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This page was generated on 2026-03-24 11:57 -0400 (Tue, 24 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: 2026-03-23 13:45 -0400 (Mon, 23 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: 2026-03-23 21:21:55 -0400 (Mon, 23 Mar 2026)
EndedAt: 2026-03-23 21:23:25 -0400 (Mon, 23 Mar 2026)
EllapsedTime: 90.1 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 24.04.3 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 23.868  1.629  17.906
* 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")
2026-03-23 21:22:47.080766 INFO::Formatting Data.
2026-03-23 21:22:47.082053 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:47.093104 INFO::Removing potential empty rows and columns
2026-03-23 21:22:47.337306 INFO::Found  0  missing values.
2026-03-23 21:22:47.340661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:47.341282 INFO::Done
2026-03-23 21:22:47.341828 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:47.352722 INFO::Starting hierarchical adjustment
2026-03-23 21:22:47.353585 INFO::Found  3  batches.
2026-03-23 21:22:47.354131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:47.355264 INFO::Using default BPPARAM
2026-03-23 21:22:47.355845 INFO::Processing subtree level 1
2026-03-23 21:22:47.45524 INFO::Adjusting the last 1 batches sequentially
2026-03-23 21:22:47.456995 INFO::Done
2026-03-23 21:22:47.457651 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:47.460159 INFO::ASW Batch was -0.032448843044917 prior to batch effect correction and is now -0.032448843044917 .
2026-03-23 21:22:47.46121 INFO::Total function execution time is  0.381117582321167  s and adjustment time is  0.103606700897217 s ( 27.18 )
2026-03-23 21:22:47.475042 INFO::Formatting Data.
2026-03-23 21:22:47.475895 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:47.47686 INFO::Removing potential empty rows and columns
2026-03-23 21:22:47.477995 INFO::Found  0  missing values.
2026-03-23 21:22:47.478965 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.
2026-03-23 21:22:47.490365 INFO::Formatting Data.
2026-03-23 21:22:47.491139 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:47.492091 INFO::Removing potential empty rows and columns
2026-03-23 21:22:47.49321 INFO::Found  0  missing values.
2026-03-23 21:22:47.49419 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.
2026-03-23 21:22:47.51143 INFO::Formatting Data.
2026-03-23 21:22:47.512238 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:47.513209 INFO::Removing potential empty rows and columns
2026-03-23 21:22:47.514307 INFO::Found  0  missing values.
2026-03-23 21:22:47.515255 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.
2026-03-23 21:22:47.519885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:47.520447 INFO::Done
2026-03-23 21:22:47.520988 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:47.523103 INFO::Starting hierarchical adjustment
2026-03-23 21:22:47.523848 INFO::Found  2  batches.
2026-03-23 21:22:47.524388 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:47.525055 INFO::Using default BPPARAM
2026-03-23 21:22:47.525608 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:47.526546 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-23 21:22:47.547955 INFO::Done
2026-03-23 21:22:47.54864 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:47.550777 INFO::ASW Batch was -0.0168209150223576 prior to batch effect correction and is now -0.106139731337918 .
2026-03-23 21:22:47.551694 INFO::Total function execution time is  0.0403382778167725  s and adjustment time is  0.024254322052002 s ( 60.13 )
2026-03-23 21:22:47.554618 INFO::Formatting Data.
2026-03-23 21:22:47.555255 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:47.564479 INFO::Formatting Data.
2026-03-23 21:22:47.565266 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:47.566235 INFO::Removing potential empty rows and columns
2026-03-23 21:22:47.567374 INFO::Found  0  missing values.
2026-03-23 21:22:47.570339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:47.570887 INFO::Done
2026-03-23 21:22:47.571421 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:47.597523 INFO::Starting hierarchical adjustment
2026-03-23 21:22:47.598913 INFO::Found  2  batches.
2026-03-23 21:22:47.599445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:47.600019 INFO::Using default BPPARAM
2026-03-23 21:22:47.600504 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:47.601393 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-23 21:22:47.615255 INFO::Done
2026-03-23 21:22:47.615852 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:47.617743 INFO::ASW Batch was -0.0319042257755275 prior to batch effect correction and is now -0.114395996763715 .
2026-03-23 21:22:47.618447 INFO::Total function execution time is  0.0540344715118408  s and adjustment time is  0.0165164470672607 s ( 30.57 )
2026-03-23 21:22:47.619411 INFO::Formatting Data.
2026-03-23 21:22:47.619993 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:47.620804 INFO::Removing potential empty rows and columns
2026-03-23 21:22:47.62174 INFO::Found  0  missing values.
2026-03-23 21:22:47.624268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:47.624779 INFO::Done
2026-03-23 21:22:47.625262 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:47.627105 INFO::Starting hierarchical adjustment
2026-03-23 21:22:47.627759 INFO::Found  2  batches.
2026-03-23 21:22:47.628229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:47.628789 INFO::Using default BPPARAM
2026-03-23 21:22:47.629271 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:47.630097 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-23 21:22:47.643879 INFO::Done
2026-03-23 21:22:47.644463 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:47.646358 INFO::ASW Batch was -0.0319042257755275 prior to batch effect correction and is now -0.114395996763715 .
2026-03-23 21:22:47.64709 INFO::Total function execution time is  0.0276727676391602  s and adjustment time is  0.016244649887085 s ( 58.7 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-23 21:22:50.4336 INFO::Formatting Data.
2026-03-23 21:22:50.434277 INFO::Recognized SummarizedExperiment
2026-03-23 21:22:50.434765 INFO::Typecasting input to dataframe.
2026-03-23 21:22:50.463561 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:50.464966 INFO::Removing potential empty rows and columns
2026-03-23 21:22:50.468785 INFO::Found  0  missing values.
2026-03-23 21:22:50.475952 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:50.47659 INFO::Done
2026-03-23 21:22:50.477115 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:50.480905 INFO::Starting hierarchical adjustment
2026-03-23 21:22:50.481656 INFO::Found  2  batches.
2026-03-23 21:22:50.482192 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:50.483329 INFO::Using default BPPARAM
2026-03-23 21:22:50.483883 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:50.484891 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-23 21:22:50.542052 INFO::Done
2026-03-23 21:22:50.542818 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:50.546519 INFO::ASW Batch was 0.00478943879446726 prior to batch effect correction and is now -0.0873591651049719 .
2026-03-23 21:22:50.547416 INFO::Total function execution time is  0.114092588424683  s and adjustment time is  0.0605275630950928 s ( 53.05 )
Warning: stack imbalance in '{', 73 then 75
2026-03-23 21:22:50.567575 INFO::Formatting Data.
2026-03-23 21:22:50.568417 INFO::Recognized SummarizedExperiment
2026-03-23 21:22:50.568989 INFO::Typecasting input to dataframe.
2026-03-23 21:22:50.578982 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:50.580288 INFO::Removing potential empty rows and columns
2026-03-23 21:22:50.584233 INFO::Found  0  missing values.
2026-03-23 21:22:50.591683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:50.592414 INFO::Done
2026-03-23 21:22:50.592971 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:50.596646 INFO::Starting hierarchical adjustment
2026-03-23 21:22:50.597423 INFO::Found  2  batches.
2026-03-23 21:22:50.597963 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:50.598572 INFO::Using default BPPARAM
2026-03-23 21:22:50.599098 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:50.600118 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-23 21:22:50.62556 INFO::Done
2026-03-23 21:22:50.626338 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:50.630283 INFO::ASW Batch was 0.00769306799308624 prior to batch effect correction and is now 0.00769306799308624 .
2026-03-23 21:22:50.631176 INFO::Total function execution time is  0.0636355876922607  s and adjustment time is  0.0282332897186279 s ( 44.37 )
2026-03-23 21:22:50.650061 INFO::Formatting Data.
2026-03-23 21:22:50.650965 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:50.651902 INFO::Removing potential empty rows and columns
2026-03-23 21:22:50.652962 INFO::Found  0  missing values.
2026-03-23 21:22:50.655985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:50.65661 INFO::Done
2026-03-23 21:22:50.65715 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:50.659228 INFO::Starting hierarchical adjustment
2026-03-23 21:22:50.659951 INFO::Found  3  batches.
2026-03-23 21:22:50.660473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:50.661098 INFO::Using default BPPARAM
2026-03-23 21:22:50.661624 INFO::Processing subtree level 1
2026-03-23 21:22:50.802496 INFO::Adjusting the last 1 batches sequentially
2026-03-23 21:22:50.804555 INFO::Done
2026-03-23 21:22:50.805343 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:50.808107 INFO::ASW Batch was -0.12865241665406 prior to batch effect correction and is now -0.195024175512771 .
2026-03-23 21:22:50.809148 INFO::Total function execution time is  0.15911340713501  s and adjustment time is  0.144718885421753 s ( 90.95 )
2026-03-23 21:22:50.824416 INFO::Skipping initial DF formatting
2026-03-23 21:22:50.82517 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:50.829288 INFO::Starting hierarchical adjustment
2026-03-23 21:22:50.830145 INFO::Found  5  batches.
2026-03-23 21:22:50.830723 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:50.831363 INFO::Using default BPPARAM
2026-03-23 21:22:50.831931 INFO::Processing subtree level 1
2026-03-23 21:22:51.074811 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:51.076835 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-23 21:22:51.098763 INFO::Done
2026-03-23 21:22:51.099746 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:51.104694 INFO::ASW Batch was 0.47124111675466 prior to batch effect correction and is now 0.47124111675466 .
2026-03-23 21:22:51.105395 INFO::ASW Label was 0.416691241260024 prior to batch effect correction and is now 0.416691241260024 .
2026-03-23 21:22:51.106648 INFO::Total function execution time is  0.281993627548218  s and adjustment time is  0.268698930740356 s ( 95.29 )
2026-03-23 21:22:51.184312 INFO::Formatting Data.
2026-03-23 21:22:51.185246 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:51.186291 INFO::Removing potential empty rows and columns
2026-03-23 21:22:51.18739 INFO::Found  0  missing values.
2026-03-23 21:22:51.191627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:51.192186 INFO::Done
2026-03-23 21:22:51.192716 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:51.196068 INFO::Starting hierarchical adjustment
2026-03-23 21:22:51.196833 INFO::Found  5  batches.
2026-03-23 21:22:51.197353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:51.197996 INFO::Using default BPPARAM
2026-03-23 21:22:51.19855 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.

2026-03-23 21:22:51.362295 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:51.364206 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-23 21:22:51.382721 INFO::Done
2026-03-23 21:22:51.383523 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:51.387492 INFO::ASW Batch was 0.553570164987083 prior to batch effect correction and is now -0.0666762093884153 .
2026-03-23 21:22:51.388209 INFO::ASW Label was 0.168213803156432 prior to batch effect correction and is now 0.714675911029906 .
2026-03-23 21:22:51.389116 INFO::Total function execution time is  0.204947471618652  s and adjustment time is  0.185980319976807 s ( 90.75 )
2026-03-23 21:22:51.390051 INFO::Formatting Data.
2026-03-23 21:22:51.390718 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:51.391685 INFO::Removing potential empty rows and columns
2026-03-23 21:22:51.392792 INFO::Found  0  missing values.
2026-03-23 21:22:51.397275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:51.397913 INFO::Done
2026-03-23 21:22:51.398514 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:51.401772 INFO::Starting hierarchical adjustment
2026-03-23 21:22:51.402485 INFO::Found  5  batches.
2026-03-23 21:22:51.403039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:51.403665 INFO::Using default BPPARAM
2026-03-23 21:22:51.404203 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.

2026-03-23 21:22:51.550297 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:51.552943 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-23 21:22:51.574373 INFO::Done
2026-03-23 21:22:51.575228 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:51.578818 INFO::ASW Batch was 0.553570164987083 prior to batch effect correction and is now -0.0666762093884153 .
2026-03-23 21:22:51.579518 INFO::ASW Label was 0.168213803156432 prior to batch effect correction and is now 0.714675911029906 .
2026-03-23 21:22:51.580383 INFO::Total function execution time is  0.190358400344849  s and adjustment time is  0.17197322845459 s ( 90.34 )
2026-03-23 21:22:51.595384 INFO::Formatting Data.
2026-03-23 21:22:51.596203 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:51.597116 INFO::Removing potential empty rows and columns
2026-03-23 21:22:51.598132 INFO::Found  0  missing values.
2026-03-23 21:22:51.602587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:51.603167 INFO::Done
2026-03-23 21:22:51.603717 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:51.607167 INFO::Starting hierarchical adjustment
2026-03-23 21:22:51.607936 INFO::Found  5  batches.
2026-03-23 21:22:51.608458 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:51.60911 INFO::Using default BPPARAM
2026-03-23 21:22:51.609665 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.

2026-03-23 21:22:51.749398 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:51.751232 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-23 21:22:51.76863 INFO::Done
2026-03-23 21:22:51.769498 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:51.773325 INFO::ASW Batch was 0.43067363153677 prior to batch effect correction and is now -0.0521631156852606 .
2026-03-23 21:22:51.773991 INFO::ASW Label was 0.321528350165625 prior to batch effect correction and is now 0.812247226242703 .
2026-03-23 21:22:51.774871 INFO::Total function execution time is  0.179535388946533  s and adjustment time is  0.160766839981079 s ( 89.55 )
2026-03-23 21:22:51.775828 INFO::Formatting Data.
2026-03-23 21:22:51.776531 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:51.777467 INFO::Removing potential empty rows and columns
2026-03-23 21:22:51.778565 INFO::Found  0  missing values.
2026-03-23 21:22:51.782847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:51.783408 INFO::Done
2026-03-23 21:22:51.783968 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:51.78722 INFO::Starting hierarchical adjustment
2026-03-23 21:22:51.78802 INFO::Found  5  batches.
2026-03-23 21:22:51.788603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:51.789256 INFO::Using default BPPARAM
2026-03-23 21:22:51.789819 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.

2026-03-23 21:22:51.938812 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:51.940935 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-23 21:22:51.961585 INFO::Done
2026-03-23 21:22:51.962545 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:51.967088 INFO::ASW Batch was 0.43067363153677 prior to batch effect correction and is now -0.0521631156852606 .
2026-03-23 21:22:51.96801 INFO::ASW Label was 0.321528350165625 prior to batch effect correction and is now 0.812247226242703 .
2026-03-23 21:22:51.969211 INFO::Total function execution time is  0.193298578262329  s and adjustment time is  0.173663854598999 s ( 89.84 )
2026-03-23 21:22:51.98735 INFO::Formatting Data.
2026-03-23 21:22:51.988331 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:51.989481 INFO::Removing potential empty rows and columns
2026-03-23 21:22:51.990777 INFO::Found  0  missing values.
2026-03-23 21:22:51.994076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:51.994717 INFO::Done
2026-03-23 21:22:51.995317 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:51.999167 INFO::Starting hierarchical adjustment
2026-03-23 21:22:52.000035 INFO::Found  2  batches.
2026-03-23 21:22:52.000659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:52.00136 INFO::Using default BPPARAM
2026-03-23 21:22:52.001966 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:52.003054 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-23 21:22:52.02065 INFO::Done
2026-03-23 21:22:52.021439 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:52.024907 INFO::ASW Batch was 0.494276718034787 prior to batch effect correction and is now 0.200958840173783 .
2026-03-23 21:22:52.025598 INFO::ASW Label was 0.648718517372673 prior to batch effect correction and is now 0.77379170408608 .
2026-03-23 21:22:52.026459 INFO::Total function execution time is  0.039323091506958  s and adjustment time is  0.0207407474517822 s ( 52.74 )
2026-03-23 21:22:52.027327 INFO::Formatting Data.
2026-03-23 21:22:52.028007 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:52.028973 INFO::Removing potential empty rows and columns
2026-03-23 21:22:52.030076 INFO::Found  0  missing values.
2026-03-23 21:22:52.033072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:52.033658 INFO::Done
2026-03-23 21:22:52.03421 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:52.03761 INFO::Starting hierarchical adjustment
2026-03-23 21:22:52.0384 INFO::Found  2  batches.
2026-03-23 21:22:52.03898 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:52.039616 INFO::Using default BPPARAM
2026-03-23 21:22:52.040171 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:52.041162 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-23 21:22:52.057721 INFO::Done
2026-03-23 21:22:52.058496 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:52.061883 INFO::ASW Batch was 0.494276718034787 prior to batch effect correction and is now 0.200958840173783 .
2026-03-23 21:22:52.062545 INFO::ASW Label was 0.648718517372673 prior to batch effect correction and is now 0.77379170408608 .
2026-03-23 21:22:52.0634 INFO::Total function execution time is  0.0360944271087646  s and adjustment time is  0.0194301605224609 s ( 53.83 )
2026-03-23 21:22:52.076245 INFO::Formatting Data.
2026-03-23 21:22:52.077164 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:52.078205 INFO::Removing potential empty rows and columns
2026-03-23 21:22:52.079235 INFO::Found  0  missing values.
2026-03-23 21:22:52.081611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:52.082205 INFO::Done
2026-03-23 21:22:52.082788 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:52.085136 INFO::Starting hierarchical adjustment
2026-03-23 21:22:52.085942 INFO::Found  2  batches.
2026-03-23 21:22:52.086523 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:52.087198 INFO::Using default BPPARAM
2026-03-23 21:22:52.087781 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:52.088796 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-23 21:22:52.126088 INFO::Done
2026-03-23 21:22:52.126973 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:52.129514 INFO::ASW Batch was 0.273860831160569 prior to batch effect correction and is now -0.159818528371203 .
2026-03-23 21:22:52.130529 INFO::Total function execution time is  0.0544257164001465  s and adjustment time is  0.0402379035949707 s ( 73.93 )
2026-03-23 21:22:52.145473 INFO::Formatting Data.
2026-03-23 21:22:52.146541 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:52.147667 INFO::Removing potential empty rows and columns
2026-03-23 21:22:52.148876 INFO::Found  0  missing values.
2026-03-23 21:22:52.1503 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.
2026-03-23 21:22:52.155643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:52.156252 INFO::Done
2026-03-23 21:22:52.156842 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:52.160586 INFO::Starting hierarchical adjustment
2026-03-23 21:22:52.1614 INFO::Found  2  batches.
2026-03-23 21:22:52.161993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:52.162667 INFO::Using default BPPARAM
2026-03-23 21:22:52.163225 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:52.164258 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-23 21:22:52.183313 INFO::Done
2026-03-23 21:22:52.184096 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:52.18739 INFO::ASW Batch was 0.250422654972371 prior to batch effect correction and is now -0.0365580290679165 .
2026-03-23 21:22:52.18805 INFO::ASW Label was 0.782354342276227 prior to batch effect correction and is now 0.945207665633134 .
2026-03-23 21:22:52.188912 INFO::Total function execution time is  0.0436563491821289  s and adjustment time is  0.0220386981964111 s ( 50.48 )
2026-03-23 21:22:52.189769 INFO::Formatting Data.
2026-03-23 21:22:52.190414 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:52.191429 INFO::Removing potential empty rows and columns
2026-03-23 21:22:52.192502 INFO::Found  0  missing values.
2026-03-23 21:22:52.193483 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.
2026-03-23 21:22:52.198297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:52.198874 INFO::Done
2026-03-23 21:22:52.199408 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:52.202565 INFO::Starting hierarchical adjustment
2026-03-23 21:22:52.203298 INFO::Found  2  batches.
2026-03-23 21:22:52.203852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:52.204461 INFO::Using default BPPARAM
2026-03-23 21:22:52.205001 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:52.205956 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-23 21:22:52.226536 INFO::Done
2026-03-23 21:22:52.227357 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:52.230599 INFO::ASW Batch was 0.250422654972371 prior to batch effect correction and is now -0.0365580290679165 .
2026-03-23 21:22:52.231238 INFO::ASW Label was 0.782354342276227 prior to batch effect correction and is now 0.945207665633134 .
2026-03-23 21:22:52.232126 INFO::Total function execution time is  0.0423679351806641  s and adjustment time is  0.0233190059661865 s ( 55.04 )
2026-03-23 21:22:52.475045 INFO::Formatting Data.
2026-03-23 21:22:52.476245 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:52.477459 INFO::Removing potential empty rows and columns
2026-03-23 21:22:52.478807 INFO::Found  0  missing values.
2026-03-23 21:22:52.482259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:52.48284 INFO::Done
2026-03-23 21:22:52.483375 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:52.486207 INFO::Starting hierarchical adjustment
2026-03-23 21:22:52.48699 INFO::Found  3  batches.
2026-03-23 21:22:52.487541 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:52.488264 INFO::Using default BPPARAM
2026-03-23 21:22:52.48882 INFO::Processing subtree level 1
2026-03-23 21:22:52.594095 INFO::Adjusting the last 1 batches sequentially
2026-03-23 21:22:52.596097 INFO::Done
2026-03-23 21:22:52.596826 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:52.599619 INFO::ASW Batch was -0.0468099059760431 prior to batch effect correction and is now -0.0468099059760431 .
2026-03-23 21:22:52.600697 INFO::Total function execution time is  0.126064777374268  s and adjustment time is  0.109257221221924 s ( 86.67 )
2026-03-23 21:22:52.601861 INFO::Formatting Data.
2026-03-23 21:22:52.602599 INFO::Typecasting input to dataframe.
2026-03-23 21:22:52.603424 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:52.604462 INFO::Removing potential empty rows and columns
2026-03-23 21:22:52.605705 INFO::Found  0  missing values.
2026-03-23 21:22:52.609139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:52.609775 INFO::Done
2026-03-23 21:22:52.610346 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:52.612772 INFO::Starting hierarchical adjustment
2026-03-23 21:22:52.61359 INFO::Found  3  batches.
2026-03-23 21:22:52.614162 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:52.614821 INFO::Using default BPPARAM
2026-03-23 21:22:52.615398 INFO::Processing subtree level 1
2026-03-23 21:22:52.710009 INFO::Adjusting the last 1 batches sequentially
2026-03-23 21:22:52.711965 INFO::Done
2026-03-23 21:22:52.71267 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:52.716197 INFO::ASW Batch was -0.0468099059760431 prior to batch effect correction and is now -0.0468099059760431 .
2026-03-23 21:22:52.717475 INFO::Total function execution time is  0.115553617477417  s and adjustment time is  0.0985321998596191 s ( 85.27 )
2026-03-23 21:22:52.732698 INFO::Formatting Data.
2026-03-23 21:22:52.733663 INFO::Typecasting input to dataframe.
2026-03-23 21:22:52.734636 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:52.735764 INFO::Removing potential empty rows and columns
2026-03-23 21:22:52.736928 INFO::Found  0  missing values.
2026-03-23 21:22:52.740173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:52.740779 INFO::Done
2026-03-23 21:22:52.741325 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:52.743531 INFO::Starting hierarchical adjustment
2026-03-23 21:22:52.744291 INFO::Found  3  batches.
2026-03-23 21:22:52.744865 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:52.745519 INFO::Using default BPPARAM
2026-03-23 21:22:52.746084 INFO::Processing subtree level 1
2026-03-23 21:22:52.838911 INFO::Adjusting the last 1 batches sequentially
2026-03-23 21:22:52.841044 INFO::Done
2026-03-23 21:22:52.841868 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:52.844942 INFO::ASW Batch was -0.135005850401601 prior to batch effect correction and is now -0.135005850401601 .
2026-03-23 21:22:52.846046 INFO::Total function execution time is  0.113418340682983  s and adjustment time is  0.0968668460845947 s ( 85.41 )
2026-03-23 21:22:53.002295 INFO::Formatting Data.
2026-03-23 21:22:53.003351 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:53.004686 INFO::Removing potential empty rows and columns
2026-03-23 21:22:53.007846 INFO::Found  1000  missing values.
2026-03-23 21:22:53.028156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:53.029036 INFO::Done
2026-03-23 21:22:53.02966 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:53.035519 INFO::Starting hierarchical adjustment
2026-03-23 21:22:53.036436 INFO::Found  10  batches.
2026-03-23 21:22:53.037033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:53.037695 INFO::Using default BPPARAM
2026-03-23 21:22:53.038256 INFO::Processing subtree level 1
2026-03-23 21:22:53.200716 INFO::Processing subtree level 2
2026-03-23 21:22:53.366734 INFO::Adjusting the last 1 batches sequentially
2026-03-23 21:22:53.368899 INFO::Done
2026-03-23 21:22:53.369608 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:53.377251 INFO::ASW Batch was 0.47273977241692 prior to batch effect correction and is now 0.47273977241692 .
2026-03-23 21:22:53.378531 INFO::ASW Label was 0.345050226572907 prior to batch effect correction and is now 0.345050226572907 .
2026-03-23 21:22:53.379728 INFO::Total function execution time is  0.377520561218262  s and adjustment time is  0.332607269287109 s ( 88.1 )
2026-03-23 21:22:53.380702 INFO::Formatting Data.
2026-03-23 21:22:53.3814 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:53.382842 INFO::Removing potential empty rows and columns
2026-03-23 21:22:53.385864 INFO::Found  1000  missing values.
2026-03-23 21:22:53.406096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:53.407008 INFO::Done
2026-03-23 21:22:53.407648 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:53.413678 INFO::Starting hierarchical adjustment
2026-03-23 21:22:53.414586 INFO::Found  10  batches.
2026-03-23 21:22:54.567667 INFO::Set up parallel execution backend with 2 workers
2026-03-23 21:22:54.569626 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-23 21:22:55.753455 INFO::Adjusting the last 2 batches sequentially
2026-03-23 21:22:55.755407 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-23 21:22:55.772271 INFO::Done
2026-03-23 21:22:55.772975 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:55.786633 INFO::ASW Batch was 0.47273977241692 prior to batch effect correction and is now 0.47273977241692 .
2026-03-23 21:22:55.787413 INFO::ASW Label was 0.345050226572907 prior to batch effect correction and is now 0.345050226572907 .
2026-03-23 21:22:55.788296 INFO::Total function execution time is  2.40763449668884  s and adjustment time is  2.35784769058228 s ( 97.93 )
2026-03-23 21:22:55.948079 INFO::Formatting Data.
2026-03-23 21:22:55.948977 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:55.950012 INFO::Removing potential empty rows and columns
2026-03-23 21:22:55.951167 INFO::Found  0  missing values.
2026-03-23 21:22:55.955266 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:55.955871 INFO::Done
2026-03-23 21:22:55.956416 INFO::Acquiring quality metrics before batch effect correction.
2026-03-23 21:22:55.959546 INFO::Starting hierarchical adjustment
2026-03-23 21:22:55.96031 INFO::Found  3  batches.
2026-03-23 21:22:55.960899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-23 21:22:55.961562 INFO::Using default BPPARAM
2026-03-23 21:22:55.962126 INFO::Processing subtree level 1
2026-03-23 21:22:56.080481 INFO::Adjusting the last 1 batches sequentially
2026-03-23 21:22:56.08264 INFO::Done
2026-03-23 21:22:56.083438 INFO::Acquiring quality metrics after batch effect correction.
2026-03-23 21:22:56.087266 INFO::ASW Batch was 0.157868827757391 prior to batch effect correction and is now -0.188900099367618 .
2026-03-23 21:22:56.088002 INFO::ASW Label was -0.175215218956607 prior to batch effect correction and is now 0.0913485346820675 .
2026-03-23 21:22:56.089081 INFO::Total function execution time is  0.14105486869812  s and adjustment time is  0.122437238693237 s ( 86.8 )
2026-03-23 21:22:56.232487 INFO::Formatting Data.
2026-03-23 21:22:56.233437 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.234567 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.235704 INFO::Found  2  missing values.
2026-03-23 21:22:56.238798 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.23941 INFO::Done
2026-03-23 21:22:56.270722 INFO::Found NA in Reference column
2026-03-23 21:22:56.281575 INFO::Require at least two references per batch.
2026-03-23 21:22:56.304384 INFO::Formatting Data.
2026-03-23 21:22:56.305281 INFO::Recognized SummarizedExperiment
2026-03-23 21:22:56.3059 INFO::Typecasting input to dataframe.
2026-03-23 21:22:56.316653 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.318036 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.321909 INFO::Found  0  missing values.
2026-03-23 21:22:56.329413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.330148 INFO::Done
2026-03-23 21:22:56.348924 INFO::Formatting Data.
2026-03-23 21:22:56.349867 INFO::Recognized SummarizedExperiment
2026-03-23 21:22:56.350488 INFO::Typecasting input to dataframe.
2026-03-23 21:22:56.371121 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.372641 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.376631 INFO::Found  0  missing values.
2026-03-23 21:22:56.388824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.389625 INFO::Done
2026-03-23 21:22:56.407683 INFO::Formatting Data.
2026-03-23 21:22:56.408577 INFO::Recognized SummarizedExperiment
2026-03-23 21:22:56.409169 INFO::Typecasting input to dataframe.
2026-03-23 21:22:56.428469 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.429769 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.431142 INFO::Found  0  missing values.
2026-03-23 21:22:56.432273 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.
2026-03-23 21:22:56.437392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.438039 INFO::Done
2026-03-23 21:22:56.449699 INFO::Formatting Data.
2026-03-23 21:22:56.450559 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.451525 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.452652 INFO::Found  0  missing values.
2026-03-23 21:22:56.455819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.456382 INFO::Done
2026-03-23 21:22:56.469462 INFO::Formatting Data.
2026-03-23 21:22:56.470475 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.471664 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.472828 INFO::Found  0  missing values.
2026-03-23 21:22:56.475966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.476583 INFO::Done
2026-03-23 21:22:56.508403 INFO::Formatting Data.
2026-03-23 21:22:56.509327 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.510421 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.511643 INFO::Found  1  missing values.
2026-03-23 21:22:56.515131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.515714 INFO::Done
2026-03-23 21:22:56.535632 INFO::Formatting Data.
2026-03-23 21:22:56.536449 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.537423 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.538395 INFO::Found  2  missing values.
2026-03-23 21:22:56.539324 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.
2026-03-23 21:22:56.541594 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.542151 INFO::Done
2026-03-23 21:22:56.552869 INFO::Formatting Data.
2026-03-23 21:22:56.553675 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.554589 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.555566 INFO::Found  2  missing values.
2026-03-23 21:22:56.557281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.557833 INFO::Done
2026-03-23 21:22:56.568898 INFO::Formatting Data.
2026-03-23 21:22:56.569705 INFO::Typecasting input to dataframe.
2026-03-23 21:22:56.570544 INFO::Replacing NaNs with NAs.
2026-03-23 21:22:56.571427 INFO::Removing potential empty rows and columns
2026-03-23 21:22:56.57245 INFO::Found  0  missing values.
2026-03-23 21:22:56.575388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-23 21:22:56.575943 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.772   3.723  21.006

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT23.868 1.62917.906
compute_asw0.0240.0020.026
count_existing0.0150.0000.015
generate_data_covariables0.0110.0020.013
generate_dataset0.0110.0020.013