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This page was generated on 2026-03-18 11:57 -0400 (Wed, 18 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: 2026-03-17 13:45 -0400 (Tue, 17 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: 2026-03-17 21:20:27 -0400 (Tue, 17 Mar 2026)
EndedAt: 2026-03-17 21:21:55 -0400 (Tue, 17 Mar 2026)
EllapsedTime: 88.0 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 25.119  1.709  18.256
* 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")
2026-03-17 21:21:19.441701 INFO::Formatting Data.
2026-03-17 21:21:19.442919 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:19.453563 INFO::Removing potential empty rows and columns
2026-03-17 21:21:19.683104 INFO::Found  0  missing values.
2026-03-17 21:21:19.686162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:19.686763 INFO::Done
2026-03-17 21:21:19.687279 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:19.697634 INFO::Starting hierarchical adjustment
2026-03-17 21:21:19.698393 INFO::Found  3  batches.
2026-03-17 21:21:19.698929 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:19.699986 INFO::Using default BPPARAM
2026-03-17 21:21:19.700504 INFO::Processing subtree level 1
2026-03-17 21:21:19.793547 INFO::Adjusting the last 1 batches sequentially
2026-03-17 21:21:19.795194 INFO::Done
2026-03-17 21:21:19.795812 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:19.798184 INFO::ASW Batch was -0.11008162742441 prior to batch effect correction and is now -0.11008162742441 .
2026-03-17 21:21:19.799198 INFO::Total function execution time is  0.358092546463013  s and adjustment time is  0.0969357490539551 s ( 27.07 )
2026-03-17 21:21:19.812026 INFO::Formatting Data.
2026-03-17 21:21:19.812733 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:19.813628 INFO::Removing potential empty rows and columns
2026-03-17 21:21:19.814764 INFO::Found  0  missing values.
2026-03-17 21:21:19.815677 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.
2026-03-17 21:21:19.825908 INFO::Formatting Data.
2026-03-17 21:21:19.826573 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:19.827416 INFO::Removing potential empty rows and columns
2026-03-17 21:21:19.828441 INFO::Found  0  missing values.
2026-03-17 21:21:19.82935 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.
2026-03-17 21:21:19.84447 INFO::Formatting Data.
2026-03-17 21:21:19.845236 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:19.846076 INFO::Removing potential empty rows and columns
2026-03-17 21:21:19.847075 INFO::Found  0  missing values.
2026-03-17 21:21:19.847951 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.
2026-03-17 21:21:19.85223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:19.852773 INFO::Done
2026-03-17 21:21:19.853278 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:19.855178 INFO::Starting hierarchical adjustment
2026-03-17 21:21:19.85586 INFO::Found  2  batches.
2026-03-17 21:21:19.856356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:19.856973 INFO::Using default BPPARAM
2026-03-17 21:21:19.857471 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:19.858354 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-17 21:21:19.878628 INFO::Done
2026-03-17 21:21:19.879294 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:19.881466 INFO::ASW Batch was -0.0274968209135592 prior to batch effect correction and is now -0.0999553040447279 .
2026-03-17 21:21:19.882265 INFO::Total function execution time is  0.0378451347351074  s and adjustment time is  0.022883415222168 s ( 60.47 )
2026-03-17 21:21:19.885051 INFO::Formatting Data.
2026-03-17 21:21:19.885687 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:19.89433 INFO::Formatting Data.
2026-03-17 21:21:19.895005 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:19.895876 INFO::Removing potential empty rows and columns
2026-03-17 21:21:19.896921 INFO::Found  0  missing values.
2026-03-17 21:21:19.899856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:19.900387 INFO::Done
2026-03-17 21:21:19.900923 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:19.925945 INFO::Starting hierarchical adjustment
2026-03-17 21:21:19.927189 INFO::Found  2  batches.
2026-03-17 21:21:19.927728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:19.928267 INFO::Using default BPPARAM
2026-03-17 21:21:19.928754 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:19.929605 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-17 21:21:19.942969 INFO::Done
2026-03-17 21:21:19.943567 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:19.945421 INFO::ASW Batch was -0.0417253763394064 prior to batch effect correction and is now -0.0991661677294827 .
2026-03-17 21:21:19.946133 INFO::Total function execution time is  0.0518343448638916  s and adjustment time is  0.0159506797790527 s ( 30.77 )
2026-03-17 21:21:19.947116 INFO::Formatting Data.
2026-03-17 21:21:19.947677 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:19.948477 INFO::Removing potential empty rows and columns
2026-03-17 21:21:19.949391 INFO::Found  0  missing values.
2026-03-17 21:21:19.951978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:19.95247 INFO::Done
2026-03-17 21:21:19.95295 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:19.954773 INFO::Starting hierarchical adjustment
2026-03-17 21:21:19.955412 INFO::Found  2  batches.
2026-03-17 21:21:19.955893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:19.956442 INFO::Using default BPPARAM
2026-03-17 21:21:19.956924 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:19.957752 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-17 21:21:19.971615 INFO::Done
2026-03-17 21:21:19.972245 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:19.974156 INFO::ASW Batch was -0.0417253763394064 prior to batch effect correction and is now -0.0991661677294827 .
2026-03-17 21:21:19.974902 INFO::Total function execution time is  0.0277769565582275  s and adjustment time is  0.0163083076477051 s ( 58.71 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-17 21:21:22.714314 INFO::Formatting Data.
2026-03-17 21:21:22.714926 INFO::Recognized SummarizedExperiment
2026-03-17 21:21:22.715391 INFO::Typecasting input to dataframe.
2026-03-17 21:21:22.744292 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:22.745571 INFO::Removing potential empty rows and columns
2026-03-17 21:21:22.749375 INFO::Found  0  missing values.
2026-03-17 21:21:22.756783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:22.757412 INFO::Done
2026-03-17 21:21:22.757962 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:22.761592 INFO::Starting hierarchical adjustment
2026-03-17 21:21:22.762308 INFO::Found  2  batches.
2026-03-17 21:21:22.762844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:22.763928 INFO::Using default BPPARAM
2026-03-17 21:21:22.764474 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:22.76544 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-17 21:21:22.821404 INFO::Done
2026-03-17 21:21:22.822097 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:22.82565 INFO::ASW Batch was 0.0361463130114458 prior to batch effect correction and is now -0.0929198840975136 .
2026-03-17 21:21:22.826467 INFO::Total function execution time is  0.112406730651855  s and adjustment time is  0.0592193603515625 s ( 52.68 )
Warning: stack imbalance in '{', 73 then 75
2026-03-17 21:21:22.84515 INFO::Formatting Data.
2026-03-17 21:21:22.845874 INFO::Recognized SummarizedExperiment
2026-03-17 21:21:22.846408 INFO::Typecasting input to dataframe.
2026-03-17 21:21:22.855468 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:22.856574 INFO::Removing potential empty rows and columns
2026-03-17 21:21:22.860245 INFO::Found  0  missing values.
2026-03-17 21:21:22.867275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:22.867867 INFO::Done
2026-03-17 21:21:22.868371 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:22.871898 INFO::Starting hierarchical adjustment
2026-03-17 21:21:22.872617 INFO::Found  2  batches.
2026-03-17 21:21:22.873137 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:22.873743 INFO::Using default BPPARAM
2026-03-17 21:21:22.874249 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:22.875192 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-17 21:21:22.899902 INFO::Done
2026-03-17 21:21:22.900604 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:22.904166 INFO::ASW Batch was -0.0072075295135186 prior to batch effect correction and is now -0.0072075295135186 .
2026-03-17 21:21:22.905004 INFO::Total function execution time is  0.0598313808441162  s and adjustment time is  0.0274074077606201 s ( 45.81 )
2026-03-17 21:21:22.922909 INFO::Formatting Data.
2026-03-17 21:21:22.923763 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:22.92467 INFO::Removing potential empty rows and columns
2026-03-17 21:21:22.925681 INFO::Found  0  missing values.
2026-03-17 21:21:22.928569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:22.929098 INFO::Done
2026-03-17 21:21:22.929598 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:22.931585 INFO::Starting hierarchical adjustment
2026-03-17 21:21:22.932261 INFO::Found  3  batches.
2026-03-17 21:21:22.932783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:22.933363 INFO::Using default BPPARAM
2026-03-17 21:21:22.933883 INFO::Processing subtree level 1
2026-03-17 21:21:23.067073 INFO::Adjusting the last 1 batches sequentially
2026-03-17 21:21:23.068864 INFO::Done
2026-03-17 21:21:23.069497 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:23.071927 INFO::ASW Batch was -0.0231021849669541 prior to batch effect correction and is now -0.149776669536576 .
2026-03-17 21:21:23.072847 INFO::Total function execution time is  0.149953842163086  s and adjustment time is  0.136721611022949 s ( 91.18 )
2026-03-17 21:21:23.087013 INFO::Skipping initial DF formatting
2026-03-17 21:21:23.0877 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:23.09166 INFO::Starting hierarchical adjustment
2026-03-17 21:21:23.092428 INFO::Found  5  batches.
2026-03-17 21:21:23.092989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:23.093611 INFO::Using default BPPARAM
2026-03-17 21:21:23.094139 INFO::Processing subtree level 1
2026-03-17 21:21:23.322406 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:23.324065 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-17 21:21:23.343845 INFO::Done
2026-03-17 21:21:23.344573 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:23.348758 INFO::ASW Batch was 0.539859189154729 prior to batch effect correction and is now 0.539859189154729 .
2026-03-17 21:21:23.349357 INFO::ASW Label was 0.358649882092256 prior to batch effect correction and is now 0.358649882092256 .
2026-03-17 21:21:23.350202 INFO::Total function execution time is  0.263248920440674  s and adjustment time is  0.251546382904053 s ( 95.55 )
2026-03-17 21:21:23.413342 INFO::Formatting Data.
2026-03-17 21:21:23.41431 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:23.415351 INFO::Removing potential empty rows and columns
2026-03-17 21:21:23.41643 INFO::Found  0  missing values.
2026-03-17 21:21:23.420631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:23.421161 INFO::Done
2026-03-17 21:21:23.421685 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:23.424825 INFO::Starting hierarchical adjustment
2026-03-17 21:21:23.425567 INFO::Found  5  batches.
2026-03-17 21:21:23.426113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:23.426748 INFO::Using default BPPARAM
2026-03-17 21:21:23.42728 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.

2026-03-17 21:21:23.570755 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:23.57285 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-17 21:21:23.59316 INFO::Done
2026-03-17 21:21:23.594043 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:23.598136 INFO::ASW Batch was 0.452114201138332 prior to batch effect correction and is now -0.0480511178446716 .
2026-03-17 21:21:23.598864 INFO::ASW Label was 0.312829263238368 prior to batch effect correction and is now 0.815570018642705 .
2026-03-17 21:21:23.599778 INFO::Total function execution time is  0.1865553855896  s and adjustment time is  0.167656660079956 s ( 89.87 )
2026-03-17 21:21:23.600749 INFO::Formatting Data.
2026-03-17 21:21:23.60149 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:23.602601 INFO::Removing potential empty rows and columns
2026-03-17 21:21:23.603977 INFO::Found  0  missing values.
2026-03-17 21:21:23.608945 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:23.609632 INFO::Done
2026-03-17 21:21:23.610198 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:23.61394 INFO::Starting hierarchical adjustment
2026-03-17 21:21:23.614767 INFO::Found  5  batches.
2026-03-17 21:21:23.615361 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:23.616059 INFO::Using default BPPARAM
2026-03-17 21:21:23.616686 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.

2026-03-17 21:21:23.802606 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:23.804218 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-17 21:21:23.820241 INFO::Done
2026-03-17 21:21:23.820957 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:23.824372 INFO::ASW Batch was 0.452114201138332 prior to batch effect correction and is now -0.0480511178446716 .
2026-03-17 21:21:23.824981 INFO::ASW Label was 0.312829263238368 prior to batch effect correction and is now 0.815570018642705 .
2026-03-17 21:21:23.82579 INFO::Total function execution time is  0.225064992904663  s and adjustment time is  0.205642700195312 s ( 91.37 )
2026-03-17 21:21:23.839175 INFO::Formatting Data.
2026-03-17 21:21:23.839966 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:23.840981 INFO::Removing potential empty rows and columns
2026-03-17 21:21:23.842073 INFO::Found  0  missing values.
2026-03-17 21:21:23.846131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:23.846679 INFO::Done
2026-03-17 21:21:23.847206 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:23.850246 INFO::Starting hierarchical adjustment
2026-03-17 21:21:23.85097 INFO::Found  5  batches.
2026-03-17 21:21:23.851525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:23.852194 INFO::Using default BPPARAM
2026-03-17 21:21:23.852783 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.

2026-03-17 21:21:23.990134 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:23.992286 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-17 21:21:24.011094 INFO::Done
2026-03-17 21:21:24.012003 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.0159 INFO::ASW Batch was 0.476447005321408 prior to batch effect correction and is now -0.0474583154520416 .
2026-03-17 21:21:24.016608 INFO::ASW Label was 0.28198562763999 prior to batch effect correction and is now 0.741061012811778 .
2026-03-17 21:21:24.017559 INFO::Total function execution time is  0.178416013717651  s and adjustment time is  0.160195112228394 s ( 89.79 )
2026-03-17 21:21:24.018475 INFO::Formatting Data.
2026-03-17 21:21:24.019154 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.020151 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.021229 INFO::Found  0  missing values.
2026-03-17 21:21:24.025675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.026284 INFO::Done
2026-03-17 21:21:24.026839 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.030193 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.031001 INFO::Found  5  batches.
2026-03-17 21:21:24.031581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.032257 INFO::Using default BPPARAM
2026-03-17 21:21:24.032835 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.

2026-03-17 21:21:24.164206 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:24.166452 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-17 21:21:24.193686 INFO::Done
2026-03-17 21:21:24.194581 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.198527 INFO::ASW Batch was 0.476447005321408 prior to batch effect correction and is now -0.0474583154520416 .
2026-03-17 21:21:24.199184 INFO::ASW Label was 0.28198562763999 prior to batch effect correction and is now 0.741061012811778 .
2026-03-17 21:21:24.200076 INFO::Total function execution time is  0.181597232818604  s and adjustment time is  0.162822723388672 s ( 89.66 )
2026-03-17 21:21:24.214529 INFO::Formatting Data.
2026-03-17 21:21:24.215327 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.216329 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.217392 INFO::Found  0  missing values.
2026-03-17 21:21:24.220271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.220842 INFO::Done
2026-03-17 21:21:24.221388 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.224562 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.225328 INFO::Found  2  batches.
2026-03-17 21:21:24.225889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.22655 INFO::Using default BPPARAM
2026-03-17 21:21:24.227105 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:24.228031 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-17 21:21:24.243449 INFO::Done
2026-03-17 21:21:24.244128 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.247271 INFO::ASW Batch was 0.689862909076662 prior to batch effect correction and is now -0.0335739504026531 .
2026-03-17 21:21:24.24796 INFO::ASW Label was 0.351493569445958 prior to batch effect correction and is now 0.882734400586509 .
2026-03-17 21:21:24.248806 INFO::Total function execution time is  0.034360408782959  s and adjustment time is  0.0182688236236572 s ( 53.17 )
2026-03-17 21:21:24.249658 INFO::Formatting Data.
2026-03-17 21:21:24.250353 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.251305 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.252383 INFO::Found  0  missing values.
2026-03-17 21:21:24.255322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.255891 INFO::Done
2026-03-17 21:21:24.256437 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.259469 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.260231 INFO::Found  2  batches.
2026-03-17 21:21:24.26081 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.261432 INFO::Using default BPPARAM
2026-03-17 21:21:24.261985 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:24.262932 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-17 21:21:24.278096 INFO::Done
2026-03-17 21:21:24.278796 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.281944 INFO::ASW Batch was 0.689862909076662 prior to batch effect correction and is now -0.0335739504026531 .
2026-03-17 21:21:24.282552 INFO::ASW Label was 0.351493569445958 prior to batch effect correction and is now 0.882734400586509 .
2026-03-17 21:21:24.283349 INFO::Total function execution time is  0.0337295532226562  s and adjustment time is  0.0180025100708008 s ( 53.37 )
2026-03-17 21:21:24.295213 INFO::Formatting Data.
2026-03-17 21:21:24.296118 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.297044 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.297992 INFO::Found  0  missing values.
2026-03-17 21:21:24.300206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.300769 INFO::Done
2026-03-17 21:21:24.301289 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.303274 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.303992 INFO::Found  2  batches.
2026-03-17 21:21:24.304537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.305144 INFO::Using default BPPARAM
2026-03-17 21:21:24.305704 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:24.306622 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-17 21:21:24.337604 INFO::Done
2026-03-17 21:21:24.338294 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.340259 INFO::ASW Batch was -0.0774047322849037 prior to batch effect correction and is now -0.173660898158732 .
2026-03-17 21:21:24.341081 INFO::Total function execution time is  0.0459551811218262  s and adjustment time is  0.0337212085723877 s ( 73.38 )
2026-03-17 21:21:24.353848 INFO::Formatting Data.
2026-03-17 21:21:24.354701 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.355686 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.35682 INFO::Found  0  missing values.
2026-03-17 21:21:24.358056 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.
2026-03-17 21:21:24.363141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.363758 INFO::Done
2026-03-17 21:21:24.36433 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.367583 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.368332 INFO::Found  2  batches.
2026-03-17 21:21:24.368912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.369553 INFO::Using default BPPARAM
2026-03-17 21:21:24.37016 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:24.371162 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-17 21:21:24.389043 INFO::Done
2026-03-17 21:21:24.389805 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.393178 INFO::ASW Batch was 0.619292688853282 prior to batch effect correction and is now -0.021896636144115 .
2026-03-17 21:21:24.393852 INFO::ASW Label was 0.451016935806205 prior to batch effect correction and is now 0.916475955839287 .
2026-03-17 21:21:24.394708 INFO::Total function execution time is  0.0409324169158936  s and adjustment time is  0.0208361148834229 s ( 50.9 )
2026-03-17 21:21:24.395593 INFO::Formatting Data.
2026-03-17 21:21:24.396238 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.397202 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.398261 INFO::Found  0  missing values.
2026-03-17 21:21:24.399242 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.
2026-03-17 21:21:24.404139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.404742 INFO::Done
2026-03-17 21:21:24.405305 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.40844 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.409232 INFO::Found  2  batches.
2026-03-17 21:21:24.409806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.410456 INFO::Using default BPPARAM
2026-03-17 21:21:24.411032 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:24.412023 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-17 21:21:24.429764 INFO::Done
2026-03-17 21:21:24.43053 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.433867 INFO::ASW Batch was 0.619292688853282 prior to batch effect correction and is now -0.021896636144115 .
2026-03-17 21:21:24.434501 INFO::ASW Label was 0.451016935806205 prior to batch effect correction and is now 0.916475955839287 .
2026-03-17 21:21:24.435352 INFO::Total function execution time is  0.0397660732269287  s and adjustment time is  0.0206754207611084 s ( 51.99 )
2026-03-17 21:21:24.641784 INFO::Formatting Data.
2026-03-17 21:21:24.642582 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.643483 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.644526 INFO::Found  0  missing values.
2026-03-17 21:21:24.647623 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.648174 INFO::Done
2026-03-17 21:21:24.648694 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.650723 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.651418 INFO::Found  3  batches.
2026-03-17 21:21:24.651945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.652547 INFO::Using default BPPARAM
2026-03-17 21:21:24.653064 INFO::Processing subtree level 1
2026-03-17 21:21:24.738924 INFO::Adjusting the last 1 batches sequentially
2026-03-17 21:21:24.740819 INFO::Done
2026-03-17 21:21:24.741553 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.744118 INFO::ASW Batch was -0.151023746185324 prior to batch effect correction and is now -0.151023746185324 .
2026-03-17 21:21:24.745139 INFO::Total function execution time is  0.103447914123535  s and adjustment time is  0.0895051956176758 s ( 86.52 )
2026-03-17 21:21:24.746255 INFO::Formatting Data.
2026-03-17 21:21:24.746947 INFO::Typecasting input to dataframe.
2026-03-17 21:21:24.747749 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.748734 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.749928 INFO::Found  0  missing values.
2026-03-17 21:21:24.753207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.753789 INFO::Done
2026-03-17 21:21:24.754326 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.756533 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.757277 INFO::Found  3  batches.
2026-03-17 21:21:24.757834 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.758481 INFO::Using default BPPARAM
2026-03-17 21:21:24.759031 INFO::Processing subtree level 1
2026-03-17 21:21:24.843932 INFO::Adjusting the last 1 batches sequentially
2026-03-17 21:21:24.84578 INFO::Done
2026-03-17 21:21:24.846462 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.848976 INFO::ASW Batch was -0.151023746185324 prior to batch effect correction and is now -0.151023746185324 .
2026-03-17 21:21:24.849944 INFO::Total function execution time is  0.10367751121521  s and adjustment time is  0.0886311531066895 s ( 85.49 )
2026-03-17 21:21:24.863117 INFO::Formatting Data.
2026-03-17 21:21:24.863914 INFO::Typecasting input to dataframe.
2026-03-17 21:21:24.864777 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:24.865698 INFO::Removing potential empty rows and columns
2026-03-17 21:21:24.866767 INFO::Found  0  missing values.
2026-03-17 21:21:24.869769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:24.870302 INFO::Done
2026-03-17 21:21:24.870839 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:24.872887 INFO::Starting hierarchical adjustment
2026-03-17 21:21:24.873609 INFO::Found  3  batches.
2026-03-17 21:21:24.874134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:24.874776 INFO::Using default BPPARAM
2026-03-17 21:21:24.875303 INFO::Processing subtree level 1
2026-03-17 21:21:24.956636 INFO::Adjusting the last 1 batches sequentially
2026-03-17 21:21:24.958349 INFO::Done
2026-03-17 21:21:24.958968 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:24.961382 INFO::ASW Batch was -0.0856123696757841 prior to batch effect correction and is now -0.0856123696757841 .
2026-03-17 21:21:24.962305 INFO::Total function execution time is  0.0992457866668701  s and adjustment time is  0.0848784446716309 s ( 85.52 )
2026-03-17 21:21:25.092847 INFO::Formatting Data.
2026-03-17 21:21:25.093657 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:25.094786 INFO::Removing potential empty rows and columns
2026-03-17 21:21:25.09757 INFO::Found  1000  missing values.
2026-03-17 21:21:25.11671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:25.117423 INFO::Done
2026-03-17 21:21:25.117994 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:25.123437 INFO::Starting hierarchical adjustment
2026-03-17 21:21:25.124258 INFO::Found  10  batches.
2026-03-17 21:21:25.124809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:25.125428 INFO::Using default BPPARAM
2026-03-17 21:21:25.125964 INFO::Processing subtree level 1
2026-03-17 21:21:25.264569 INFO::Processing subtree level 2
2026-03-17 21:21:25.404959 INFO::Adjusting the last 1 batches sequentially
2026-03-17 21:21:25.407085 INFO::Done
2026-03-17 21:21:25.407794 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:25.413551 INFO::ASW Batch was 0.566583345434445 prior to batch effect correction and is now 0.566583345434445 .
2026-03-17 21:21:25.414217 INFO::ASW Label was 0.290161366164398 prior to batch effect correction and is now 0.290161366164398 .
2026-03-17 21:21:25.415602 INFO::Total function execution time is  0.322671890258789  s and adjustment time is  0.282964944839478 s ( 87.69 )
2026-03-17 21:21:25.416699 INFO::Formatting Data.
2026-03-17 21:21:25.417393 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:25.418747 INFO::Removing potential empty rows and columns
2026-03-17 21:21:25.421656 INFO::Found  1000  missing values.
2026-03-17 21:21:25.440616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:25.441389 INFO::Done
2026-03-17 21:21:25.44197 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:25.447614 INFO::Starting hierarchical adjustment
2026-03-17 21:21:25.44843 INFO::Found  10  batches.
2026-03-17 21:21:26.359558 INFO::Set up parallel execution backend with 2 workers
2026-03-17 21:21:26.361496 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-17 21:21:27.406386 INFO::Adjusting the last 2 batches sequentially
2026-03-17 21:21:27.408062 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-17 21:21:27.423677 INFO::Done
2026-03-17 21:21:27.424296 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:27.42865 INFO::ASW Batch was 0.566583345434445 prior to batch effect correction and is now 0.566583345434445 .
2026-03-17 21:21:27.429201 INFO::ASW Label was 0.290161366164398 prior to batch effect correction and is now 0.290161366164398 .
2026-03-17 21:21:27.42991 INFO::Total function execution time is  2.01327848434448  s and adjustment time is  1.97539854049683 s ( 98.12 )
2026-03-17 21:21:27.568127 INFO::Formatting Data.
2026-03-17 21:21:27.568903 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:27.569788 INFO::Removing potential empty rows and columns
2026-03-17 21:21:27.570812 INFO::Found  0  missing values.
2026-03-17 21:21:27.574217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:27.574739 INFO::Done
2026-03-17 21:21:27.575225 INFO::Acquiring quality metrics before batch effect correction.
2026-03-17 21:21:27.577809 INFO::Starting hierarchical adjustment
2026-03-17 21:21:27.578467 INFO::Found  3  batches.
2026-03-17 21:21:27.578966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-17 21:21:27.579543 INFO::Using default BPPARAM
2026-03-17 21:21:27.580035 INFO::Processing subtree level 1
2026-03-17 21:21:27.679796 INFO::Adjusting the last 1 batches sequentially
2026-03-17 21:21:27.681529 INFO::Done
2026-03-17 21:21:27.682144 INFO::Acquiring quality metrics after batch effect correction.
2026-03-17 21:21:27.685253 INFO::ASW Batch was 0.218745533779461 prior to batch effect correction and is now -0.136140280871877 .
2026-03-17 21:21:27.685872 INFO::ASW Label was -0.212779153248609 prior to batch effect correction and is now -0.0444274926664619 .
2026-03-17 21:21:27.686773 INFO::Total function execution time is  0.118707418441772  s and adjustment time is  0.103152990341187 s ( 86.9 )
2026-03-17 21:21:27.803997 INFO::Formatting Data.
2026-03-17 21:21:27.804855 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:27.805771 INFO::Removing potential empty rows and columns
2026-03-17 21:21:27.806776 INFO::Found  2  missing values.
2026-03-17 21:21:27.809615 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:27.81015 INFO::Done
2026-03-17 21:21:27.839129 INFO::Found NA in Reference column
2026-03-17 21:21:27.848903 INFO::Require at least two references per batch.
2026-03-17 21:21:27.869233 INFO::Formatting Data.
2026-03-17 21:21:27.869975 INFO::Recognized SummarizedExperiment
2026-03-17 21:21:27.870527 INFO::Typecasting input to dataframe.
2026-03-17 21:21:27.880002 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:27.881176 INFO::Removing potential empty rows and columns
2026-03-17 21:21:27.884516 INFO::Found  0  missing values.
2026-03-17 21:21:27.890969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:27.891567 INFO::Done
2026-03-17 21:21:27.907408 INFO::Formatting Data.
2026-03-17 21:21:27.908242 INFO::Recognized SummarizedExperiment
2026-03-17 21:21:27.908818 INFO::Typecasting input to dataframe.
2026-03-17 21:21:27.925976 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:27.927221 INFO::Removing potential empty rows and columns
2026-03-17 21:21:27.930537 INFO::Found  0  missing values.
2026-03-17 21:21:27.940526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:27.941129 INFO::Done
2026-03-17 21:21:27.955699 INFO::Formatting Data.
2026-03-17 21:21:27.956358 INFO::Recognized SummarizedExperiment
2026-03-17 21:21:27.956869 INFO::Typecasting input to dataframe.
2026-03-17 21:21:27.972164 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:27.973126 INFO::Removing potential empty rows and columns
2026-03-17 21:21:27.974126 INFO::Found  0  missing values.
2026-03-17 21:21:27.974989 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.
2026-03-17 21:21:27.979035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:27.979535 INFO::Done
2026-03-17 21:21:27.988831 INFO::Formatting Data.
2026-03-17 21:21:27.989501 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:27.990296 INFO::Removing potential empty rows and columns
2026-03-17 21:21:27.99122 INFO::Found  0  missing values.
2026-03-17 21:21:27.993841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:27.994339 INFO::Done
2026-03-17 21:21:28.004833 INFO::Formatting Data.
2026-03-17 21:21:28.005558 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:28.006479 INFO::Removing potential empty rows and columns
2026-03-17 21:21:28.007437 INFO::Found  0  missing values.
2026-03-17 21:21:28.010116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:28.010636 INFO::Done
2026-03-17 21:21:28.03845 INFO::Formatting Data.
2026-03-17 21:21:28.039296 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:28.040417 INFO::Removing potential empty rows and columns
2026-03-17 21:21:28.041546 INFO::Found  1  missing values.
2026-03-17 21:21:28.044071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:28.044591 INFO::Done
2026-03-17 21:21:28.062427 INFO::Formatting Data.
2026-03-17 21:21:28.06324 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:28.064065 INFO::Removing potential empty rows and columns
2026-03-17 21:21:28.064987 INFO::Found  2  missing values.
2026-03-17 21:21:28.065865 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.
2026-03-17 21:21:28.068034 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:28.068558 INFO::Done
2026-03-17 21:21:28.078086 INFO::Formatting Data.
2026-03-17 21:21:28.078811 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:28.079626 INFO::Removing potential empty rows and columns
2026-03-17 21:21:28.080498 INFO::Found  2  missing values.
2026-03-17 21:21:28.082059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:28.082581 INFO::Done
2026-03-17 21:21:28.092358 INFO::Formatting Data.
2026-03-17 21:21:28.093149 INFO::Typecasting input to dataframe.
2026-03-17 21:21:28.093925 INFO::Replacing NaNs with NAs.
2026-03-17 21:21:28.094723 INFO::Removing potential empty rows and columns
2026-03-17 21:21:28.095651 INFO::Found  0  missing values.
2026-03-17 21:21:28.098367 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-17 21:21:28.09888 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.040   3.126  19.865

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT25.119 1.70918.256
compute_asw0.0240.0010.024
count_existing0.0120.0010.013
generate_data_covariables0.0100.0020.012
generate_dataset0.0110.0000.012