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This page was generated on 2026-04-08 11:57 -0400 (Wed, 08 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4897
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Package 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-04-07 13:45 -0400 (Tue, 07 Apr 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: 2026-04-07 21:21:39 -0400 (Tue, 07 Apr 2026)
EndedAt: 2026-04-07 21:23:08 -0400 (Tue, 07 Apr 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 24.919  1.309  17.755
* 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")
2026-04-07 21:22:31.029258 INFO::Formatting Data.
2026-04-07 21:22:31.030469 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:31.041081 INFO::Removing potential empty rows and columns
2026-04-07 21:22:31.277186 INFO::Found  0  missing values.
2026-04-07 21:22:31.280416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:31.281008 INFO::Done
2026-04-07 21:22:31.281552 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:31.29246 INFO::Starting hierarchical adjustment
2026-04-07 21:22:31.293295 INFO::Found  3  batches.
2026-04-07 21:22:31.293828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:31.294902 INFO::Using default BPPARAM
2026-04-07 21:22:31.295449 INFO::Processing subtree level 1
2026-04-07 21:22:31.392596 INFO::Adjusting the last 1 batches sequentially
2026-04-07 21:22:31.394289 INFO::Done
2026-04-07 21:22:31.394922 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:31.397325 INFO::ASW Batch was -0.103874291483699 prior to batch effect correction and is now -0.103874291483699 .
2026-04-07 21:22:31.398348 INFO::Total function execution time is  0.369699001312256  s and adjustment time is  0.101153612136841 s ( 27.36 )
2026-04-07 21:22:31.411934 INFO::Formatting Data.
2026-04-07 21:22:31.412684 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:31.413611 INFO::Removing potential empty rows and columns
2026-04-07 21:22:31.414771 INFO::Found  0  missing values.
2026-04-07 21:22:31.4157 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.
2026-04-07 21:22:31.426658 INFO::Formatting Data.
2026-04-07 21:22:31.427369 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:31.428224 INFO::Removing potential empty rows and columns
2026-04-07 21:22:31.429216 INFO::Found  0  missing values.
2026-04-07 21:22:31.430129 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.
2026-04-07 21:22:31.44615 INFO::Formatting Data.
2026-04-07 21:22:31.44688 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:31.447771 INFO::Removing potential empty rows and columns
2026-04-07 21:22:31.44883 INFO::Found  0  missing values.
2026-04-07 21:22:31.449769 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.
2026-04-07 21:22:31.454154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:31.45469 INFO::Done
2026-04-07 21:22:31.455208 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:31.457206 INFO::Starting hierarchical adjustment
2026-04-07 21:22:31.457885 INFO::Found  2  batches.
2026-04-07 21:22:31.458433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:31.459049 INFO::Using default BPPARAM
2026-04-07 21:22:31.459595 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:31.460502 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-07 21:22:31.481032 INFO::Done
2026-04-07 21:22:31.481712 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:31.483887 INFO::ASW Batch was 0.0801848697293989 prior to batch effect correction and is now -0.094492928055232 .
2026-04-07 21:22:31.4847 INFO::Total function execution time is  0.038604736328125  s and adjustment time is  0.0232546329498291 s ( 60.24 )
2026-04-07 21:22:31.487438 INFO::Formatting Data.
2026-04-07 21:22:31.488053 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:31.496743 INFO::Formatting Data.
2026-04-07 21:22:31.497431 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:31.498304 INFO::Removing potential empty rows and columns
2026-04-07 21:22:31.499311 INFO::Found  0  missing values.
2026-04-07 21:22:31.502208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:31.502756 INFO::Done
2026-04-07 21:22:31.503267 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:31.526022 INFO::Starting hierarchical adjustment
2026-04-07 21:22:31.527198 INFO::Found  2  batches.
2026-04-07 21:22:31.527706 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:31.528239 INFO::Using default BPPARAM
2026-04-07 21:22:31.52871 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:31.52955 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-07 21:22:31.542895 INFO::Done
2026-04-07 21:22:31.543497 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:31.545318 INFO::ASW Batch was -0.0201035756783867 prior to batch effect correction and is now -0.131587703523851 .
2026-04-07 21:22:31.546017 INFO::Total function execution time is  0.0493118762969971  s and adjustment time is  0.0158565044403076 s ( 32.16 )
2026-04-07 21:22:31.546962 INFO::Formatting Data.
2026-04-07 21:22:31.547526 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:31.548299 INFO::Removing potential empty rows and columns
2026-04-07 21:22:31.54921 INFO::Found  0  missing values.
2026-04-07 21:22:31.551764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:31.552243 INFO::Done
2026-04-07 21:22:31.552724 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:31.554516 INFO::Starting hierarchical adjustment
2026-04-07 21:22:31.555161 INFO::Found  2  batches.
2026-04-07 21:22:31.555665 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:31.556223 INFO::Using default BPPARAM
2026-04-07 21:22:31.556727 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:31.55756 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-07 21:22:31.571684 INFO::Done
2026-04-07 21:22:31.572317 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:31.574124 INFO::ASW Batch was -0.0201035756783867 prior to batch effect correction and is now -0.131587703523851 .
2026-04-07 21:22:31.574841 INFO::Total function execution time is  0.0278749465942383  s and adjustment time is  0.0166332721710205 s ( 59.67 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-07 21:22:34.339945 INFO::Formatting Data.
2026-04-07 21:22:34.340709 INFO::Recognized SummarizedExperiment
2026-04-07 21:22:34.341213 INFO::Typecasting input to dataframe.
2026-04-07 21:22:34.371556 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:34.373054 INFO::Removing potential empty rows and columns
2026-04-07 21:22:34.376974 INFO::Found  0  missing values.
2026-04-07 21:22:34.384301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:34.384984 INFO::Done
2026-04-07 21:22:34.385539 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:34.38924 INFO::Starting hierarchical adjustment
2026-04-07 21:22:34.39 INFO::Found  2  batches.
2026-04-07 21:22:34.390541 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:34.391688 INFO::Using default BPPARAM
2026-04-07 21:22:34.392233 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:34.393286 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-07 21:22:34.452328 INFO::Done
2026-04-07 21:22:34.453092 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:34.456896 INFO::ASW Batch was -0.0168256267963809 prior to batch effect correction and is now -0.0911700132400521 .
2026-04-07 21:22:34.457809 INFO::Total function execution time is  0.118145942687988  s and adjustment time is  0.0624074935913086 s ( 52.82 )
Warning: stack imbalance in '{', 73 then 75
2026-04-07 21:22:34.477621 INFO::Formatting Data.
2026-04-07 21:22:34.478457 INFO::Recognized SummarizedExperiment
2026-04-07 21:22:34.479024 INFO::Typecasting input to dataframe.
2026-04-07 21:22:34.488362 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:34.489516 INFO::Removing potential empty rows and columns
2026-04-07 21:22:34.49341 INFO::Found  0  missing values.
2026-04-07 21:22:34.500511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:34.501096 INFO::Done
2026-04-07 21:22:34.501622 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:34.505167 INFO::Starting hierarchical adjustment
2026-04-07 21:22:34.50588 INFO::Found  2  batches.
2026-04-07 21:22:34.506403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:34.506995 INFO::Using default BPPARAM
2026-04-07 21:22:34.507514 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:34.50852 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-07 21:22:34.534437 INFO::Done
2026-04-07 21:22:34.535252 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:34.539261 INFO::ASW Batch was -0.00840804765433343 prior to batch effect correction and is now -0.00840804765433343 .
2026-04-07 21:22:34.540179 INFO::Total function execution time is  0.0625526905059814  s and adjustment time is  0.0286412239074707 s ( 45.79 )
2026-04-07 21:22:34.559917 INFO::Formatting Data.
2026-04-07 21:22:34.56077 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:34.561696 INFO::Removing potential empty rows and columns
2026-04-07 21:22:34.562778 INFO::Found  0  missing values.
2026-04-07 21:22:34.565834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:34.566374 INFO::Done
2026-04-07 21:22:34.566875 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:34.568955 INFO::Starting hierarchical adjustment
2026-04-07 21:22:34.569663 INFO::Found  3  batches.
2026-04-07 21:22:34.570173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:34.570791 INFO::Using default BPPARAM
2026-04-07 21:22:34.571311 INFO::Processing subtree level 1
2026-04-07 21:22:34.714045 INFO::Adjusting the last 1 batches sequentially
2026-04-07 21:22:34.715729 INFO::Done
2026-04-07 21:22:34.716345 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:34.718697 INFO::ASW Batch was -0.0642754429981953 prior to batch effect correction and is now -0.174622555287972 .
2026-04-07 21:22:34.7196 INFO::Total function execution time is  0.159734964370728  s and adjustment time is  0.146211624145508 s ( 91.53 )
2026-04-07 21:22:34.733593 INFO::Skipping initial DF formatting
2026-04-07 21:22:34.734243 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:34.738164 INFO::Starting hierarchical adjustment
2026-04-07 21:22:34.738908 INFO::Found  5  batches.
2026-04-07 21:22:34.739457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:34.740063 INFO::Using default BPPARAM
2026-04-07 21:22:34.740597 INFO::Processing subtree level 1
2026-04-07 21:22:34.961802 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:34.96339 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-07 21:22:34.983359 INFO::Done
2026-04-07 21:22:34.984122 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:34.988437 INFO::ASW Batch was 0.466742425672097 prior to batch effect correction and is now 0.466742425672097 .
2026-04-07 21:22:34.989077 INFO::ASW Label was 0.443185696744958 prior to batch effect correction and is now 0.443185696744958 .
2026-04-07 21:22:34.989935 INFO::Total function execution time is  0.25639009475708  s and adjustment time is  0.244539737701416 s ( 95.38 )
2026-04-07 21:22:35.052308 INFO::Formatting Data.
2026-04-07 21:22:35.053087 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.053979 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.054955 INFO::Found  0  missing values.
2026-04-07 21:22:35.059087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.059619 INFO::Done
2026-04-07 21:22:35.060106 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.062926 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.063623 INFO::Found  5  batches.
2026-04-07 21:22:35.064122 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.064723 INFO::Using default BPPARAM
2026-04-07 21:22:35.065227 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.

2026-04-07 21:22:35.197561 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.199157 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-07 21:22:35.216553 INFO::Done
2026-04-07 21:22:35.217324 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.220783 INFO::ASW Batch was 0.262564305207354 prior to batch effect correction and is now -0.0733372675350586 .
2026-04-07 21:22:35.221503 INFO::ASW Label was 0.519759572044401 prior to batch effect correction and is now 0.789847411375521 .
2026-04-07 21:22:35.222376 INFO::Total function execution time is  0.170129060745239  s and adjustment time is  0.153027296066284 s ( 89.95 )
2026-04-07 21:22:35.223247 INFO::Formatting Data.
2026-04-07 21:22:35.223906 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.224825 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.225923 INFO::Found  0  missing values.
2026-04-07 21:22:35.230408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.230957 INFO::Done
2026-04-07 21:22:35.231492 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.234568 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.235304 INFO::Found  5  batches.
2026-04-07 21:22:35.235862 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.236485 INFO::Using default BPPARAM
2026-04-07 21:22:35.237035 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.

2026-04-07 21:22:35.361198 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.362732 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-07 21:22:35.378691 INFO::Done
2026-04-07 21:22:35.379411 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.382728 INFO::ASW Batch was 0.262564305207354 prior to batch effect correction and is now -0.0733372675350586 .
2026-04-07 21:22:35.383335 INFO::ASW Label was 0.519759572044401 prior to batch effect correction and is now 0.789847411375521 .
2026-04-07 21:22:35.384111 INFO::Total function execution time is  0.160876750946045  s and adjustment time is  0.14354133605957 s ( 89.22 )
2026-04-07 21:22:35.397717 INFO::Formatting Data.
2026-04-07 21:22:35.398517 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.399409 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.400395 INFO::Found  0  missing values.
2026-04-07 21:22:35.404376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.404904 INFO::Done
2026-04-07 21:22:35.405432 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.408431 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.409139 INFO::Found  5  batches.
2026-04-07 21:22:35.409692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.410314 INFO::Using default BPPARAM
2026-04-07 21:22:35.41088 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.

2026-04-07 21:22:35.530974 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.532584 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-07 21:22:35.548265 INFO::Done
2026-04-07 21:22:35.549053 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.552443 INFO::ASW Batch was 0.428532160361087 prior to batch effect correction and is now -0.0356047345524454 .
2026-04-07 21:22:35.553046 INFO::ASW Label was 0.360617322161536 prior to batch effect correction and is now 0.789115663871735 .
2026-04-07 21:22:35.553847 INFO::Total function execution time is  0.156201362609863  s and adjustment time is  0.1392502784729 s ( 89.15 )
2026-04-07 21:22:35.554674 INFO::Formatting Data.
2026-04-07 21:22:35.555323 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.556214 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.557237 INFO::Found  0  missing values.
2026-04-07 21:22:35.561327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.561858 INFO::Done
2026-04-07 21:22:35.562391 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.565268 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.565976 INFO::Found  5  batches.
2026-04-07 21:22:35.566527 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.567131 INFO::Using default BPPARAM
2026-04-07 21:22:35.567668 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.

2026-04-07 21:22:35.688252 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.689942 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-07 21:22:35.707731 INFO::Done
2026-04-07 21:22:35.708548 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.712418 INFO::ASW Batch was 0.428532160361087 prior to batch effect correction and is now -0.0356047345524454 .
2026-04-07 21:22:35.713004 INFO::ASW Label was 0.360617322161536 prior to batch effect correction and is now 0.789115663871735 .
2026-04-07 21:22:35.713841 INFO::Total function execution time is  0.159168481826782  s and adjustment time is  0.141854524612427 s ( 89.12 )
2026-04-07 21:22:35.727482 INFO::Formatting Data.
2026-04-07 21:22:35.728235 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.729153 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.730138 INFO::Found  0  missing values.
2026-04-07 21:22:35.732794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.733328 INFO::Done
2026-04-07 21:22:35.733834 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.736718 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.737432 INFO::Found  2  batches.
2026-04-07 21:22:35.737954 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.73857 INFO::Using default BPPARAM
2026-04-07 21:22:35.739091 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.739958 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-07 21:22:35.754037 INFO::Done
2026-04-07 21:22:35.754655 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.757459 INFO::ASW Batch was 0.667232689703624 prior to batch effect correction and is now -0.0128676937922038 .
2026-04-07 21:22:35.758016 INFO::ASW Label was 0.374284394684859 prior to batch effect correction and is now 0.863907990795409 .
2026-04-07 21:22:35.758766 INFO::Total function execution time is  0.0313897132873535  s and adjustment time is  0.0167598724365234 s ( 53.39 )
2026-04-07 21:22:35.759515 INFO::Formatting Data.
2026-04-07 21:22:35.76011 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.760933 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.761871 INFO::Found  0  missing values.
2026-04-07 21:22:35.764445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.764977 INFO::Done
2026-04-07 21:22:35.765496 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.768317 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.769001 INFO::Found  2  batches.
2026-04-07 21:22:35.769539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.770124 INFO::Using default BPPARAM
2026-04-07 21:22:35.770642 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.771542 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-07 21:22:35.785896 INFO::Done
2026-04-07 21:22:35.78652 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.789297 INFO::ASW Batch was 0.667232689703624 prior to batch effect correction and is now -0.0128676937922038 .
2026-04-07 21:22:35.789855 INFO::ASW Label was 0.374284394684859 prior to batch effect correction and is now 0.863907990795409 .
2026-04-07 21:22:35.790604 INFO::Total function execution time is  0.0311033725738525  s and adjustment time is  0.0170307159423828 s ( 54.76 )
2026-04-07 21:22:35.801429 INFO::Formatting Data.
2026-04-07 21:22:35.802092 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.802908 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.803765 INFO::Found  0  missing values.
2026-04-07 21:22:35.805771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.806309 INFO::Done
2026-04-07 21:22:35.806827 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.808652 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.809319 INFO::Found  2  batches.
2026-04-07 21:22:35.809826 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.810408 INFO::Using default BPPARAM
2026-04-07 21:22:35.810921 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.811793 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-07 21:22:35.841913 INFO::Done
2026-04-07 21:22:35.842654 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.844647 INFO::ASW Batch was -0.0252752774217695 prior to batch effect correction and is now -0.164938080045852 .
2026-04-07 21:22:35.845478 INFO::Total function execution time is  0.044161319732666  s and adjustment time is  0.0327081680297852 s ( 74.07 )
2026-04-07 21:22:35.857514 INFO::Formatting Data.
2026-04-07 21:22:35.858262 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.85914 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.860157 INFO::Found  0  missing values.
2026-04-07 21:22:35.861342 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.
2026-04-07 21:22:35.865821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.866361 INFO::Done
2026-04-07 21:22:35.866865 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.869946 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.870651 INFO::Found  2  batches.
2026-04-07 21:22:35.871196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.87182 INFO::Using default BPPARAM
2026-04-07 21:22:35.872364 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.873298 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-07 21:22:35.890863 INFO::Done
2026-04-07 21:22:35.89161 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.894659 INFO::ASW Batch was 0.517997235055329 prior to batch effect correction and is now -0.0206948116180195 .
2026-04-07 21:22:35.895268 INFO::ASW Label was 0.515721427303235 prior to batch effect correction and is now 0.916009949917193 .
2026-04-07 21:22:35.896084 INFO::Total function execution time is  0.038661003112793  s and adjustment time is  0.0203192234039307 s ( 52.56 )
2026-04-07 21:22:35.896914 INFO::Formatting Data.
2026-04-07 21:22:35.897565 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:35.898531 INFO::Removing potential empty rows and columns
2026-04-07 21:22:35.899565 INFO::Found  0  missing values.
2026-04-07 21:22:35.900614 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.
2026-04-07 21:22:35.905553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:35.906101 INFO::Done
2026-04-07 21:22:35.906643 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:35.909496 INFO::Starting hierarchical adjustment
2026-04-07 21:22:35.910171 INFO::Found  2  batches.
2026-04-07 21:22:35.910678 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:35.911261 INFO::Using default BPPARAM
2026-04-07 21:22:35.911771 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:35.912678 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-07 21:22:35.92931 INFO::Done
2026-04-07 21:22:35.930048 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:35.933111 INFO::ASW Batch was 0.517997235055329 prior to batch effect correction and is now -0.0206948116180195 .
2026-04-07 21:22:35.933733 INFO::ASW Label was 0.515721427303235 prior to batch effect correction and is now 0.916009949917193 .
2026-04-07 21:22:35.93454 INFO::Total function execution time is  0.037651538848877  s and adjustment time is  0.0192408561706543 s ( 51.1 )
2026-04-07 21:22:36.143056 INFO::Formatting Data.
2026-04-07 21:22:36.143873 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:36.144754 INFO::Removing potential empty rows and columns
2026-04-07 21:22:36.145775 INFO::Found  0  missing values.
2026-04-07 21:22:36.14875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:36.149283 INFO::Done
2026-04-07 21:22:36.149792 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:36.151804 INFO::Starting hierarchical adjustment
2026-04-07 21:22:36.152493 INFO::Found  3  batches.
2026-04-07 21:22:36.153009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:36.153616 INFO::Using default BPPARAM
2026-04-07 21:22:36.154118 INFO::Processing subtree level 1
2026-04-07 21:22:36.237204 INFO::Adjusting the last 1 batches sequentially
2026-04-07 21:22:36.238946 INFO::Done
2026-04-07 21:22:36.239616 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:36.242137 INFO::ASW Batch was -0.138141256018151 prior to batch effect correction and is now -0.138141256018151 .
2026-04-07 21:22:36.243057 INFO::Total function execution time is  0.100084066390991  s and adjustment time is  0.086575984954834 s ( 86.5 )
2026-04-07 21:22:36.244091 INFO::Formatting Data.
2026-04-07 21:22:36.244749 INFO::Typecasting input to dataframe.
2026-04-07 21:22:36.245496 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:36.246395 INFO::Removing potential empty rows and columns
2026-04-07 21:22:36.247463 INFO::Found  0  missing values.
2026-04-07 21:22:36.250505 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:36.251038 INFO::Done
2026-04-07 21:22:36.251569 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:36.253575 INFO::Starting hierarchical adjustment
2026-04-07 21:22:36.254268 INFO::Found  3  batches.
2026-04-07 21:22:36.254813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:36.255423 INFO::Using default BPPARAM
2026-04-07 21:22:36.255945 INFO::Processing subtree level 1
2026-04-07 21:22:36.336724 INFO::Adjusting the last 1 batches sequentially
2026-04-07 21:22:36.338392 INFO::Done
2026-04-07 21:22:36.339019 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:36.341389 INFO::ASW Batch was -0.138141256018151 prior to batch effect correction and is now -0.138141256018151 .
2026-04-07 21:22:36.342307 INFO::Total function execution time is  0.098193883895874  s and adjustment time is  0.0842342376708984 s ( 85.78 )
2026-04-07 21:22:36.3558 INFO::Formatting Data.
2026-04-07 21:22:36.356662 INFO::Typecasting input to dataframe.
2026-04-07 21:22:36.357555 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:36.358492 INFO::Removing potential empty rows and columns
2026-04-07 21:22:36.359591 INFO::Found  0  missing values.
2026-04-07 21:22:36.362697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:36.363254 INFO::Done
2026-04-07 21:22:36.363791 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:36.365818 INFO::Starting hierarchical adjustment
2026-04-07 21:22:36.36653 INFO::Found  3  batches.
2026-04-07 21:22:36.367068 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:36.367686 INFO::Using default BPPARAM
2026-04-07 21:22:36.368205 INFO::Processing subtree level 1
2026-04-07 21:22:36.453814 INFO::Adjusting the last 1 batches sequentially
2026-04-07 21:22:36.455549 INFO::Done
2026-04-07 21:22:36.456171 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:36.458637 INFO::ASW Batch was -0.055568348130987 prior to batch effect correction and is now -0.055568348130987 .
2026-04-07 21:22:36.459544 INFO::Total function execution time is  0.103819131851196  s and adjustment time is  0.0891497135162354 s ( 85.87 )
2026-04-07 21:22:36.592802 INFO::Formatting Data.
2026-04-07 21:22:36.593675 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:36.594915 INFO::Removing potential empty rows and columns
2026-04-07 21:22:36.597826 INFO::Found  1000  missing values.
2026-04-07 21:22:36.617366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:36.61819 INFO::Done
2026-04-07 21:22:36.618765 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:36.624587 INFO::Starting hierarchical adjustment
2026-04-07 21:22:36.625404 INFO::Found  10  batches.
2026-04-07 21:22:36.625952 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:36.62658 INFO::Using default BPPARAM
2026-04-07 21:22:36.627117 INFO::Processing subtree level 1
2026-04-07 21:22:36.771766 INFO::Processing subtree level 2
2026-04-07 21:22:36.913222 INFO::Adjusting the last 1 batches sequentially
2026-04-07 21:22:36.915468 INFO::Done
2026-04-07 21:22:36.916179 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:36.922262 INFO::ASW Batch was 0.543721071174544 prior to batch effect correction and is now 0.543721071174544 .
2026-04-07 21:22:36.923002 INFO::ASW Label was 0.359431330736964 prior to batch effect correction and is now 0.359431330736964 .
2026-04-07 21:22:36.924016 INFO::Total function execution time is  0.331271886825562  s and adjustment time is  0.290217638015747 s ( 87.61 )
2026-04-07 21:22:36.924917 INFO::Formatting Data.
2026-04-07 21:22:36.925628 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:36.926985 INFO::Removing potential empty rows and columns
2026-04-07 21:22:36.930027 INFO::Found  1000  missing values.
2026-04-07 21:22:36.950986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:36.951778 INFO::Done
2026-04-07 21:22:36.952409 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:36.958252 INFO::Starting hierarchical adjustment
2026-04-07 21:22:36.959054 INFO::Found  10  batches.
2026-04-07 21:22:37.987432 INFO::Set up parallel execution backend with 2 workers
2026-04-07 21:22:37.98976 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-07 21:22:39.393655 INFO::Adjusting the last 2 batches sequentially
2026-04-07 21:22:39.39564 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-07 21:22:39.413133 INFO::Done
2026-04-07 21:22:39.414006 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:39.419003 INFO::ASW Batch was 0.543721071174544 prior to batch effect correction and is now 0.543721071174544 .
2026-04-07 21:22:39.419668 INFO::ASW Label was 0.359431330736964 prior to batch effect correction and is now 0.359431330736964 .
2026-04-07 21:22:39.420447 INFO::Total function execution time is  2.49556994438171  s and adjustment time is  2.45416831970215 s ( 98.34 )
2026-04-07 21:22:39.590189 INFO::Formatting Data.
2026-04-07 21:22:39.591207 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:39.592329 INFO::Removing potential empty rows and columns
2026-04-07 21:22:39.593546 INFO::Found  0  missing values.
2026-04-07 21:22:39.597463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:39.59808 INFO::Done
2026-04-07 21:22:39.59865 INFO::Acquiring quality metrics before batch effect correction.
2026-04-07 21:22:39.601787 INFO::Starting hierarchical adjustment
2026-04-07 21:22:39.602545 INFO::Found  3  batches.
2026-04-07 21:22:39.60307 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-07 21:22:39.603702 INFO::Using default BPPARAM
2026-04-07 21:22:39.604234 INFO::Processing subtree level 1
2026-04-07 21:22:39.73034 INFO::Adjusting the last 1 batches sequentially
2026-04-07 21:22:39.732465 INFO::Done
2026-04-07 21:22:39.733175 INFO::Acquiring quality metrics after batch effect correction.
2026-04-07 21:22:39.737073 INFO::ASW Batch was 0.242821771750645 prior to batch effect correction and is now -0.14749601675622 .
2026-04-07 21:22:39.737824 INFO::ASW Label was -0.188108574180765 prior to batch effect correction and is now -0.07059097773777 .
2026-04-07 21:22:39.738911 INFO::Total function execution time is  0.148848533630371  s and adjustment time is  0.130046606063843 s ( 87.37 )
2026-04-07 21:22:39.911479 INFO::Formatting Data.
2026-04-07 21:22:39.912999 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:39.91447 INFO::Removing potential empty rows and columns
2026-04-07 21:22:39.916034 INFO::Found  2  missing values.
2026-04-07 21:22:39.919884 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:39.920604 INFO::Done
2026-04-07 21:22:39.953117 INFO::Found NA in Reference column
2026-04-07 21:22:39.964893 INFO::Require at least two references per batch.
2026-04-07 21:22:39.987211 INFO::Formatting Data.
2026-04-07 21:22:39.988105 INFO::Recognized SummarizedExperiment
2026-04-07 21:22:39.988713 INFO::Typecasting input to dataframe.
2026-04-07 21:22:40 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.001512 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.005206 INFO::Found  0  missing values.
2026-04-07 21:22:40.012506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.013311 INFO::Done
2026-04-07 21:22:40.030828 INFO::Formatting Data.
2026-04-07 21:22:40.031747 INFO::Recognized SummarizedExperiment
2026-04-07 21:22:40.032336 INFO::Typecasting input to dataframe.
2026-04-07 21:22:40.051164 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.052676 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.056417 INFO::Found  0  missing values.
2026-04-07 21:22:40.067351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.068169 INFO::Done
2026-04-07 21:22:40.084686 INFO::Formatting Data.
2026-04-07 21:22:40.085545 INFO::Recognized SummarizedExperiment
2026-04-07 21:22:40.086056 INFO::Typecasting input to dataframe.
2026-04-07 21:22:40.103206 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.104382 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.105488 INFO::Found  0  missing values.
2026-04-07 21:22:40.10644 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.
2026-04-07 21:22:40.110954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.111548 INFO::Done
2026-04-07 21:22:40.122703 INFO::Formatting Data.
2026-04-07 21:22:40.123691 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.124792 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.125908 INFO::Found  0  missing values.
2026-04-07 21:22:40.128936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.129572 INFO::Done
2026-04-07 21:22:40.142071 INFO::Formatting Data.
2026-04-07 21:22:40.143053 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.144062 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.145292 INFO::Found  0  missing values.
2026-04-07 21:22:40.148529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.149117 INFO::Done
2026-04-07 21:22:40.197366 INFO::Formatting Data.
2026-04-07 21:22:40.198412 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.199701 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.201097 INFO::Found  1  missing values.
2026-04-07 21:22:40.204071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.20469 INFO::Done
2026-04-07 21:22:40.227614 INFO::Formatting Data.
2026-04-07 21:22:40.228587 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.229542 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.230581 INFO::Found  2  missing values.
2026-04-07 21:22:40.231556 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.
2026-04-07 21:22:40.23398 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.234554 INFO::Done
2026-04-07 21:22:40.246429 INFO::Formatting Data.
2026-04-07 21:22:40.247356 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.248316 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.249254 INFO::Found  2  missing values.
2026-04-07 21:22:40.250937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.251494 INFO::Done
2026-04-07 21:22:40.263243 INFO::Formatting Data.
2026-04-07 21:22:40.264154 INFO::Typecasting input to dataframe.
2026-04-07 21:22:40.265019 INFO::Replacing NaNs with NAs.
2026-04-07 21:22:40.265946 INFO::Removing potential empty rows and columns
2026-04-07 21:22:40.266983 INFO::Found  0  missing values.
2026-04-07 21:22:40.270082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-07 21:22:40.270754 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.751   3.419  20.872

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT24.919 1.30917.755
compute_asw0.0230.0020.024
count_existing0.0130.0000.014
generate_data_covariables0.0110.0010.012
generate_dataset0.0110.0010.011