Back to Multiple platform build/check report for BioC 3.23:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2026-04-29 10:14 -0400 (Wed, 29 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4988
kjohnson3macOS 13.7.7 Venturaarm644.6.0 Patched (2026-04-24 r89963) -- "Because it was There" 4694
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 171/2415HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.8.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-04-28 14:14 -0400 (Tue, 28 Apr 2026)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_23
git_last_commit: 0c9135c
git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
See other builds for BERT in R Universe.

CHECK results for BERT on nebbiolo1

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: 1.8.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.8.0.tar.gz
StartedAt: 2026-04-28 22:02:21 -0400 (Tue, 28 Apr 2026)
EndedAt: 2026-04-28 22:03:55 -0400 (Tue, 28 Apr 2026)
EllapsedTime: 94.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-29 02:02:21 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.8.0’
* 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 25.294  2.027  18.781
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.8.0’
** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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")
2026-04-28 22:03:15.787132 INFO::Formatting Data.
2026-04-28 22:03:15.788496 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:15.799908 INFO::Removing potential empty rows and columns
2026-04-28 22:03:16.176361 INFO::Found  0  missing values.
2026-04-28 22:03:16.179842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:16.180747 INFO::Done
2026-04-28 22:03:16.181478 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:16.195644 INFO::Starting hierarchical adjustment
2026-04-28 22:03:16.196626 INFO::Found  3  batches.
2026-04-28 22:03:16.19728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:16.19842 INFO::Using default BPPARAM
2026-04-28 22:03:16.199032 INFO::Processing subtree level 1
2026-04-28 22:03:16.306059 INFO::Adjusting the last 1 batches sequentially
2026-04-28 22:03:16.308499 INFO::Done
2026-04-28 22:03:16.309417 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:16.3127 INFO::ASW Batch was -0.056520605607336 prior to batch effect correction and is now -0.056520605607336 .
2026-04-28 22:03:16.314055 INFO::Total function execution time is  0.527426481246948  s and adjustment time is  0.112015247344971 s ( 21.24 )
2026-04-28 22:03:16.331064 INFO::Formatting Data.
2026-04-28 22:03:16.332173 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:16.333329 INFO::Removing potential empty rows and columns
2026-04-28 22:03:16.334624 INFO::Found  0  missing values.
2026-04-28 22:03:16.335808 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.
2026-04-28 22:03:16.348185 INFO::Formatting Data.
2026-04-28 22:03:16.349183 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:16.350324 INFO::Removing potential empty rows and columns
2026-04-28 22:03:16.351616 INFO::Found  0  missing values.
2026-04-28 22:03:16.352695 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.
2026-04-28 22:03:16.370594 INFO::Formatting Data.
2026-04-28 22:03:16.371539 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:16.372577 INFO::Removing potential empty rows and columns
2026-04-28 22:03:16.37375 INFO::Found  0  missing values.
2026-04-28 22:03:16.374798 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.
2026-04-28 22:03:16.379953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:16.380666 INFO::Done
2026-04-28 22:03:16.381295 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:16.383666 INFO::Starting hierarchical adjustment
2026-04-28 22:03:16.384491 INFO::Found  2  batches.
2026-04-28 22:03:16.385121 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:16.385881 INFO::Using default BPPARAM
2026-04-28 22:03:16.386493 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:16.387589 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-28 22:03:16.412013 INFO::Done
2026-04-28 22:03:16.412948 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:16.415447 INFO::ASW Batch was 0.0706627983166764 prior to batch effect correction and is now -0.095375905464998 .
2026-04-28 22:03:16.416443 INFO::Total function execution time is  0.0459752082824707  s and adjustment time is  0.0276241302490234 s ( 60.08 )
2026-04-28 22:03:16.419882 INFO::Formatting Data.
2026-04-28 22:03:16.420643 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:16.430926 INFO::Formatting Data.
2026-04-28 22:03:16.43188 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:16.43296 INFO::Removing potential empty rows and columns
2026-04-28 22:03:16.434185 INFO::Found  0  missing values.
2026-04-28 22:03:16.437449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:16.43808 INFO::Done
2026-04-28 22:03:16.438656 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:16.441015 INFO::Starting hierarchical adjustment
2026-04-28 22:03:16.441814 INFO::Found  2  batches.
2026-04-28 22:03:16.442402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:16.443112 INFO::Using default BPPARAM
2026-04-28 22:03:16.443712 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:16.444762 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-28 22:03:16.462476 INFO::Done
2026-04-28 22:03:16.463417 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:16.465883 INFO::ASW Batch was 0.00899659121217408 prior to batch effect correction and is now -0.128601485497358 .
2026-04-28 22:03:16.466934 INFO::Total function execution time is  0.0361106395721436  s and adjustment time is  0.0207817554473877 s ( 57.55 )
2026-04-28 22:03:16.468237 INFO::Formatting Data.
2026-04-28 22:03:16.468982 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:16.469997 INFO::Removing potential empty rows and columns
2026-04-28 22:03:16.471172 INFO::Found  0  missing values.
2026-04-28 22:03:16.474402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:16.475051 INFO::Done
2026-04-28 22:03:16.475652 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:16.478137 INFO::Starting hierarchical adjustment
2026-04-28 22:03:16.478998 INFO::Found  2  batches.
2026-04-28 22:03:16.479613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:16.480331 INFO::Using default BPPARAM
2026-04-28 22:03:16.480971 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:16.482049 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-28 22:03:16.499133 INFO::Done
2026-04-28 22:03:16.500065 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:16.502546 INFO::ASW Batch was 0.00899659121217408 prior to batch effect correction and is now -0.128601485497358 .
2026-04-28 22:03:16.503486 INFO::Total function execution time is  0.0352489948272705  s and adjustment time is  0.0202662944793701 s ( 57.49 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-28 22:03:20.47789 INFO::Formatting Data.
2026-04-28 22:03:20.478747 INFO::Recognized SummarizedExperiment
2026-04-28 22:03:20.479292 INFO::Typecasting input to dataframe.
2026-04-28 22:03:20.510512 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:20.511889 INFO::Removing potential empty rows and columns
2026-04-28 22:03:20.515363 INFO::Found  0  missing values.
2026-04-28 22:03:20.521941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:20.522547 INFO::Done
2026-04-28 22:03:20.523105 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:20.526505 INFO::Starting hierarchical adjustment
2026-04-28 22:03:20.527264 INFO::Found  2  batches.
2026-04-28 22:03:20.527815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:20.528971 INFO::Using default BPPARAM
2026-04-28 22:03:20.529508 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:20.530478 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-28 22:03:20.583544 INFO::Done
2026-04-28 22:03:20.584405 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:20.588045 INFO::ASW Batch was 0.0308164078027551 prior to batch effect correction and is now -0.0929479540741734 .
2026-04-28 22:03:20.588985 INFO::Total function execution time is  0.111393213272095  s and adjustment time is  0.0564072132110596 s ( 50.64 )
Warning: stack imbalance in '{', 73 then 75
2026-04-28 22:03:20.607428 INFO::Formatting Data.
2026-04-28 22:03:20.608254 INFO::Recognized SummarizedExperiment
2026-04-28 22:03:20.608842 INFO::Typecasting input to dataframe.
2026-04-28 22:03:20.617836 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:20.619047 INFO::Removing potential empty rows and columns
2026-04-28 22:03:20.622418 INFO::Found  0  missing values.
2026-04-28 22:03:20.629222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:20.62987 INFO::Done
2026-04-28 22:03:20.630419 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:20.633928 INFO::Starting hierarchical adjustment
2026-04-28 22:03:20.634647 INFO::Found  2  batches.
2026-04-28 22:03:20.635195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:20.635841 INFO::Using default BPPARAM
2026-04-28 22:03:20.636413 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:20.637426 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-28 22:03:20.66286 INFO::Done
2026-04-28 22:03:20.663715 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:20.66753 INFO::ASW Batch was 0.00428875745535641 prior to batch effect correction and is now 0.00428875745535641 .
2026-04-28 22:03:20.66849 INFO::Total function execution time is  0.0610408782958984  s and adjustment time is  0.0282964706420898 s ( 46.36 )
2026-04-28 22:03:20.688546 INFO::Formatting Data.
2026-04-28 22:03:20.689486 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:20.690502 INFO::Removing potential empty rows and columns
2026-04-28 22:03:20.691613 INFO::Found  0  missing values.
2026-04-28 22:03:20.69479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:20.69536 INFO::Done
2026-04-28 22:03:20.695922 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:20.698136 INFO::Starting hierarchical adjustment
2026-04-28 22:03:20.698897 INFO::Found  3  batches.
2026-04-28 22:03:20.699452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:20.70011 INFO::Using default BPPARAM
2026-04-28 22:03:20.700668 INFO::Processing subtree level 1
2026-04-28 22:03:20.851847 INFO::Adjusting the last 1 batches sequentially
2026-04-28 22:03:20.854069 INFO::Done
2026-04-28 22:03:20.854847 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:20.857745 INFO::ASW Batch was -0.154404174762763 prior to batch effect correction and is now -0.195472185537957 .
2026-04-28 22:03:20.858818 INFO::Total function execution time is  0.170326709747314  s and adjustment time is  0.155312299728394 s ( 91.18 )
2026-04-28 22:03:20.874554 INFO::Skipping initial DF formatting
2026-04-28 22:03:20.875365 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:20.879618 INFO::Starting hierarchical adjustment
2026-04-28 22:03:20.88046 INFO::Found  5  batches.
2026-04-28 22:03:20.88106 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:20.881741 INFO::Using default BPPARAM
2026-04-28 22:03:20.882324 INFO::Processing subtree level 1
2026-04-28 22:03:21.010242 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.012162 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-28 22:03:21.033083 INFO::Done
2026-04-28 22:03:21.033964 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.038687 INFO::ASW Batch was 0.516111949435554 prior to batch effect correction and is now 0.516111949435554 .
2026-04-28 22:03:21.039449 INFO::ASW Label was 0.375413350737675 prior to batch effect correction and is now 0.375413350737675 .
2026-04-28 22:03:21.040428 INFO::Total function execution time is  0.165962934494019  s and adjustment time is  0.152744770050049 s ( 92.04 )
2026-04-28 22:03:21.060386 INFO::Formatting Data.
2026-04-28 22:03:21.061451 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.062541 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.063645 INFO::Found  0  missing values.
2026-04-28 22:03:21.068123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.068747 INFO::Done
2026-04-28 22:03:21.069312 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.072665 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.073443 INFO::Found  5  batches.
2026-04-28 22:03:21.074024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.074709 INFO::Using default BPPARAM
2026-04-28 22:03:21.075292 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.

2026-04-28 22:03:21.190186 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.191968 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-28 22:03:21.208697 INFO::Done
2026-04-28 22:03:21.209518 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.212877 INFO::ASW Batch was 0.404249298309631 prior to batch effect correction and is now -0.0769267183541395 .
2026-04-28 22:03:21.213533 INFO::ASW Label was 0.358618962361992 prior to batch effect correction and is now 0.855172150368941 .
2026-04-28 22:03:21.214416 INFO::Total function execution time is  0.154191970825195  s and adjustment time is  0.135363340377808 s ( 87.79 )
2026-04-28 22:03:21.215301 INFO::Formatting Data.
2026-04-28 22:03:21.215986 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.216925 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.21799 INFO::Found  0  missing values.
2026-04-28 22:03:21.222209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.222812 INFO::Done
2026-04-28 22:03:21.22337 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.226434 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.227195 INFO::Found  5  batches.
2026-04-28 22:03:21.227777 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.228453 INFO::Using default BPPARAM
2026-04-28 22:03:21.229041 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.

2026-04-28 22:03:21.34658 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.34844 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-28 22:03:21.36524 INFO::Done
2026-04-28 22:03:21.366066 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.369699 INFO::ASW Batch was 0.404249298309631 prior to batch effect correction and is now -0.0769267183541395 .
2026-04-28 22:03:21.370412 INFO::ASW Label was 0.358618962361992 prior to batch effect correction and is now 0.855172150368941 .
2026-04-28 22:03:21.371365 INFO::Total function execution time is  0.156047105789185  s and adjustment time is  0.138148307800293 s ( 88.53 )
2026-04-28 22:03:21.386182 INFO::Formatting Data.
2026-04-28 22:03:21.387106 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.388117 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.389218 INFO::Found  0  missing values.
2026-04-28 22:03:21.393476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.394083 INFO::Done
2026-04-28 22:03:21.394686 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.397902 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.39867 INFO::Found  5  batches.
2026-04-28 22:03:21.399264 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.399958 INFO::Using default BPPARAM
2026-04-28 22:03:21.400532 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.

2026-04-28 22:03:21.518702 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.520504 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-28 22:03:21.53706 INFO::Done
2026-04-28 22:03:21.537903 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.541494 INFO::ASW Batch was 0.260787827726938 prior to batch effect correction and is now -0.0791471600574637 .
2026-04-28 22:03:21.542217 INFO::ASW Label was 0.479494203088773 prior to batch effect correction and is now 0.851248509990768 .
2026-04-28 22:03:21.543138 INFO::Total function execution time is  0.157052040100098  s and adjustment time is  0.138496160507202 s ( 88.18 )
2026-04-28 22:03:21.544072 INFO::Formatting Data.
2026-04-28 22:03:21.544758 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.545771 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.546873 INFO::Found  0  missing values.
2026-04-28 22:03:21.551305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.551957 INFO::Done
2026-04-28 22:03:21.552539 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.556294 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.557114 INFO::Found  5  batches.
2026-04-28 22:03:21.557739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.558435 INFO::Using default BPPARAM
2026-04-28 22:03:21.559066 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.

2026-04-28 22:03:21.684126 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.686133 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-28 22:03:21.70362 INFO::Done
2026-04-28 22:03:21.704503 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.708151 INFO::ASW Batch was 0.260787827726938 prior to batch effect correction and is now -0.0791471600574637 .
2026-04-28 22:03:21.708867 INFO::ASW Label was 0.479494203088773 prior to batch effect correction and is now 0.851248509990768 .
2026-04-28 22:03:21.709835 INFO::Total function execution time is  0.165751934051514  s and adjustment time is  0.146622180938721 s ( 88.46 )
2026-04-28 22:03:21.725515 INFO::Formatting Data.
2026-04-28 22:03:21.726722 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.727885 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.729082 INFO::Found  0  missing values.
2026-04-28 22:03:21.732268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.732932 INFO::Done
2026-04-28 22:03:21.733516 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.737168 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.737973 INFO::Found  2  batches.
2026-04-28 22:03:21.738569 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.739287 INFO::Using default BPPARAM
2026-04-28 22:03:21.739938 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.740989 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-28 22:03:21.757026 INFO::Done
2026-04-28 22:03:21.757839 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.761114 INFO::ASW Batch was 0.705375762313262 prior to batch effect correction and is now 0.0372014549549747 .
2026-04-28 22:03:21.761804 INFO::ASW Label was 0.36265925275462 prior to batch effect correction and is now 0.843856555444367 .
2026-04-28 22:03:21.762732 INFO::Total function execution time is  0.0373706817626953  s and adjustment time is  0.0191972255706787 s ( 51.37 )
2026-04-28 22:03:21.763812 INFO::Formatting Data.
2026-04-28 22:03:21.764496 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.765459 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.76652 INFO::Found  0  missing values.
2026-04-28 22:03:21.769401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.770052 INFO::Done
2026-04-28 22:03:21.77062 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.773757 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.774512 INFO::Found  2  batches.
2026-04-28 22:03:21.775121 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.7758 INFO::Using default BPPARAM
2026-04-28 22:03:21.776403 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.77739 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-28 22:03:21.793657 INFO::Done
2026-04-28 22:03:21.794513 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.798182 INFO::ASW Batch was 0.705375762313262 prior to batch effect correction and is now 0.0372014549549747 .
2026-04-28 22:03:21.798871 INFO::ASW Label was 0.36265925275462 prior to batch effect correction and is now 0.843856555444367 .
2026-04-28 22:03:21.799892 INFO::Total function execution time is  0.0361001491546631  s and adjustment time is  0.0192489624023438 s ( 53.32 )
2026-04-28 22:03:21.81293 INFO::Formatting Data.
2026-04-28 22:03:21.813908 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.814948 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.815975 INFO::Found  0  missing values.
2026-04-28 22:03:21.818347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.818981 INFO::Done
2026-04-28 22:03:21.819563 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.821706 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.823319 INFO::Found  2  batches.
2026-04-28 22:03:21.824585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.825299 INFO::Using default BPPARAM
2026-04-28 22:03:21.825914 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.826991 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-28 22:03:21.860877 INFO::Done
2026-04-28 22:03:21.861745 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.863978 INFO::ASW Batch was 0.0698657351546242 prior to batch effect correction and is now -0.145921504285967 .
2026-04-28 22:03:21.864864 INFO::Total function execution time is  0.0520763397216797  s and adjustment time is  0.0382039546966553 s ( 73.36 )
2026-04-28 22:03:21.878281 INFO::Formatting Data.
2026-04-28 22:03:21.879261 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.880293 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.881375 INFO::Found  0  missing values.
2026-04-28 22:03:21.882629 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.
2026-04-28 22:03:21.887723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.888361 INFO::Done
2026-04-28 22:03:21.888942 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.892188 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.892977 INFO::Found  2  batches.
2026-04-28 22:03:21.893552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.894241 INFO::Using default BPPARAM
2026-04-28 22:03:21.89482 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.895872 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-28 22:03:21.914351 INFO::Done
2026-04-28 22:03:21.915258 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.918592 INFO::ASW Batch was 0.616134860441836 prior to batch effect correction and is now 0.121804011957245 .
2026-04-28 22:03:21.919242 INFO::ASW Label was 0.537349744898091 prior to batch effect correction and is now 0.872255287739876 .
2026-04-28 22:03:21.920152 INFO::Total function execution time is  0.0420279502868652  s and adjustment time is  0.0214660167694092 s ( 51.08 )
2026-04-28 22:03:21.921063 INFO::Formatting Data.
2026-04-28 22:03:21.921784 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:21.922789 INFO::Removing potential empty rows and columns
2026-04-28 22:03:21.923858 INFO::Found  0  missing values.
2026-04-28 22:03:21.924869 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.
2026-04-28 22:03:21.929926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:21.930554 INFO::Done
2026-04-28 22:03:21.931137 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:21.93453 INFO::Starting hierarchical adjustment
2026-04-28 22:03:21.935309 INFO::Found  2  batches.
2026-04-28 22:03:21.935945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:21.936611 INFO::Using default BPPARAM
2026-04-28 22:03:21.937198 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:21.938231 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-28 22:03:21.956972 INFO::Done
2026-04-28 22:03:21.957901 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:21.961274 INFO::ASW Batch was 0.616134860441836 prior to batch effect correction and is now 0.121804011957245 .
2026-04-28 22:03:21.961984 INFO::ASW Label was 0.537349744898091 prior to batch effect correction and is now 0.872255287739876 .
2026-04-28 22:03:21.962878 INFO::Total function execution time is  0.0418455600738525  s and adjustment time is  0.0217523574829102 s ( 51.98 )
2026-04-28 22:03:22.186801 INFO::Formatting Data.
2026-04-28 22:03:22.187874 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:22.188895 INFO::Removing potential empty rows and columns
2026-04-28 22:03:22.190054 INFO::Found  0  missing values.
2026-04-28 22:03:22.193265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:22.193847 INFO::Done
2026-04-28 22:03:22.194403 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:22.196712 INFO::Starting hierarchical adjustment
2026-04-28 22:03:22.197468 INFO::Found  3  batches.
2026-04-28 22:03:22.198048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:22.198749 INFO::Using default BPPARAM
2026-04-28 22:03:22.199309 INFO::Processing subtree level 1
2026-04-28 22:03:22.293438 INFO::Adjusting the last 1 batches sequentially
2026-04-28 22:03:22.295396 INFO::Done
2026-04-28 22:03:22.296074 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:22.298697 INFO::ASW Batch was -0.0539217915840901 prior to batch effect correction and is now -0.0539217915840901 .
2026-04-28 22:03:22.29974 INFO::Total function execution time is  0.113124370574951  s and adjustment time is  0.0980873107910156 s ( 86.71 )
2026-04-28 22:03:22.300875 INFO::Formatting Data.
2026-04-28 22:03:22.301599 INFO::Typecasting input to dataframe.
2026-04-28 22:03:22.302432 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:22.30343 INFO::Removing potential empty rows and columns
2026-04-28 22:03:22.304592 INFO::Found  0  missing values.
2026-04-28 22:03:22.307854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:22.308496 INFO::Done
2026-04-28 22:03:22.309083 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:22.311347 INFO::Starting hierarchical adjustment
2026-04-28 22:03:22.312122 INFO::Found  3  batches.
2026-04-28 22:03:22.312714 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:22.313396 INFO::Using default BPPARAM
2026-04-28 22:03:22.314029 INFO::Processing subtree level 1
2026-04-28 22:03:22.407371 INFO::Adjusting the last 1 batches sequentially
2026-04-28 22:03:22.409461 INFO::Done
2026-04-28 22:03:22.410203 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:22.413033 INFO::ASW Batch was -0.0539217915840901 prior to batch effect correction and is now -0.0539217915840901 .
2026-04-28 22:03:22.414091 INFO::Total function execution time is  0.113215923309326  s and adjustment time is  0.0974855422973633 s ( 86.11 )
2026-04-28 22:03:22.42889 INFO::Formatting Data.
2026-04-28 22:03:22.429846 INFO::Typecasting input to dataframe.
2026-04-28 22:03:22.430784 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:22.431873 INFO::Removing potential empty rows and columns
2026-04-28 22:03:22.433039 INFO::Found  0  missing values.
2026-04-28 22:03:22.436317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:22.436899 INFO::Done
2026-04-28 22:03:22.437468 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:22.439719 INFO::Starting hierarchical adjustment
2026-04-28 22:03:22.440474 INFO::Found  3  batches.
2026-04-28 22:03:22.441064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:22.441758 INFO::Using default BPPARAM
2026-04-28 22:03:22.442329 INFO::Processing subtree level 1
2026-04-28 22:03:22.544068 INFO::Adjusting the last 1 batches sequentially
2026-04-28 22:03:22.546122 INFO::Done
2026-04-28 22:03:22.546886 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:22.549812 INFO::ASW Batch was 0.0564110141731781 prior to batch effect correction and is now 0.0564110141731781 .
2026-04-28 22:03:22.550883 INFO::Total function execution time is  0.122086048126221  s and adjustment time is  0.105789661407471 s ( 86.65 )
2026-04-28 22:03:22.69963 INFO::Formatting Data.
2026-04-28 22:03:22.700692 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:22.701948 INFO::Removing potential empty rows and columns
2026-04-28 22:03:22.704934 INFO::Found  1000  missing values.
2026-04-28 22:03:22.724972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:22.725838 INFO::Done
2026-04-28 22:03:22.726444 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:22.732203 INFO::Starting hierarchical adjustment
2026-04-28 22:03:22.733018 INFO::Found  10  batches.
2026-04-28 22:03:22.733606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:22.734317 INFO::Using default BPPARAM
2026-04-28 22:03:22.734906 INFO::Processing subtree level 1
2026-04-28 22:03:22.883219 INFO::Processing subtree level 2
2026-04-28 22:03:23.03465 INFO::Adjusting the last 1 batches sequentially
2026-04-28 22:03:23.036822 INFO::Done
2026-04-28 22:03:23.03752 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:23.043423 INFO::ASW Batch was 0.4807640301935 prior to batch effect correction and is now 0.4807640301935 .
2026-04-28 22:03:23.044164 INFO::ASW Label was 0.342292456237802 prior to batch effect correction and is now 0.342292456237802 .
2026-04-28 22:03:23.04517 INFO::Total function execution time is  0.345637321472168  s and adjustment time is  0.30396032333374 s ( 87.94 )
2026-04-28 22:03:23.046075 INFO::Formatting Data.
2026-04-28 22:03:23.046792 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:23.048095 INFO::Removing potential empty rows and columns
2026-04-28 22:03:23.051166 INFO::Found  1000  missing values.
2026-04-28 22:03:23.071292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:23.072175 INFO::Done
2026-04-28 22:03:23.072787 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:23.078476 INFO::Starting hierarchical adjustment
2026-04-28 22:03:23.079301 INFO::Found  10  batches.
2026-04-28 22:03:24.396264 INFO::Set up parallel execution backend with 2 workers
2026-04-28 22:03:24.399531 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-28 22:03:25.666203 INFO::Adjusting the last 2 batches sequentially
2026-04-28 22:03:25.669501 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-28 22:03:25.686287 INFO::Done
2026-04-28 22:03:25.68701 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:25.691612 INFO::ASW Batch was 0.4807640301935 prior to batch effect correction and is now 0.4807640301935 .
2026-04-28 22:03:25.69223 INFO::ASW Label was 0.342292456237802 prior to batch effect correction and is now 0.342292456237802 .
2026-04-28 22:03:25.692986 INFO::Total function execution time is  2.64696192741394  s and adjustment time is  2.60712361335754 s ( 98.49 )
2026-04-28 22:03:25.841934 INFO::Formatting Data.
2026-04-28 22:03:25.842846 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:25.843909 INFO::Removing potential empty rows and columns
2026-04-28 22:03:25.84515 INFO::Found  0  missing values.
2026-04-28 22:03:25.84909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:25.849692 INFO::Done
2026-04-28 22:03:25.850262 INFO::Acquiring quality metrics before batch effect correction.
2026-04-28 22:03:25.853254 INFO::Starting hierarchical adjustment
2026-04-28 22:03:25.854012 INFO::Found  3  batches.
2026-04-28 22:03:25.854596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-28 22:03:25.855292 INFO::Using default BPPARAM
2026-04-28 22:03:25.855928 INFO::Processing subtree level 1
2026-04-28 22:03:25.964844 INFO::Adjusting the last 1 batches sequentially
2026-04-28 22:03:25.966751 INFO::Done
2026-04-28 22:03:25.967455 INFO::Acquiring quality metrics after batch effect correction.
2026-04-28 22:03:25.970716 INFO::ASW Batch was 0.231265000674714 prior to batch effect correction and is now -0.145495586948763 .
2026-04-28 22:03:25.971337 INFO::ASW Label was -0.191223834600331 prior to batch effect correction and is now -0.0456428372479805 .
2026-04-28 22:03:25.972261 INFO::Total function execution time is  0.130403995513916  s and adjustment time is  0.112845420837402 s ( 86.54 )
2026-04-28 22:03:26.096641 INFO::Formatting Data.
2026-04-28 22:03:26.097536 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.098479 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.099553 INFO::Found  2  missing values.
2026-04-28 22:03:26.10242 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.103018 INFO::Done
2026-04-28 22:03:26.130392 INFO::Found NA in Reference column
2026-04-28 22:03:26.139931 INFO::Require at least two references per batch.
2026-04-28 22:03:26.160353 INFO::Formatting Data.
2026-04-28 22:03:26.161273 INFO::Recognized SummarizedExperiment
2026-04-28 22:03:26.161904 INFO::Typecasting input to dataframe.
2026-04-28 22:03:26.172133 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.173448 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.177285 INFO::Found  0  missing values.
2026-04-28 22:03:26.184475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.185142 INFO::Done
2026-04-28 22:03:26.201746 INFO::Formatting Data.
2026-04-28 22:03:26.202653 INFO::Recognized SummarizedExperiment
2026-04-28 22:03:26.203268 INFO::Typecasting input to dataframe.
2026-04-28 22:03:26.221559 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.223128 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.227173 INFO::Found  0  missing values.
2026-04-28 22:03:26.238944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.239625 INFO::Done
2026-04-28 22:03:26.256495 INFO::Formatting Data.
2026-04-28 22:03:26.257369 INFO::Recognized SummarizedExperiment
2026-04-28 22:03:26.257988 INFO::Typecasting input to dataframe.
2026-04-28 22:03:26.275922 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.277139 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.278406 INFO::Found  0  missing values.
2026-04-28 22:03:26.279403 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.
2026-04-28 22:03:26.284106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.284721 INFO::Done
2026-04-28 22:03:26.29572 INFO::Formatting Data.
2026-04-28 22:03:26.296571 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.297608 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.298738 INFO::Found  0  missing values.
2026-04-28 22:03:26.301893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.302515 INFO::Done
2026-04-28 22:03:26.31407 INFO::Formatting Data.
2026-04-28 22:03:26.314949 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.315867 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.316967 INFO::Found  0  missing values.
2026-04-28 22:03:26.319861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.320419 INFO::Done
2026-04-28 22:03:26.351135 INFO::Formatting Data.
2026-04-28 22:03:26.352117 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.35324 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.354467 INFO::Found  1  missing values.
2026-04-28 22:03:26.357332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.357958 INFO::Done
2026-04-28 22:03:26.377298 INFO::Formatting Data.
2026-04-28 22:03:26.378191 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.379089 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.380095 INFO::Found  2  missing values.
2026-04-28 22:03:26.381044 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.
2026-04-28 22:03:26.383352 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.383941 INFO::Done
2026-04-28 22:03:26.394031 INFO::Formatting Data.
2026-04-28 22:03:26.394852 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.395761 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.396723 INFO::Found  2  missing values.
2026-04-28 22:03:26.398354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.398992 INFO::Done
2026-04-28 22:03:26.410213 INFO::Formatting Data.
2026-04-28 22:03:26.411095 INFO::Typecasting input to dataframe.
2026-04-28 22:03:26.411944 INFO::Replacing NaNs with NAs.
2026-04-28 22:03:26.412875 INFO::Removing potential empty rows and columns
2026-04-28 22:03:26.413957 INFO::Found  0  missing values.
2026-04-28 22:03:26.416894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-28 22:03:26.417456 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 19.132   4.308  23.181

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT25.294 2.02718.781
compute_asw0.0250.0000.025
count_existing0.0140.0000.014
generate_data_covariables0.0100.0020.012
generate_dataset0.0090.0030.012