and columns
2026-03-25 21:27:19.739866 INFO::Found  0  missing values.
2026-03-25 21:27:19.744333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:19.745131 INFO::Done
2026-03-25 21:27:19.745805 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:19.749175 INFO::Starting hierarchical adjustment
2026-03-25 21:27:19.74997 INFO::Found  5  batches.
2026-03-25 21:27:19.750563 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:19.751235 INFO::Using default BPPARAM
2026-03-25 21:27:19.751818 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.

2026-03-25 21:27:19.880516 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:19.882227 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-25 21:27:19.899048 INFO::Done
2026-03-25 21:27:19.899916 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:19.903185 INFO::ASW Batch was 0.370716227642519 prior to batch effect correction and is now -0.0897174692581621 .
2026-03-25 21:27:19.903783 INFO::ASW Label was 0.336792840452985 prior to batch effect correction and is now 0.888530461254082 .
2026-03-25 21:27:19.904589 INFO::Total function execution time is  0.167438268661499  s and adjustment time is  0.149179458618164 s ( 89.1 )
2026-03-25 21:27:19.917728 INFO::Formatting Data.
2026-03-25 21:27:19.918483 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:19.9194 INFO::Removing potential empty rows and columns
2026-03-25 21:27:19.920419 INFO::Found  0  missing values.
2026-03-25 21:27:19.923049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:19.923586 INFO::Done
2026-03-25 21:27:19.924103 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:19.926953 INFO::Starting hierarchical adjustment
2026-03-25 21:27:19.92767 INFO::Found  2  batches.
2026-03-25 21:27:19.92819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:19.928805 INFO::Using default BPPARAM
2026-03-25 21:27:19.929332 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:19.930205 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-25 21:27:19.944232 INFO::Done
2026-03-25 21:27:19.944867 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:19.947662 INFO::ASW Batch was 0.437537399547402 prior to batch effect correction and is now 0.0338491604027562 .
2026-03-25 21:27:19.948223 INFO::ASW Label was 0.649601514294398 prior to batch effect correction and is now 0.902793004596177 .
2026-03-25 21:27:19.948956 INFO::Total function execution time is  0.0313074588775635  s and adjustment time is  0.0166997909545898 s ( 53.34 )
2026-03-25 21:27:19.949706 INFO::Formatting Data.
2026-03-25 21:27:19.950306 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:19.951119 INFO::Removing potential empty rows and columns
2026-03-25 21:27:19.95206 INFO::Found  0  missing values.
2026-03-25 21:27:19.954564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:19.955098 INFO::Done
2026-03-25 21:27:19.955609 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:19.958331 INFO::Starting hierarchical adjustment
2026-03-25 21:27:19.958997 INFO::Found  2  batches.
2026-03-25 21:27:19.959512 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:19.960083 INFO::Using default BPPARAM
2026-03-25 21:27:19.960591 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:19.961462 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-25 21:27:19.975199 INFO::Done
2026-03-25 21:27:19.975844 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:19.978604 INFO::ASW Batch was 0.437537399547402 prior to batch effect correction and is now 0.0338491604027562 .
2026-03-25 21:27:19.97918 INFO::ASW Label was 0.649601514294398 prior to batch effect correction and is now 0.902793004596177 .
2026-03-25 21:27:19.979912 INFO::Total function execution time is  0.0302176475524902  s and adjustment time is  0.0163233280181885 s ( 54.02 )
2026-03-25 21:27:19.990696 INFO::Formatting Data.
2026-03-25 21:27:19.991415 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:19.992232 INFO::Removing potential empty rows and columns
2026-03-25 21:27:19.993172 INFO::Found  0  missing values.
2026-03-25 21:27:19.995191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:19.995708 INFO::Done
2026-03-25 21:27:19.996199 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:19.998013 INFO::Starting hierarchical adjustment
2026-03-25 21:27:19.998682 INFO::Found  2  batches.
2026-03-25 21:27:19.999187 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:19.999771 INFO::Using default BPPARAM
2026-03-25 21:27:20.00028 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:20.001107 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-25 21:27:20.030504 INFO::Done
2026-03-25 21:27:20.031158 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:20.033017 INFO::ASW Batch was -0.0976266560457427 prior to batch effect correction and is now -0.194922924056628 .
2026-03-25 21:27:20.033787 INFO::Total function execution time is  0.0431632995605469  s and adjustment time is  0.031930685043335 s ( 73.98 )
2026-03-25 21:27:20.045078 INFO::Formatting Data.
2026-03-25 21:27:20.045809 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:20.046741 INFO::Removing potential empty rows and columns
2026-03-25 21:27:20.047715 INFO::Found  0  missing values.
2026-03-25 21:27:20.048829 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.
2026-03-25 21:27:20.053157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:20.053692 INFO::Done
2026-03-25 21:27:20.054177 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:20.056929 INFO::Starting hierarchical adjustment
2026-03-25 21:27:20.057605 INFO::Found  2  batches.
2026-03-25 21:27:20.058104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:20.058682 INFO::Using default BPPARAM
2026-03-25 21:27:20.059163 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:20.060032 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-25 21:27:20.075491 INFO::Done
2026-03-25 21:27:20.076124 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:20.078865 INFO::ASW Batch was 0.354231668933677 prior to batch effect correction and is now 0.0631263787276241 .
2026-03-25 21:27:20.079426 INFO::ASW Label was 0.71458061911608 prior to batch effect correction and is now 0.881495142259908 .
2026-03-25 21:27:20.080141 INFO::Total function execution time is  0.0351624488830566  s and adjustment time is  0.0179972648620605 s ( 51.18 )
2026-03-25 21:27:20.080881 INFO::Formatting Data.
2026-03-25 21:27:20.081453 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:20.082304 INFO::Removing potential empty rows and columns
2026-03-25 21:27:20.083215 INFO::Found  0  missing values.
2026-03-25 21:27:20.084064 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.
2026-03-25 21:27:20.088229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:20.088768 INFO::Done
2026-03-25 21:27:20.089251 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:20.092014 INFO::Starting hierarchical adjustment
2026-03-25 21:27:20.092701 INFO::Found  2  batches.
2026-03-25 21:27:20.093212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:20.093792 INFO::Using default BPPARAM
2026-03-25 21:27:20.094283 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:20.095156 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-25 21:27:20.119841 INFO::Done
2026-03-25 21:27:20.120711 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:20.123838 INFO::ASW Batch was 0.354231668933677 prior to batch effect correction and is now 0.0631263787276241 .
2026-03-25 21:27:20.124454 INFO::ASW Label was 0.71458061911608 prior to batch effect correction and is now 0.881495142259908 .
2026-03-25 21:27:20.125244 INFO::Total function execution time is  0.0443496704101562  s and adjustment time is  0.0270991325378418 s ( 61.1 )
2026-03-25 21:27:20.33069 INFO::Formatting Data.
2026-03-25 21:27:20.331482 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:20.332441 INFO::Removing potential empty rows and columns
2026-03-25 21:27:20.333505 INFO::Found  0  missing values.
2026-03-25 21:27:20.33651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:20.337042 INFO::Done
2026-03-25 21:27:20.337573 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:20.339555 INFO::Starting hierarchical adjustment
2026-03-25 21:27:20.340236 INFO::Found  3  batches.
2026-03-25 21:27:20.34078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:20.341464 INFO::Using default BPPARAM
2026-03-25 21:27:20.342002 INFO::Processing subtree level 1
2026-03-25 21:27:20.433933 INFO::Adjusting the last 1 batches sequentially
2026-03-25 21:27:20.435932 INFO::Done
2026-03-25 21:27:20.436662 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:20.439376 INFO::ASW Batch was -0.0176451659708502 prior to batch effect correction and is now -0.0176451659708502 .
2026-03-25 21:27:20.440429 INFO::Total function execution time is  0.109710931777954  s and adjustment time is  0.0957834720611572 s ( 87.31 )
2026-03-25 21:27:20.441631 INFO::Formatting Data.
2026-03-25 21:27:20.442344 INFO::Typecasting input to dataframe.
2026-03-25 21:27:20.443158 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:20.44415 INFO::Removing potential empty rows and columns
2026-03-25 21:27:20.445335 INFO::Found  0  missing values.
2026-03-25 21:27:20.448624 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:20.449196 INFO::Done
2026-03-25 21:27:20.44975 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:20.451943 INFO::Starting hierarchical adjustment
2026-03-25 21:27:20.452694 INFO::Found  3  batches.
2026-03-25 21:27:20.453228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:20.45469 INFO::Using default BPPARAM
2026-03-25 21:27:20.455561 INFO::Processing subtree level 1
2026-03-25 21:27:20.541144 INFO::Adjusting the last 1 batches sequentially
2026-03-25 21:27:20.543138 INFO::Done
2026-03-25 21:27:20.543882 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:20.546564 INFO::ASW Batch was -0.0176451659708502 prior to batch effect correction and is now -0.0176451659708502 .
2026-03-25 21:27:20.547588 INFO::Total function execution time is  0.105952501296997  s and adjustment time is  0.090576171875 s ( 85.49 )
2026-03-25 21:27:20.562318 INFO::Formatting Data.
2026-03-25 21:27:20.563269 INFO::Typecasting input to dataframe.
2026-03-25 21:27:20.564197 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:20.565184 INFO::Removing potential empty rows and columns
2026-03-25 21:27:20.566325 INFO::Found  0  missing values.
2026-03-25 21:27:20.569366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:20.569922 INFO::Done
2026-03-25 21:27:20.570461 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:20.572654 INFO::Starting hierarchical adjustment
2026-03-25 21:27:20.573383 INFO::Found  3  batches.
2026-03-25 21:27:20.573919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:20.574566 INFO::Using default BPPARAM
2026-03-25 21:27:20.575099 INFO::Processing subtree level 1
2026-03-25 21:27:20.661485 INFO::Adjusting the last 1 batches sequentially
2026-03-25 21:27:20.663554 INFO::Done
2026-03-25 21:27:20.664333 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:20.667178 INFO::ASW Batch was -0.139575915597126 prior to batch effect correction and is now -0.139575915597126 .
2026-03-25 21:27:20.668216 INFO::Total function execution time is  0.106041193008423  s and adjustment time is  0.0902941226959229 s ( 85.15 )
2026-03-25 21:27:20.814057 INFO::Formatting Data.
2026-03-25 21:27:20.814926 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:20.816066 INFO::Removing potential empty rows and columns
2026-03-25 21:27:20.818883 INFO::Found  1000  missing values.
2026-03-25 21:27:20.838658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:20.839583 INFO::Done
2026-03-25 21:27:20.840222 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:20.846059 INFO::Starting hierarchical adjustment
2026-03-25 21:27:20.846902 INFO::Found  10  batches.
2026-03-25 21:27:20.847509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:20.848144 INFO::Using default BPPARAM
2026-03-25 21:27:20.848706 INFO::Processing subtree level 1
2026-03-25 21:27:20.988904 INFO::Processing subtree level 2
2026-03-25 21:27:21.133516 INFO::Adjusting the last 1 batches sequentially
2026-03-25 21:27:21.13569 INFO::Done
2026-03-25 21:27:21.136434 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:21.142402 INFO::ASW Batch was 0.449538402887416 prior to batch effect correction and is now 0.449538402887416 .
2026-03-25 21:27:21.143125 INFO::ASW Label was 0.365056267188337 prior to batch effect correction and is now 0.365056267188337 .
2026-03-25 21:27:21.144124 INFO::Total function execution time is  0.330113887786865  s and adjustment time is  0.288935422897339 s ( 87.53 )
2026-03-25 21:27:21.145063 INFO::Formatting Data.
2026-03-25 21:27:21.145746 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:21.147198 INFO::Removing potential empty rows and columns
2026-03-25 21:27:21.150076 INFO::Found  1000  missing values.
2026-03-25 21:27:21.169748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:21.170596 INFO::Done
2026-03-25 21:27:21.17117 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:21.176939 INFO::Starting hierarchical adjustment
2026-03-25 21:27:21.177784 INFO::Found  10  batches.
2026-03-25 21:27:22.579299 INFO::Set up parallel execution backend with 2 workers
2026-03-25 21:27:22.581161 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-25 21:27:23.950341 INFO::Adjusting the last 2 batches sequentially
2026-03-25 21:27:23.952083 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-25 21:27:23.968347 INFO::Done
2026-03-25 21:27:23.968978 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:23.97357 INFO::ASW Batch was 0.449538402887416 prior to batch effect correction and is now 0.449538402887416 .
2026-03-25 21:27:23.974147 INFO::ASW Label was 0.365056267188337 prior to batch effect correction and is now 0.365056267188337 .
2026-03-25 21:27:23.974868 INFO::Total function execution time is  2.82985210418701  s and adjustment time is  2.79071617126465 s ( 98.62 )
2026-03-25 21:27:24.112433 INFO::Formatting Data.
2026-03-25 21:27:24.113237 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.114147 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.115193 INFO::Found  0  missing values.
2026-03-25 21:27:24.11869 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.119222 INFO::Done
2026-03-25 21:27:24.119727 INFO::Acquiring quality metrics before batch effect correction.
2026-03-25 21:27:24.122371 INFO::Starting hierarchical adjustment
2026-03-25 21:27:24.123041 INFO::Found  3  batches.
2026-03-25 21:27:24.12355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-25 21:27:24.124124 INFO::Using default BPPARAM
2026-03-25 21:27:24.124628 INFO::Processing subtree level 1
2026-03-25 21:27:24.225053 INFO::Adjusting the last 1 batches sequentially
2026-03-25 21:27:24.226848 INFO::Done
2026-03-25 21:27:24.227513 INFO::Acquiring quality metrics after batch effect correction.
2026-03-25 21:27:24.230615 INFO::ASW Batch was 0.164746937196035 prior to batch effect correction and is now -0.135353873569583 .
2026-03-25 21:27:24.231225 INFO::ASW Label was -0.155989283825996 prior to batch effect correction and is now -0.0616546022294573 .
2026-03-25 21:27:24.232118 INFO::Total function execution time is  0.119754552841187  s and adjustment time is  0.103914260864258 s ( 86.77 )
2026-03-25 21:27:24.349673 INFO::Formatting Data.
2026-03-25 21:27:24.350514 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.351446 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.352483 INFO::Found  2  missing values.
2026-03-25 21:27:24.35524 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.35577 INFO::Done
2026-03-25 21:27:24.382615 INFO::Found NA in Reference column
2026-03-25 21:27:24.391894 INFO::Require at least two references per batch.
2026-03-25 21:27:24.41156 INFO::Formatting Data.
2026-03-25 21:27:24.412314 INFO::Recognized SummarizedExperiment
2026-03-25 21:27:24.41283 INFO::Typecasting input to dataframe.
2026-03-25 21:27:24.422229 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.42343 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.426727 INFO::Found  0  missing values.
2026-03-25 21:27:24.433214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.433823 INFO::Done
2026-03-25 21:27:24.450183 INFO::Formatting Data.
2026-03-25 21:27:24.451043 INFO::Recognized SummarizedExperiment
2026-03-25 21:27:24.451604 INFO::Typecasting input to dataframe.
2026-03-25 21:27:24.469374 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.470654 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.474138 INFO::Found  0  missing values.
2026-03-25 21:27:24.484629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.485336 INFO::Done
2026-03-25 21:27:24.501356 INFO::Formatting Data.
2026-03-25 21:27:24.502179 INFO::Recognized SummarizedExperiment
2026-03-25 21:27:24.502747 INFO::Typecasting input to dataframe.
2026-03-25 21:27:24.519464 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.520555 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.521686 INFO::Found  0  missing values.
2026-03-25 21:27:24.531812 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.
2026-03-25 21:27:24.536961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.537681 INFO::Done
2026-03-25 21:27:24.549347 INFO::Formatting Data.
2026-03-25 21:27:24.550194 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.551141 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.552291 INFO::Found  0  missing values.
2026-03-25 21:27:24.555316 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.555871 INFO::Done
2026-03-25 21:27:24.56847 INFO::Formatting Data.
2026-03-25 21:27:24.56941 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.570496 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.571622 INFO::Found  0  missing values.
2026-03-25 21:27:24.57462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.575171 INFO::Done
2026-03-25 21:27:24.608204 INFO::Formatting Data.
2026-03-25 21:27:24.609344 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.610559 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.611807 INFO::Found  1  missing values.
2026-03-25 21:27:24.614701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.615257 INFO::Done
2026-03-25 21:27:24.636881 INFO::Formatting Data.
2026-03-25 21:27:24.637824 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.638818 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.639933 INFO::Found  2  missing values.
2026-03-25 21:27:24.640982 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.
2026-03-25 21:27:24.643494 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.644061 INFO::Done
2026-03-25 21:27:24.655228 INFO::Formatting Data.
2026-03-25 21:27:24.656106 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.657049 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.657985 INFO::Found  2  missing values.
2026-03-25 21:27:24.659716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.66025 INFO::Done
2026-03-25 21:27:24.671396 INFO::Formatting Data.
2026-03-25 21:27:24.672263 INFO::Typecasting input to dataframe.
2026-03-25 21:27:24.673149 INFO::Replacing NaNs with NAs.
2026-03-25 21:27:24.674049 INFO::Removing potential empty rows and columns
2026-03-25 21:27:24.675119 INFO::Found  0  missing values.
2026-03-25 21:27:24.678138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-25 21:27:24.678718 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.196   4.154  21.109

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT23.976 1.32317.322
compute_asw0.0230.0020.025
count_existing0.0140.0000.013
generate_data_covariables0.0110.0010.012
generate_dataset0.0120.0000.011