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This page was generated on 2026-03-12 11:57 -0400 (Thu, 12 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4892
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Package 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-03-11 13:45 -0400 (Wed, 11 Mar 2026)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_22
git_last_commit: 49dbe48
git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
See other builds for BERT in R Universe.

CHECK results for BERT on nebbiolo2

To the developers/maintainers of the BERT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BERT
Version: 1.6.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
StartedAt: 2026-03-11 21:28:19 -0400 (Wed, 11 Mar 2026)
EndedAt: 2026-03-11 21:29:55 -0400 (Wed, 11 Mar 2026)
EllapsedTime: 96.1 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 25.464  1.734  18.353
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.6.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


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

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2026-03-11 21:29:13.422289 INFO::Formatting Data.
2026-03-11 21:29:13.423553 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:13.434224 INFO::Removing potential empty rows and columns
2026-03-11 21:29:13.680712 INFO::Found  0  missing values.
2026-03-11 21:29:13.684192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:13.684915 INFO::Done
2026-03-11 21:29:13.685519 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:13.697186 INFO::Starting hierarchical adjustment
2026-03-11 21:29:13.698116 INFO::Found  3  batches.
2026-03-11 21:29:13.698695 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:13.699896 INFO::Using default BPPARAM
2026-03-11 21:29:13.700484 INFO::Processing subtree level 1
2026-03-11 21:29:13.809304 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:29:13.811131 INFO::Done
2026-03-11 21:29:13.811821 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:13.814416 INFO::ASW Batch was -0.135886979155632 prior to batch effect correction and is now -0.135886979155632 .
2026-03-11 21:29:13.81554 INFO::Total function execution time is  0.393854141235352  s and adjustment time is  0.113204956054688 s ( 28.74 )
2026-03-11 21:29:13.8305 INFO::Formatting Data.
2026-03-11 21:29:13.831307 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:13.832285 INFO::Removing potential empty rows and columns
2026-03-11 21:29:13.833503 INFO::Found  0  missing values.
2026-03-11 21:29:13.8345 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-11 21:29:13.845758 INFO::Formatting Data.
2026-03-11 21:29:13.846435 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:13.847343 INFO::Removing potential empty rows and columns
2026-03-11 21:29:13.84848 INFO::Found  0  missing values.
2026-03-11 21:29:13.849428 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-11 21:29:13.866628 INFO::Formatting Data.
2026-03-11 21:29:13.867378 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:13.868315 INFO::Removing potential empty rows and columns
2026-03-11 21:29:13.869412 INFO::Found  0  missing values.
2026-03-11 21:29:13.870335 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-11 21:29:13.874989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:13.875541 INFO::Done
2026-03-11 21:29:13.876075 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:13.878193 INFO::Starting hierarchical adjustment
2026-03-11 21:29:13.878924 INFO::Found  2  batches.
2026-03-11 21:29:13.879454 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:13.880148 INFO::Using default BPPARAM
2026-03-11 21:29:13.88072 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:13.881675 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:29:13.903153 INFO::Done
2026-03-11 21:29:13.903818 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:13.905997 INFO::ASW Batch was -0.0360561167468885 prior to batch effect correction and is now -0.122596020635266 .
2026-03-11 21:29:13.9068 INFO::Total function execution time is  0.0402488708496094  s and adjustment time is  0.0243818759918213 s ( 60.58 )
2026-03-11 21:29:13.909662 INFO::Formatting Data.
2026-03-11 21:29:13.910288 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:13.919092 INFO::Formatting Data.
2026-03-11 21:29:13.919759 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:13.92063 INFO::Removing potential empty rows and columns
2026-03-11 21:29:13.921671 INFO::Found  0  missing values.
2026-03-11 21:29:13.924647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:13.925182 INFO::Done
2026-03-11 21:29:13.92572 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:13.952959 INFO::Starting hierarchical adjustment
2026-03-11 21:29:13.95465 INFO::Found  2  batches.
2026-03-11 21:29:13.955221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:13.955805 INFO::Using default BPPARAM
2026-03-11 21:29:13.956317 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:13.957242 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:29:13.972914 INFO::Done
2026-03-11 21:29:13.973605 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:13.97581 INFO::ASW Batch was -0.0267597311225905 prior to batch effect correction and is now -0.12072903704138 .
2026-03-11 21:29:13.976654 INFO::Total function execution time is  0.0575454235076904  s and adjustment time is  0.0184743404388428 s ( 32.1 )
2026-03-11 21:29:13.977779 INFO::Formatting Data.
2026-03-11 21:29:13.978416 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:13.97935 INFO::Removing potential empty rows and columns
2026-03-11 21:29:13.980411 INFO::Found  0  missing values.
2026-03-11 21:29:13.983313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:13.983873 INFO::Done
2026-03-11 21:29:13.98438 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:13.986577 INFO::Starting hierarchical adjustment
2026-03-11 21:29:13.987277 INFO::Found  2  batches.
2026-03-11 21:29:13.987805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:13.988413 INFO::Using default BPPARAM
2026-03-11 21:29:13.988947 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:13.989876 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:29:14.005284 INFO::Done
2026-03-11 21:29:14.005906 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:14.007905 INFO::ASW Batch was -0.0267597311225905 prior to batch effect correction and is now -0.12072903704138 .
2026-03-11 21:29:14.008696 INFO::Total function execution time is  0.0309123992919922  s and adjustment time is  0.0181534290313721 s ( 58.73 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-11 21:29:16.983999 INFO::Formatting Data.
2026-03-11 21:29:16.984794 INFO::Recognized SummarizedExperiment
2026-03-11 21:29:16.985309 INFO::Typecasting input to dataframe.
2026-03-11 21:29:17.017285 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:17.018715 INFO::Removing potential empty rows and columns
2026-03-11 21:29:17.023171 INFO::Found  0  missing values.
2026-03-11 21:29:17.030758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:17.031449 INFO::Done
2026-03-11 21:29:17.032029 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:17.035966 INFO::Starting hierarchical adjustment
2026-03-11 21:29:17.036742 INFO::Found  2  batches.
2026-03-11 21:29:17.037277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:17.038549 INFO::Using default BPPARAM
2026-03-11 21:29:17.039104 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:17.040173 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:29:17.100874 INFO::Done
2026-03-11 21:29:17.101689 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:17.105694 INFO::ASW Batch was 0.0153717407825487 prior to batch effect correction and is now -0.0956452833964639 .
2026-03-11 21:29:17.10672 INFO::Total function execution time is  0.12301230430603  s and adjustment time is  0.0642549991607666 s ( 52.23 )
Warning: stack imbalance in '{', 73 then 75
2026-03-11 21:29:17.127798 INFO::Formatting Data.
2026-03-11 21:29:17.128928 INFO::Recognized SummarizedExperiment
2026-03-11 21:29:17.129543 INFO::Typecasting input to dataframe.
2026-03-11 21:29:17.139699 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:17.140968 INFO::Removing potential empty rows and columns
2026-03-11 21:29:17.144796 INFO::Found  0  missing values.
2026-03-11 21:29:17.152366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:17.153091 INFO::Done
2026-03-11 21:29:17.153641 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:17.15755 INFO::Starting hierarchical adjustment
2026-03-11 21:29:17.158301 INFO::Found  2  batches.
2026-03-11 21:29:17.158836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:17.159434 INFO::Using default BPPARAM
2026-03-11 21:29:17.15997 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:17.160976 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:29:17.18736 INFO::Done
2026-03-11 21:29:17.188181 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:17.192229 INFO::ASW Batch was -0.00151068606372413 prior to batch effect correction and is now -0.00151068606372413 .
2026-03-11 21:29:17.193253 INFO::Total function execution time is  0.0654730796813965  s and adjustment time is  0.0291643142700195 s ( 44.54 )
2026-03-11 21:29:17.213711 INFO::Formatting Data.
2026-03-11 21:29:17.214565 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:17.215545 INFO::Removing potential empty rows and columns
2026-03-11 21:29:17.216604 INFO::Found  0  missing values.
2026-03-11 21:29:17.219686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:17.220237 INFO::Done
2026-03-11 21:29:17.220775 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:17.222951 INFO::Starting hierarchical adjustment
2026-03-11 21:29:17.223664 INFO::Found  3  batches.
2026-03-11 21:29:17.224178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:17.224799 INFO::Using default BPPARAM
2026-03-11 21:29:17.225309 INFO::Processing subtree level 1
2026-03-11 21:29:17.376906 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:29:17.378733 INFO::Done
2026-03-11 21:29:17.379361 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:17.381857 INFO::ASW Batch was -0.0609059421700561 prior to batch effect correction and is now -0.185891226939333 .
2026-03-11 21:29:17.382766 INFO::Total function execution time is  0.169170141220093  s and adjustment time is  0.15521764755249 s ( 91.75 )
2026-03-11 21:29:17.398968 INFO::Skipping initial DF formatting
2026-03-11 21:29:17.399716 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:17.404011 INFO::Starting hierarchical adjustment
2026-03-11 21:29:17.404871 INFO::Found  5  batches.
2026-03-11 21:29:17.405432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:17.406102 INFO::Using default BPPARAM
2026-03-11 21:29:17.406646 INFO::Processing subtree level 1
2026-03-11 21:29:17.705794 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:17.708694 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:29:17.73592 INFO::Done
2026-03-11 21:29:17.737017 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:17.812829 INFO::ASW Batch was 0.524078751810546 prior to batch effect correction and is now 0.524078751810546 .
2026-03-11 21:29:17.815056 INFO::ASW Label was 0.382333178030747 prior to batch effect correction and is now 0.382333178030747 .
2026-03-11 21:29:17.816449 INFO::Total function execution time is  0.417518854141235  s and adjustment time is  0.331122159957886 s ( 79.31 )
2026-03-11 21:29:17.837832 INFO::Formatting Data.
2026-03-11 21:29:17.838826 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:17.839961 INFO::Removing potential empty rows and columns
2026-03-11 21:29:17.841128 INFO::Found  0  missing values.
2026-03-11 21:29:17.847862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:17.848815 INFO::Done
2026-03-11 21:29:17.849684 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:17.854275 INFO::Starting hierarchical adjustment
2026-03-11 21:29:17.855215 INFO::Found  5  batches.
2026-03-11 21:29:17.855872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:17.856558 INFO::Using default BPPARAM
2026-03-11 21:29:17.857124 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

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

2026-03-11 21:29:18.047973 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:18.050533 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:29:18.07486 INFO::Done
2026-03-11 21:29:18.075812 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:18.080347 INFO::ASW Batch was 0.0674155441032274 prior to batch effect correction and is now -0.0429174212261514 .
2026-03-11 21:29:18.081209 INFO::ASW Label was 0.642285037505156 prior to batch effect correction and is now 0.876282532367433 .
2026-03-11 21:29:18.082315 INFO::Total function execution time is  0.244621515274048  s and adjustment time is  0.219801664352417 s ( 89.85 )
2026-03-11 21:29:18.083364 INFO::Formatting Data.
2026-03-11 21:29:18.084172 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:18.085296 INFO::Removing potential empty rows and columns
2026-03-11 21:29:18.086642 INFO::Found  0  missing values.
2026-03-11 21:29:18.09193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:18.092622 INFO::Done
2026-03-11 21:29:18.093263 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:18.097148 INFO::Starting hierarchical adjustment
2026-03-11 21:29:18.097997 INFO::Found  5  batches.
2026-03-11 21:29:18.098582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:18.099315 INFO::Using default BPPARAM
2026-03-11 21:29:18.099911 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

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

2026-03-11 21:29:18.262215 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:18.264547 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:29:18.28599 INFO::Done
2026-03-11 21:29:18.287022 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:18.291831 INFO::ASW Batch was 0.0674155441032274 prior to batch effect correction and is now -0.0429174212261514 .
2026-03-11 21:29:18.292687 INFO::ASW Label was 0.642285037505156 prior to batch effect correction and is now 0.876282532367433 .
2026-03-11 21:29:18.293828 INFO::Total function execution time is  0.210464954376221  s and adjustment time is  0.188088655471802 s ( 89.37 )
2026-03-11 21:29:18.328526 INFO::Formatting Data.
2026-03-11 21:29:18.329728 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:18.330966 INFO::Removing potential empty rows and columns
2026-03-11 21:29:18.332342 INFO::Found  0  missing values.
2026-03-11 21:29:18.337382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:18.338024 INFO::Done
2026-03-11 21:29:18.338659 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:18.342993 INFO::Starting hierarchical adjustment
2026-03-11 21:29:18.343941 INFO::Found  5  batches.
2026-03-11 21:29:18.344591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:18.34539 INFO::Using default BPPARAM
2026-03-11 21:29:18.346024 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

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

2026-03-11 21:29:18.536088 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:18.539304 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:29:18.567057 INFO::Done
2026-03-11 21:29:18.568066 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:18.572004 INFO::ASW Batch was 0.5006966563712 prior to batch effect correction and is now -0.0375476426057573 .
2026-03-11 21:29:18.572752 INFO::ASW Label was 0.362731470730992 prior to batch effect correction and is now 0.696932078352753 .
2026-03-11 21:29:18.57372 INFO::Total function execution time is  0.245580911636353  s and adjustment time is  0.223269939422607 s ( 90.92 )
2026-03-11 21:29:18.574674 INFO::Formatting Data.
2026-03-11 21:29:18.575387 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:18.576482 INFO::Removing potential empty rows and columns
2026-03-11 21:29:18.577816 INFO::Found  0  missing values.
2026-03-11 21:29:18.584908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:18.585701 INFO::Done
2026-03-11 21:29:18.586402 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:18.59078 INFO::Starting hierarchical adjustment
2026-03-11 21:29:18.591615 INFO::Found  5  batches.
2026-03-11 21:29:18.592218 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:18.592967 INFO::Using default BPPARAM
2026-03-11 21:29:18.593591 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

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

2026-03-11 21:29:18.81871 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:18.821401 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:29:18.847173 INFO::Done
2026-03-11 21:29:18.848248 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:18.852644 INFO::ASW Batch was 0.5006966563712 prior to batch effect correction and is now -0.0375476426057573 .
2026-03-11 21:29:18.853491 INFO::ASW Label was 0.362731470730992 prior to batch effect correction and is now 0.696932078352753 .
2026-03-11 21:29:18.854612 INFO::Total function execution time is  0.279894590377808  s and adjustment time is  0.255623579025269 s ( 91.33 )
2026-03-11 21:29:18.872631 INFO::Formatting Data.
2026-03-11 21:29:18.873736 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:18.874953 INFO::Removing potential empty rows and columns
2026-03-11 21:29:18.87622 INFO::Found  0  missing values.
2026-03-11 21:29:18.879347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:18.879977 INFO::Done
2026-03-11 21:29:18.880565 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:18.884045 INFO::Starting hierarchical adjustment
2026-03-11 21:29:18.88486 INFO::Found  2  batches.
2026-03-11 21:29:18.88546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:18.886198 INFO::Using default BPPARAM
2026-03-11 21:29:18.886814 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:18.887866 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:29:18.905015 INFO::Done
2026-03-11 21:29:18.905837 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:18.909463 INFO::ASW Batch was 0.597668881025475 prior to batch effect correction and is now 0.0442437467361431 .
2026-03-11 21:29:18.910176 INFO::ASW Label was 0.493030980443461 prior to batch effect correction and is now 0.848736363152063 .
2026-03-11 21:29:18.911091 INFO::Total function execution time is  0.0387217998504639  s and adjustment time is  0.0202968120574951 s ( 52.42 )
2026-03-11 21:29:18.912085 INFO::Formatting Data.
2026-03-11 21:29:18.912831 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:18.913877 INFO::Removing potential empty rows and columns
2026-03-11 21:29:18.915094 INFO::Found  0  missing values.
2026-03-11 21:29:18.918271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:18.918908 INFO::Done
2026-03-11 21:29:18.919524 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:18.922882 INFO::Starting hierarchical adjustment
2026-03-11 21:29:18.923672 INFO::Found  2  batches.
2026-03-11 21:29:18.924248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:18.924912 INFO::Using default BPPARAM
2026-03-11 21:29:18.925473 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:18.926493 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-11 21:29:18.944063 INFO::Done
2026-03-11 21:29:18.944896 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:18.948557 INFO::ASW Batch was 0.597668881025475 prior to batch effect correction and is now 0.0442437467361431 .
2026-03-11 21:29:18.949219 INFO::ASW Label was 0.493030980443461 prior to batch effect correction and is now 0.848736363152063 .
2026-03-11 21:29:18.950105 INFO::Total function execution time is  0.0380451679229736  s and adjustment time is  0.0205233097076416 s ( 53.94 )
2026-03-11 21:29:18.963797 INFO::Formatting Data.
2026-03-11 21:29:18.964706 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:18.965772 INFO::Removing potential empty rows and columns
2026-03-11 21:29:18.966832 INFO::Found  0  missing values.
2026-03-11 21:29:18.969206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:18.969807 INFO::Done
2026-03-11 21:29:18.970356 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:18.972683 INFO::Starting hierarchical adjustment
2026-03-11 21:29:18.97347 INFO::Found  2  batches.
2026-03-11 21:29:18.974062 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:18.974746 INFO::Using default BPPARAM
2026-03-11 21:29:18.975317 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:18.97631 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:29:19.013341 INFO::Done
2026-03-11 21:29:19.014369 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:19.016977 INFO::ASW Batch was 0.322553225333282 prior to batch effect correction and is now -0.191720867644184 .
2026-03-11 21:29:19.01801 INFO::Total function execution time is  0.0543463230133057  s and adjustment time is  0.0399355888366699 s ( 73.48 )
2026-03-11 21:29:19.033865 INFO::Formatting Data.
2026-03-11 21:29:19.035004 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:19.036199 INFO::Removing potential empty rows and columns
2026-03-11 21:29:19.0375 INFO::Found  0  missing values.
2026-03-11 21:29:19.03906 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-11 21:29:19.044745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:19.045407 INFO::Done
2026-03-11 21:29:19.046024 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:19.049861 INFO::Starting hierarchical adjustment
2026-03-11 21:29:19.0507 INFO::Found  2  batches.
2026-03-11 21:29:19.051295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:19.052046 INFO::Using default BPPARAM
2026-03-11 21:29:19.052678 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:19.05383 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:29:19.075219 INFO::Done
2026-03-11 21:29:19.07623 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:19.080295 INFO::ASW Batch was 0.745414155330394 prior to batch effect correction and is now 0.0740096957647594 .
2026-03-11 21:29:19.081151 INFO::ASW Label was 0.354137333422405 prior to batch effect correction and is now 0.8579167332894 .
2026-03-11 21:29:19.082166 INFO::Total function execution time is  0.0485405921936035  s and adjustment time is  0.0246176719665527 s ( 50.72 )
2026-03-11 21:29:19.083167 INFO::Formatting Data.
2026-03-11 21:29:19.083913 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:19.085077 INFO::Removing potential empty rows and columns
2026-03-11 21:29:19.086325 INFO::Found  0  missing values.
2026-03-11 21:29:19.087475 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-11 21:29:19.093002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:19.093691 INFO::Done
2026-03-11 21:29:19.094285 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:19.098102 INFO::Starting hierarchical adjustment
2026-03-11 21:29:19.098943 INFO::Found  2  batches.
2026-03-11 21:29:19.099542 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:19.10026 INFO::Using default BPPARAM
2026-03-11 21:29:19.100876 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:19.102032 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:29:19.123127 INFO::Done
2026-03-11 21:29:19.12414 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:19.127924 INFO::ASW Batch was 0.745414155330394 prior to batch effect correction and is now 0.0740096957647594 .
2026-03-11 21:29:19.128672 INFO::ASW Label was 0.354137333422405 prior to batch effect correction and is now 0.8579167332894 .
2026-03-11 21:29:19.129707 INFO::Total function execution time is  0.0465459823608398  s and adjustment time is  0.0242607593536377 s ( 52.12 )
2026-03-11 21:29:19.39749 INFO::Formatting Data.
2026-03-11 21:29:19.399167 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:19.400755 INFO::Removing potential empty rows and columns
2026-03-11 21:29:19.402293 INFO::Found  0  missing values.
2026-03-11 21:29:19.406895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:19.407839 INFO::Done
2026-03-11 21:29:19.40875 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:19.412406 INFO::Starting hierarchical adjustment
2026-03-11 21:29:19.413295 INFO::Found  3  batches.
2026-03-11 21:29:19.413893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:19.415096 INFO::Using default BPPARAM
2026-03-11 21:29:19.41568 INFO::Processing subtree level 1
2026-03-11 21:29:19.537163 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:29:19.539652 INFO::Done
2026-03-11 21:29:19.540498 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:19.544177 INFO::ASW Batch was -0.0325275142824266 prior to batch effect correction and is now -0.0325275142824266 .
2026-03-11 21:29:19.545492 INFO::Total function execution time is  0.148339509963989  s and adjustment time is  0.126539468765259 s ( 85.3 )
2026-03-11 21:29:19.546935 INFO::Formatting Data.
2026-03-11 21:29:19.547747 INFO::Typecasting input to dataframe.
2026-03-11 21:29:19.548693 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:19.549963 INFO::Removing potential empty rows and columns
2026-03-11 21:29:19.551379 INFO::Found  0  missing values.
2026-03-11 21:29:19.555389 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:19.556095 INFO::Done
2026-03-11 21:29:19.556703 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:19.559325 INFO::Starting hierarchical adjustment
2026-03-11 21:29:19.560123 INFO::Found  3  batches.
2026-03-11 21:29:19.560806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:19.561607 INFO::Using default BPPARAM
2026-03-11 21:29:19.562271 INFO::Processing subtree level 1
2026-03-11 21:29:19.678303 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:29:19.68056 INFO::Done
2026-03-11 21:29:19.681297 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:19.684316 INFO::ASW Batch was -0.0325275142824266 prior to batch effect correction and is now -0.0325275142824266 .
2026-03-11 21:29:19.685415 INFO::Total function execution time is  0.138483285903931  s and adjustment time is  0.120563507080078 s ( 87.06 )
2026-03-11 21:29:19.701776 INFO::Formatting Data.
2026-03-11 21:29:19.702739 INFO::Typecasting input to dataframe.
2026-03-11 21:29:19.703724 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:19.704801 INFO::Removing potential empty rows and columns
2026-03-11 21:29:19.706059 INFO::Found  0  missing values.
2026-03-11 21:29:19.709576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:19.71017 INFO::Done
2026-03-11 21:29:19.710769 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:19.713122 INFO::Starting hierarchical adjustment
2026-03-11 21:29:19.713906 INFO::Found  3  batches.
2026-03-11 21:29:19.71448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:19.71519 INFO::Using default BPPARAM
2026-03-11 21:29:19.715792 INFO::Processing subtree level 1
2026-03-11 21:29:19.823405 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:29:19.82553 INFO::Done
2026-03-11 21:29:19.826242 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:19.829073 INFO::ASW Batch was -0.0555688665990018 prior to batch effect correction and is now -0.0555688665990018 .
2026-03-11 21:29:19.830176 INFO::Total function execution time is  0.128533840179443  s and adjustment time is  0.111735343933105 s ( 86.93 )
2026-03-11 21:29:19.986316 INFO::Formatting Data.
2026-03-11 21:29:19.987278 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:19.98864 INFO::Removing potential empty rows and columns
2026-03-11 21:29:19.991547 INFO::Found  1000  missing values.
2026-03-11 21:29:20.010981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:20.011885 INFO::Done
2026-03-11 21:29:20.012492 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:20.018484 INFO::Starting hierarchical adjustment
2026-03-11 21:29:20.019431 INFO::Found  10  batches.
2026-03-11 21:29:20.020009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:20.020674 INFO::Using default BPPARAM
2026-03-11 21:29:20.021214 INFO::Processing subtree level 1
2026-03-11 21:29:20.201981 INFO::Processing subtree level 2
2026-03-11 21:29:20.358186 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:29:20.360627 INFO::Done
2026-03-11 21:29:20.361394 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:20.367435 INFO::ASW Batch was 0.468681974360755 prior to batch effect correction and is now 0.468681974360755 .
2026-03-11 21:29:20.36817 INFO::ASW Label was 0.345677250482151 prior to batch effect correction and is now 0.345677250482151 .
2026-03-11 21:29:20.369218 INFO::Total function execution time is  0.383048057556152  s and adjustment time is  0.341319799423218 s ( 89.11 )
2026-03-11 21:29:20.370223 INFO::Formatting Data.
2026-03-11 21:29:20.370928 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:20.372302 INFO::Removing potential empty rows and columns
2026-03-11 21:29:20.375239 INFO::Found  1000  missing values.
2026-03-11 21:29:20.396523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:20.397563 INFO::Done
2026-03-11 21:29:20.398185 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:20.40425 INFO::Starting hierarchical adjustment
2026-03-11 21:29:20.405132 INFO::Found  10  batches.
2026-03-11 21:29:22.046883 INFO::Set up parallel execution backend with 2 workers
2026-03-11 21:29:22.049577 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-11 21:29:23.718314 INFO::Adjusting the last 2 batches sequentially
2026-03-11 21:29:23.721458 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-11 21:29:23.743071 INFO::Done
2026-03-11 21:29:23.744146 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:23.750434 INFO::ASW Batch was 0.468681974360755 prior to batch effect correction and is now 0.468681974360755 .
2026-03-11 21:29:23.751297 INFO::ASW Label was 0.345677250482151 prior to batch effect correction and is now 0.345677250482151 .
2026-03-11 21:29:23.75227 INFO::Total function execution time is  3.38207840919495  s and adjustment time is  3.33801221847534 s ( 98.7 )
2026-03-11 21:29:23.978983 INFO::Formatting Data.
2026-03-11 21:29:23.980368 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:23.981716 INFO::Removing potential empty rows and columns
2026-03-11 21:29:23.983178 INFO::Found  0  missing values.
2026-03-11 21:29:23.987806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:23.988551 INFO::Done
2026-03-11 21:29:23.989193 INFO::Acquiring quality metrics before batch effect correction.
2026-03-11 21:29:23.992837 INFO::Starting hierarchical adjustment
2026-03-11 21:29:23.993697 INFO::Found  3  batches.
2026-03-11 21:29:23.994295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-11 21:29:23.994989 INFO::Using default BPPARAM
2026-03-11 21:29:23.995573 INFO::Processing subtree level 1
2026-03-11 21:29:24.134654 INFO::Adjusting the last 1 batches sequentially
2026-03-11 21:29:24.137218 INFO::Done
2026-03-11 21:29:24.138039 INFO::Acquiring quality metrics after batch effect correction.
2026-03-11 21:29:24.142239 INFO::ASW Batch was 0.148495274055706 prior to batch effect correction and is now -0.149717303949056 .
2026-03-11 21:29:24.14301 INFO::ASW Label was -0.190237337119544 prior to batch effect correction and is now 0.0170164846217587 .
2026-03-11 21:29:24.14421 INFO::Total function execution time is  0.165433168411255  s and adjustment time is  0.143658638000488 s ( 86.84 )
2026-03-11 21:29:24.310944 INFO::Formatting Data.
2026-03-11 21:29:24.312112 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.313301 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.314656 INFO::Found  2  missing values.
2026-03-11 21:29:24.31806 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.318691 INFO::Done
2026-03-11 21:29:24.352458 INFO::Found NA in Reference column
2026-03-11 21:29:24.363797 INFO::Require at least two references per batch.
2026-03-11 21:29:24.387841 INFO::Formatting Data.
2026-03-11 21:29:24.388787 INFO::Recognized SummarizedExperiment
2026-03-11 21:29:24.389415 INFO::Typecasting input to dataframe.
2026-03-11 21:29:24.400925 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.402426 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.406197 INFO::Found  0  missing values.
2026-03-11 21:29:24.413704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.414386 INFO::Done
2026-03-11 21:29:24.433053 INFO::Formatting Data.
2026-03-11 21:29:24.434054 INFO::Recognized SummarizedExperiment
2026-03-11 21:29:24.434731 INFO::Typecasting input to dataframe.
2026-03-11 21:29:24.455217 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.45686 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.460768 INFO::Found  0  missing values.
2026-03-11 21:29:24.472545 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.473334 INFO::Done
2026-03-11 21:29:24.491978 INFO::Formatting Data.
2026-03-11 21:29:24.492914 INFO::Recognized SummarizedExperiment
2026-03-11 21:29:24.493473 INFO::Typecasting input to dataframe.
2026-03-11 21:29:24.523924 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.526107 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.527427 INFO::Found  0  missing values.
2026-03-11 21:29:24.528548 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-11 21:29:24.533014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.533571 INFO::Done
2026-03-11 21:29:24.546367 INFO::Formatting Data.
2026-03-11 21:29:24.547299 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.548167 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.549263 INFO::Found  0  missing values.
2026-03-11 21:29:24.552611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.553252 INFO::Done
2026-03-11 21:29:24.567725 INFO::Formatting Data.
2026-03-11 21:29:24.568804 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.569968 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.571021 INFO::Found  0  missing values.
2026-03-11 21:29:24.574082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.574673 INFO::Done
2026-03-11 21:29:24.61143 INFO::Formatting Data.
2026-03-11 21:29:24.612425 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.613706 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.615056 INFO::Found  1  missing values.
2026-03-11 21:29:24.617987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.618541 INFO::Done
2026-03-11 21:29:24.638954 INFO::Formatting Data.
2026-03-11 21:29:24.640018 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.640958 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.641967 INFO::Found  2  missing values.
2026-03-11 21:29:24.642997 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-11 21:29:24.645557 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.646128 INFO::Done
2026-03-11 21:29:24.656222 INFO::Formatting Data.
2026-03-11 21:29:24.657166 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.658134 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.6592 INFO::Found  2  missing values.
2026-03-11 21:29:24.661124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.661709 INFO::Done
2026-03-11 21:29:24.673177 INFO::Formatting Data.
2026-03-11 21:29:24.673977 INFO::Typecasting input to dataframe.
2026-03-11 21:29:24.674823 INFO::Replacing NaNs with NAs.
2026-03-11 21:29:24.675725 INFO::Removing potential empty rows and columns
2026-03-11 21:29:24.676751 INFO::Found  0  missing values.
2026-03-11 21:29:24.679757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-11 21:29:24.680296 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 21.035   4.758  25.053

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT25.464 1.73418.353
compute_asw0.0240.0000.025
count_existing0.0140.0000.014
generate_data_covariables0.0130.0010.013
generate_dataset0.0130.0000.013