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This page was generated on 2026-01-08 11:58 -0500 (Thu, 08 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4671
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 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-01-05 13:45 -0500 (Mon, 05 Jan 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 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

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: 2026-01-05 21:20:06 -0500 (Mon, 05 Jan 2026)
EndedAt: 2026-01-05 21:21:35 -0500 (Mon, 05 Jan 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
BERT 23.71  1.171   16.89
* 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")
2026-01-05 21:20:57.641318 INFO::Formatting Data.
2026-01-05 21:20:57.642669 INFO::Replacing NaNs with NAs.
2026-01-05 21:20:57.654963 INFO::Removing potential empty rows and columns
2026-01-05 21:20:57.913446 INFO::Found  0  missing values.
2026-01-05 21:20:57.916903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:20:57.917565 INFO::Done
2026-01-05 21:20:57.91814 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:20:57.929476 INFO::Starting hierarchical adjustment
2026-01-05 21:20:57.930309 INFO::Found  3  batches.
2026-01-05 21:20:57.930872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:20:57.93202 INFO::Using default BPPARAM
2026-01-05 21:20:57.932588 INFO::Processing subtree level 1
2026-01-05 21:20:58.033436 INFO::Adjusting the last 1 batches sequentially
2026-01-05 21:20:58.035281 INFO::Done
2026-01-05 21:20:58.035949 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:20:58.038528 INFO::ASW Batch was -0.0896187884830782 prior to batch effect correction and is now -0.0896187884830782 .
2026-01-05 21:20:58.039611 INFO::Total function execution time is  0.39898943901062  s and adjustment time is  0.10512113571167 s ( 26.35 )
2026-01-05 21:20:58.05332 INFO::Formatting Data.
2026-01-05 21:20:58.054107 INFO::Replacing NaNs with NAs.
2026-01-05 21:20:58.055069 INFO::Removing potential empty rows and columns
2026-01-05 21:20:58.056269 INFO::Found  0  missing values.
2026-01-05 21:20:58.05721 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-01-05 21:20:58.068377 INFO::Formatting Data.
2026-01-05 21:20:58.069055 INFO::Replacing NaNs with NAs.
2026-01-05 21:20:58.069937 INFO::Removing potential empty rows and columns
2026-01-05 21:20:58.070965 INFO::Found  0  missing values.
2026-01-05 21:20:58.071899 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-01-05 21:20:58.088323 INFO::Formatting Data.
2026-01-05 21:20:58.089061 INFO::Replacing NaNs with NAs.
2026-01-05 21:20:58.089942 INFO::Removing potential empty rows and columns
2026-01-05 21:20:58.091005 INFO::Found  0  missing values.
2026-01-05 21:20:58.091955 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-01-05 21:20:58.096684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:20:58.097234 INFO::Done
2026-01-05 21:20:58.097773 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:20:58.099783 INFO::Starting hierarchical adjustment
2026-01-05 21:20:58.100492 INFO::Found  2  batches.
2026-01-05 21:20:58.101021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:20:58.101666 INFO::Using default BPPARAM
2026-01-05 21:20:58.102206 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:20:58.10313 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-05 21:20:58.124125 INFO::Done
2026-01-05 21:20:58.124862 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:20:58.126964 INFO::ASW Batch was 0.0373631996623414 prior to batch effect correction and is now -0.116478454099463 .
2026-01-05 21:20:58.127771 INFO::Total function execution time is  0.0395059585571289  s and adjustment time is  0.0237395763397217 s ( 60.09 )
2026-01-05 21:20:58.130616 INFO::Formatting Data.
2026-01-05 21:20:58.131239 INFO::Replacing NaNs with NAs.
2026-01-05 21:20:58.140023 INFO::Formatting Data.
2026-01-05 21:20:58.140684 INFO::Replacing NaNs with NAs.
2026-01-05 21:20:58.141556 INFO::Removing potential empty rows and columns
2026-01-05 21:20:58.142632 INFO::Found  0  missing values.
2026-01-05 21:20:58.14558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:20:58.146118 INFO::Done
2026-01-05 21:20:58.146652 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:20:58.148627 INFO::Starting hierarchical adjustment
2026-01-05 21:20:58.149336 INFO::Found  2  batches.
2026-01-05 21:20:58.149882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:20:58.172612 INFO::Using default BPPARAM
2026-01-05 21:20:58.174663 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:20:58.175583 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-05 21:20:58.189219 INFO::Done
2026-01-05 21:20:58.189789 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:20:58.191643 INFO::ASW Batch was -0.0119385801692608 prior to batch effect correction and is now -0.11851240330309 .
2026-01-05 21:20:58.192369 INFO::Total function execution time is  0.0523662567138672  s and adjustment time is  0.0400323867797852 s ( 76.45 )
2026-01-05 21:20:58.193375 INFO::Formatting Data.
2026-01-05 21:20:58.193935 INFO::Replacing NaNs with NAs.
2026-01-05 21:20:58.19471 INFO::Removing potential empty rows and columns
2026-01-05 21:20:58.195661 INFO::Found  0  missing values.
2026-01-05 21:20:58.198263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:20:58.198781 INFO::Done
2026-01-05 21:20:58.199265 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:20:58.201126 INFO::Starting hierarchical adjustment
2026-01-05 21:20:58.201789 INFO::Found  2  batches.
2026-01-05 21:20:58.202284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:20:58.202863 INFO::Using default BPPARAM
2026-01-05 21:20:58.203358 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:20:58.204183 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-05 21:20:58.218268 INFO::Done
2026-01-05 21:20:58.218859 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:20:58.220732 INFO::ASW Batch was -0.0119385801692608 prior to batch effect correction and is now -0.11851240330309 .
2026-01-05 21:20:58.221465 INFO::Total function execution time is  0.0280895233154297  s and adjustment time is  0.016606330871582 s ( 59.12 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-05 21:21:01.037352 INFO::Formatting Data.
2026-01-05 21:21:01.038 INFO::Recognized SummarizedExperiment
2026-01-05 21:21:01.038451 INFO::Typecasting input to dataframe.
2026-01-05 21:21:01.066328 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:01.067536 INFO::Removing potential empty rows and columns
2026-01-05 21:21:01.071295 INFO::Found  0  missing values.
2026-01-05 21:21:01.078432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:01.079033 INFO::Done
2026-01-05 21:21:01.079559 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:01.083121 INFO::Starting hierarchical adjustment
2026-01-05 21:21:01.083841 INFO::Found  2  batches.
2026-01-05 21:21:01.084347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:01.085418 INFO::Using default BPPARAM
2026-01-05 21:21:01.085959 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:01.086928 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-05 21:21:01.142422 INFO::Done
2026-01-05 21:21:01.143137 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:01.146754 INFO::ASW Batch was 0.0156119417655233 prior to batch effect correction and is now -0.0865435100575501 .
2026-01-05 21:21:01.147602 INFO::Total function execution time is  0.110487699508667  s and adjustment time is  0.0586903095245361 s ( 53.12 )
Warning: stack imbalance in '{', 73 then 75
2026-01-05 21:21:01.166279 INFO::Formatting Data.
2026-01-05 21:21:01.167032 INFO::Recognized SummarizedExperiment
2026-01-05 21:21:01.167585 INFO::Typecasting input to dataframe.
2026-01-05 21:21:01.1769 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:01.178059 INFO::Removing potential empty rows and columns
2026-01-05 21:21:01.181792 INFO::Found  0  missing values.
2026-01-05 21:21:01.188924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:01.189523 INFO::Done
2026-01-05 21:21:01.190043 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:01.193655 INFO::Starting hierarchical adjustment
2026-01-05 21:21:01.194361 INFO::Found  2  batches.
2026-01-05 21:21:01.194885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:01.195474 INFO::Using default BPPARAM
2026-01-05 21:21:01.195996 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:01.196978 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-05 21:21:01.222224 INFO::Done
2026-01-05 21:21:01.222925 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:01.226521 INFO::ASW Batch was -0.0165509336453789 prior to batch effect correction and is now -0.0165509336453789 .
2026-01-05 21:21:01.227376 INFO::Total function execution time is  0.0610682964324951  s and adjustment time is  0.0279755592346191 s ( 45.81 )
2026-01-05 21:21:01.245483 INFO::Formatting Data.
2026-01-05 21:21:01.246259 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:01.247133 INFO::Removing potential empty rows and columns
2026-01-05 21:21:01.248199 INFO::Found  0  missing values.
2026-01-05 21:21:01.251189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:01.251743 INFO::Done
2026-01-05 21:21:01.252238 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:01.254208 INFO::Starting hierarchical adjustment
2026-01-05 21:21:01.254908 INFO::Found  3  batches.
2026-01-05 21:21:01.255524 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:01.256123 INFO::Using default BPPARAM
2026-01-05 21:21:01.256653 INFO::Processing subtree level 1
2026-01-05 21:21:01.400122 INFO::Adjusting the last 1 batches sequentially
2026-01-05 21:21:01.402156 INFO::Done
2026-01-05 21:21:01.402911 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:01.405736 INFO::ASW Batch was -0.127977862217096 prior to batch effect correction and is now -0.159398515101636 .
2026-01-05 21:21:01.406804 INFO::Total function execution time is  0.161316394805908  s and adjustment time is  0.147339105606079 s ( 91.34 )
2026-01-05 21:21:01.423284 INFO::Skipping initial DF formatting
2026-01-05 21:21:01.4241 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:01.428385 INFO::Starting hierarchical adjustment
2026-01-05 21:21:01.429198 INFO::Found  5  batches.
2026-01-05 21:21:01.429769 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:01.430394 INFO::Using default BPPARAM
2026-01-05 21:21:01.430955 INFO::Processing subtree level 1
2026-01-05 21:21:01.665478 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:01.667858 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-05 21:21:01.697454 INFO::Done
2026-01-05 21:21:01.698545 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:01.704704 INFO::ASW Batch was 0.562057987724119 prior to batch effect correction and is now 0.562057987724119 .
2026-01-05 21:21:01.705554 INFO::ASW Label was 0.361210713725691 prior to batch effect correction and is now 0.361210713725691 .
2026-01-05 21:21:01.706734 INFO::Total function execution time is  0.283524513244629  s and adjustment time is  0.268366813659668 s ( 94.65 )
2026-01-05 21:21:01.782668 INFO::Formatting Data.
2026-01-05 21:21:01.783443 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:01.784408 INFO::Removing potential empty rows and columns
2026-01-05 21:21:01.785397 INFO::Found  0  missing values.
2026-01-05 21:21:01.789288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:01.789843 INFO::Done
2026-01-05 21:21:01.790345 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:01.793343 INFO::Starting hierarchical adjustment
2026-01-05 21:21:01.794084 INFO::Found  5  batches.
2026-01-05 21:21:01.794613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:01.795198 INFO::Using default BPPARAM
2026-01-05 21:21:01.795707 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2026-01-05 21:21:01.936858 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:01.938456 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-05 21:21:01.95547 INFO::Done
2026-01-05 21:21:01.956183 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:01.959792 INFO::ASW Batch was 0.3380734834947 prior to batch effect correction and is now -0.106988049138622 .
2026-01-05 21:21:01.960416 INFO::ASW Label was 0.26207027585396 prior to batch effect correction and is now 0.81538154667552 .
2026-01-05 21:21:01.961249 INFO::Total function execution time is  0.178699493408203  s and adjustment time is  0.161534309387207 s ( 90.39 )
2026-01-05 21:21:01.962126 INFO::Formatting Data.
2026-01-05 21:21:01.962765 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:01.9637 INFO::Removing potential empty rows and columns
2026-01-05 21:21:01.964775 INFO::Found  0  missing values.
2026-01-05 21:21:01.969297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:01.969865 INFO::Done
2026-01-05 21:21:01.970379 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:01.973529 INFO::Starting hierarchical adjustment
2026-01-05 21:21:01.974269 INFO::Found  5  batches.
2026-01-05 21:21:01.974825 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:01.975448 INFO::Using default BPPARAM
2026-01-05 21:21:01.976022 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2026-01-05 21:21:02.114258 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:02.116396 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-05 21:21:02.136132 INFO::Done
2026-01-05 21:21:02.137111 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:02.141261 INFO::ASW Batch was 0.3380734834947 prior to batch effect correction and is now -0.106988049138622 .
2026-01-05 21:21:02.142141 INFO::ASW Label was 0.26207027585396 prior to batch effect correction and is now 0.81538154667552 .
2026-01-05 21:21:02.143141 INFO::Total function execution time is  0.18098783493042  s and adjustment time is  0.161934852600098 s ( 89.47 )
2026-01-05 21:21:02.186746 INFO::Formatting Data.
2026-01-05 21:21:02.188393 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:02.190015 INFO::Removing potential empty rows and columns
2026-01-05 21:21:02.191758 INFO::Found  0  missing values.
2026-01-05 21:21:02.197194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:02.198052 INFO::Done
2026-01-05 21:21:02.19873 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:02.203868 INFO::Starting hierarchical adjustment
2026-01-05 21:21:02.204922 INFO::Found  5  batches.
2026-01-05 21:21:02.205582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:02.206447 INFO::Using default BPPARAM
2026-01-05 21:21:02.207062 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2026-01-05 21:21:02.362447 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:02.364295 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-05 21:21:02.382411 INFO::Done
2026-01-05 21:21:02.383322 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:02.3871 INFO::ASW Batch was 0.262670343032987 prior to batch effect correction and is now -0.0442100066150213 .
2026-01-05 21:21:02.387939 INFO::ASW Label was 0.393242779082243 prior to batch effect correction and is now 0.816607116368861 .
2026-01-05 21:21:02.388944 INFO::Total function execution time is  0.20366382598877  s and adjustment time is  0.177675724029541 s ( 87.24 )
2026-01-05 21:21:02.389939 INFO::Formatting Data.
2026-01-05 21:21:02.39069 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:02.391741 INFO::Removing potential empty rows and columns
2026-01-05 21:21:02.392907 INFO::Found  0  missing values.
2026-01-05 21:21:02.397433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:02.398182 INFO::Done
2026-01-05 21:21:02.398771 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:02.402236 INFO::Starting hierarchical adjustment
2026-01-05 21:21:02.403128 INFO::Found  5  batches.
2026-01-05 21:21:02.403741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:02.404431 INFO::Using default BPPARAM
2026-01-05 21:21:02.405005 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2026-01-05 21:21:02.555238 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:02.557155 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-05 21:21:02.576263 INFO::Done
2026-01-05 21:21:02.577379 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:02.58153 INFO::ASW Batch was 0.262670343032987 prior to batch effect correction and is now -0.0442100066150213 .
2026-01-05 21:21:02.5824 INFO::ASW Label was 0.393242779082243 prior to batch effect correction and is now 0.816607116368861 .
2026-01-05 21:21:02.583557 INFO::Total function execution time is  0.193570137023926  s and adjustment time is  0.173240661621094 s ( 89.5 )
2026-01-05 21:21:02.602458 INFO::Formatting Data.
2026-01-05 21:21:02.603582 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:02.604809 INFO::Removing potential empty rows and columns
2026-01-05 21:21:02.606152 INFO::Found  0  missing values.
2026-01-05 21:21:02.609597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:02.610263 INFO::Done
2026-01-05 21:21:02.610884 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:02.61446 INFO::Starting hierarchical adjustment
2026-01-05 21:21:02.615342 INFO::Found  2  batches.
2026-01-05 21:21:02.615972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:02.616681 INFO::Using default BPPARAM
2026-01-05 21:21:02.617283 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:02.618407 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-05 21:21:02.635684 INFO::Done
2026-01-05 21:21:02.636559 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:02.63994 INFO::ASW Batch was 0.524147883084397 prior to batch effect correction and is now -0.00496331072391081 .
2026-01-05 21:21:02.640676 INFO::ASW Label was 0.462485562040934 prior to batch effect correction and is now 0.893489321093218 .
2026-01-05 21:21:02.64157 INFO::Total function execution time is  0.0393037796020508  s and adjustment time is  0.0204520225524902 s ( 52.04 )
2026-01-05 21:21:02.642431 INFO::Formatting Data.
2026-01-05 21:21:02.643123 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:02.644108 INFO::Removing potential empty rows and columns
2026-01-05 21:21:02.645188 INFO::Found  0  missing values.
2026-01-05 21:21:02.648081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:02.648719 INFO::Done
2026-01-05 21:21:02.649304 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:02.652663 INFO::Starting hierarchical adjustment
2026-01-05 21:21:02.65345 INFO::Found  2  batches.
2026-01-05 21:21:02.654047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:02.654756 INFO::Using default BPPARAM
2026-01-05 21:21:02.655349 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:02.656369 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-05 21:21:02.672764 INFO::Done
2026-01-05 21:21:02.673546 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:02.676759 INFO::ASW Batch was 0.524147883084397 prior to batch effect correction and is now -0.00496331072391081 .
2026-01-05 21:21:02.677449 INFO::ASW Label was 0.462485562040934 prior to batch effect correction and is now 0.893489321093218 .
2026-01-05 21:21:02.678315 INFO::Total function execution time is  0.0358977317810059  s and adjustment time is  0.0194311141967773 s ( 54.13 )
2026-01-05 21:21:02.691396 INFO::Formatting Data.
2026-01-05 21:21:02.69237 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:02.693347 INFO::Removing potential empty rows and columns
2026-01-05 21:21:02.694309 INFO::Found  0  missing values.
2026-01-05 21:21:02.696563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:02.697096 INFO::Done
2026-01-05 21:21:02.697628 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:02.699775 INFO::Starting hierarchical adjustment
2026-01-05 21:21:02.700502 INFO::Found  2  batches.
2026-01-05 21:21:02.70104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:02.701642 INFO::Using default BPPARAM
2026-01-05 21:21:02.70217 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:02.703095 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-05 21:21:02.736614 INFO::Done
2026-01-05 21:21:02.737421 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:02.739678 INFO::ASW Batch was 0.0455875281344225 prior to batch effect correction and is now -0.134465108496776 .
2026-01-05 21:21:02.740576 INFO::Total function execution time is  0.0493335723876953  s and adjustment time is  0.0361800193786621 s ( 73.34 )
2026-01-05 21:21:02.753692 INFO::Formatting Data.
2026-01-05 21:21:02.754538 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:02.755485 INFO::Removing potential empty rows and columns
2026-01-05 21:21:02.756551 INFO::Found  0  missing values.
2026-01-05 21:21:02.75778 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-01-05 21:21:02.762542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:02.763089 INFO::Done
2026-01-05 21:21:02.763621 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:02.766677 INFO::Starting hierarchical adjustment
2026-01-05 21:21:02.767355 INFO::Found  2  batches.
2026-01-05 21:21:02.767869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:02.76844 INFO::Using default BPPARAM
2026-01-05 21:21:02.768954 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:02.769866 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-05 21:21:02.786615 INFO::Done
2026-01-05 21:21:02.787307 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:02.790296 INFO::ASW Batch was 0.36313737359625 prior to batch effect correction and is now -0.0381765687882626 .
2026-01-05 21:21:02.790885 INFO::ASW Label was 0.726678596951914 prior to batch effect correction and is now 0.969621493365486 .
2026-01-05 21:21:02.791656 INFO::Total function execution time is  0.0380935668945312  s and adjustment time is  0.0193653106689453 s ( 50.84 )
2026-01-05 21:21:02.792426 INFO::Formatting Data.
2026-01-05 21:21:02.79304 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:02.793934 INFO::Removing potential empty rows and columns
2026-01-05 21:21:02.794915 INFO::Found  0  missing values.
2026-01-05 21:21:02.795826 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-01-05 21:21:02.800375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:02.800945 INFO::Done
2026-01-05 21:21:02.80145 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:02.804394 INFO::Starting hierarchical adjustment
2026-01-05 21:21:02.805094 INFO::Found  2  batches.
2026-01-05 21:21:02.805613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:02.806206 INFO::Using default BPPARAM
2026-01-05 21:21:02.806723 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:02.807619 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-05 21:21:02.823807 INFO::Done
2026-01-05 21:21:02.82446 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:02.827423 INFO::ASW Batch was 0.36313737359625 prior to batch effect correction and is now -0.0381765687882626 .
2026-01-05 21:21:02.828034 INFO::ASW Label was 0.726678596951914 prior to batch effect correction and is now 0.969621493365486 .
2026-01-05 21:21:02.828861 INFO::Total function execution time is  0.036442756652832  s and adjustment time is  0.0188393592834473 s ( 51.7 )
2026-01-05 21:21:03.056984 INFO::Formatting Data.
2026-01-05 21:21:03.05815 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:03.059311 INFO::Removing potential empty rows and columns
2026-01-05 21:21:03.060479 INFO::Found  0  missing values.
2026-01-05 21:21:03.063746 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:03.064332 INFO::Done
2026-01-05 21:21:03.064888 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:03.067566 INFO::Starting hierarchical adjustment
2026-01-05 21:21:03.068357 INFO::Found  3  batches.
2026-01-05 21:21:03.068896 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:03.06957 INFO::Using default BPPARAM
2026-01-05 21:21:03.070097 INFO::Processing subtree level 1
2026-01-05 21:21:03.165479 INFO::Adjusting the last 1 batches sequentially
2026-01-05 21:21:03.167488 INFO::Done
2026-01-05 21:21:03.168219 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:03.170954 INFO::ASW Batch was -0.125318356669343 prior to batch effect correction and is now -0.125318356669343 .
2026-01-05 21:21:03.172019 INFO::Total function execution time is  0.115226745605469  s and adjustment time is  0.0992915630340576 s ( 86.17 )
2026-01-05 21:21:03.173146 INFO::Formatting Data.
2026-01-05 21:21:03.173828 INFO::Typecasting input to dataframe.
2026-01-05 21:21:03.174651 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:03.175675 INFO::Removing potential empty rows and columns
2026-01-05 21:21:03.176869 INFO::Found  0  missing values.
2026-01-05 21:21:03.180184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:03.180841 INFO::Done
2026-01-05 21:21:03.181392 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:03.183706 INFO::Starting hierarchical adjustment
2026-01-05 21:21:03.184484 INFO::Found  3  batches.
2026-01-05 21:21:03.185078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:03.185739 INFO::Using default BPPARAM
2026-01-05 21:21:03.186278 INFO::Processing subtree level 1
2026-01-05 21:21:03.285666 INFO::Adjusting the last 1 batches sequentially
2026-01-05 21:21:03.287776 INFO::Done
2026-01-05 21:21:03.288607 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:03.291361 INFO::ASW Batch was -0.125318356669343 prior to batch effect correction and is now -0.125318356669343 .
2026-01-05 21:21:03.292433 INFO::Total function execution time is  0.119259595870972  s and adjustment time is  0.103416442871094 s ( 86.72 )
2026-01-05 21:21:03.308438 INFO::Formatting Data.
2026-01-05 21:21:03.309415 INFO::Typecasting input to dataframe.
2026-01-05 21:21:03.310371 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:03.311418 INFO::Removing potential empty rows and columns
2026-01-05 21:21:03.312628 INFO::Found  0  missing values.
2026-01-05 21:21:03.316125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:03.316729 INFO::Done
2026-01-05 21:21:03.317283 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:03.319679 INFO::Starting hierarchical adjustment
2026-01-05 21:21:03.320437 INFO::Found  3  batches.
2026-01-05 21:21:03.321005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:03.321684 INFO::Using default BPPARAM
2026-01-05 21:21:03.322238 INFO::Processing subtree level 1
2026-01-05 21:21:03.418774 INFO::Adjusting the last 1 batches sequentially
2026-01-05 21:21:03.420803 INFO::Done
2026-01-05 21:21:03.421494 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:03.42419 INFO::ASW Batch was -0.0142328603153314 prior to batch effect correction and is now -0.0142328603153314 .
2026-01-05 21:21:03.425188 INFO::Total function execution time is  0.116875410079956  s and adjustment time is  0.100512981414795 s ( 86 )
2026-01-05 21:21:03.572081 INFO::Formatting Data.
2026-01-05 21:21:03.573064 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:03.574263 INFO::Removing potential empty rows and columns
2026-01-05 21:21:03.577081 INFO::Found  1000  missing values.
2026-01-05 21:21:03.59639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:03.597151 INFO::Done
2026-01-05 21:21:03.59772 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:03.603429 INFO::Starting hierarchical adjustment
2026-01-05 21:21:03.60421 INFO::Found  10  batches.
2026-01-05 21:21:03.604758 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:03.605394 INFO::Using default BPPARAM
2026-01-05 21:21:03.60594 INFO::Processing subtree level 1
2026-01-05 21:21:03.745556 INFO::Processing subtree level 2
2026-01-05 21:21:03.893641 INFO::Adjusting the last 1 batches sequentially
2026-01-05 21:21:03.896105 INFO::Done
2026-01-05 21:21:03.896869 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:03.902688 INFO::ASW Batch was 0.509114807447709 prior to batch effect correction and is now 0.509114807447709 .
2026-01-05 21:21:03.903436 INFO::ASW Label was 0.302022549357554 prior to batch effect correction and is now 0.302022549357554 .
2026-01-05 21:21:03.904472 INFO::Total function execution time is  0.332544326782227  s and adjustment time is  0.291984558105469 s ( 87.8 )
2026-01-05 21:21:03.905374 INFO::Formatting Data.
2026-01-05 21:21:03.906048 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:03.907392 INFO::Removing potential empty rows and columns
2026-01-05 21:21:03.910217 INFO::Found  1000  missing values.
2026-01-05 21:21:03.929873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:03.930684 INFO::Done
2026-01-05 21:21:03.931262 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:03.937105 INFO::Starting hierarchical adjustment
2026-01-05 21:21:03.938003 INFO::Found  10  batches.
2026-01-05 21:21:05.046317 INFO::Set up parallel execution backend with 2 workers
2026-01-05 21:21:05.048427 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-05 21:21:06.488845 INFO::Adjusting the last 2 batches sequentially
2026-01-05 21:21:06.491211 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-05 21:21:06.508773 INFO::Done
2026-01-05 21:21:06.509543 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:06.514522 INFO::ASW Batch was 0.509114807447709 prior to batch effect correction and is now 0.509114807447709 .
2026-01-05 21:21:06.515184 INFO::ASW Label was 0.302022549357554 prior to batch effect correction and is now 0.302022549357554 .
2026-01-05 21:21:06.515991 INFO::Total function execution time is  2.61065673828125  s and adjustment time is  2.57091546058655 s ( 98.48 )
2026-01-05 21:21:06.688902 INFO::Formatting Data.
2026-01-05 21:21:06.689939 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:06.69102 INFO::Removing potential empty rows and columns
2026-01-05 21:21:06.692187 INFO::Found  0  missing values.
2026-01-05 21:21:06.696133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:06.696719 INFO::Done
2026-01-05 21:21:06.697253 INFO::Acquiring quality metrics before batch effect correction.
2026-01-05 21:21:06.700359 INFO::Starting hierarchical adjustment
2026-01-05 21:21:06.70111 INFO::Found  3  batches.
2026-01-05 21:21:06.701667 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-05 21:21:06.702294 INFO::Using default BPPARAM
2026-01-05 21:21:06.702879 INFO::Processing subtree level 1
2026-01-05 21:21:06.815032 INFO::Adjusting the last 1 batches sequentially
2026-01-05 21:21:06.816942 INFO::Done
2026-01-05 21:21:06.817645 INFO::Acquiring quality metrics after batch effect correction.
2026-01-05 21:21:06.821101 INFO::ASW Batch was 0.21050154863784 prior to batch effect correction and is now -0.145619947139816 .
2026-01-05 21:21:06.82179 INFO::ASW Label was -0.211822086040297 prior to batch effect correction and is now -0.0220454184253174 .
2026-01-05 21:21:06.822747 INFO::Total function execution time is  0.133981227874756  s and adjustment time is  0.115958452224731 s ( 86.55 )
2026-01-05 21:21:06.999325 INFO::Formatting Data.
2026-01-05 21:21:07.000266 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.001198 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.002247 INFO::Found  2  missing values.
2026-01-05 21:21:07.005184 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.005734 INFO::Done
2026-01-05 21:21:07.033676 INFO::Found NA in Reference column
2026-01-05 21:21:07.043108 INFO::Require at least two references per batch.
2026-01-05 21:21:07.063708 INFO::Formatting Data.
2026-01-05 21:21:07.064482 INFO::Recognized SummarizedExperiment
2026-01-05 21:21:07.065032 INFO::Typecasting input to dataframe.
2026-01-05 21:21:07.075119 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.076329 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.079748 INFO::Found  0  missing values.
2026-01-05 21:21:07.086189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.086775 INFO::Done
2026-01-05 21:21:07.102407 INFO::Formatting Data.
2026-01-05 21:21:07.103212 INFO::Recognized SummarizedExperiment
2026-01-05 21:21:07.103772 INFO::Typecasting input to dataframe.
2026-01-05 21:21:07.12109 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.122403 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.125846 INFO::Found  0  missing values.
2026-01-05 21:21:07.136286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.136956 INFO::Done
2026-01-05 21:21:07.152679 INFO::Formatting Data.
2026-01-05 21:21:07.153419 INFO::Recognized SummarizedExperiment
2026-01-05 21:21:07.153946 INFO::Typecasting input to dataframe.
2026-01-05 21:21:07.171257 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.172425 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.173573 INFO::Found  0  missing values.
2026-01-05 21:21:07.174538 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-01-05 21:21:07.178967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.179523 INFO::Done
2026-01-05 21:21:07.19096 INFO::Formatting Data.
2026-01-05 21:21:07.191937 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.193228 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.194911 INFO::Found  0  missing values.
2026-01-05 21:21:07.199774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.200641 INFO::Done
2026-01-05 21:21:07.216491 INFO::Formatting Data.
2026-01-05 21:21:07.217446 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.218376 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.219463 INFO::Found  0  missing values.
2026-01-05 21:21:07.222427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.222968 INFO::Done
2026-01-05 21:21:07.253962 INFO::Formatting Data.
2026-01-05 21:21:07.254877 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.255973 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.257169 INFO::Found  1  missing values.
2026-01-05 21:21:07.260126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.260664 INFO::Done
2026-01-05 21:21:07.280622 INFO::Formatting Data.
2026-01-05 21:21:07.281501 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.282441 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.283406 INFO::Found  2  missing values.
2026-01-05 21:21:07.284324 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-01-05 21:21:07.286591 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.287113 INFO::Done
2026-01-05 21:21:07.297343 INFO::Formatting Data.
2026-01-05 21:21:07.298204 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.299148 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.300118 INFO::Found  2  missing values.
2026-01-05 21:21:07.301795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.302319 INFO::Done
2026-01-05 21:21:07.313629 INFO::Formatting Data.
2026-01-05 21:21:07.314814 INFO::Typecasting input to dataframe.
2026-01-05 21:21:07.316067 INFO::Replacing NaNs with NAs.
2026-01-05 21:21:07.31736 INFO::Removing potential empty rows and columns
2026-01-05 21:21:07.318884 INFO::Found  0  missing values.
2026-01-05 21:21:07.323418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-05 21:21:07.324298 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.704   3.510  20.773

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT23.710 1.17116.890
compute_asw0.0220.0020.025
count_existing0.0130.0010.014
generate_data_covariables0.0120.0000.013
generate_dataset0.0100.0030.012