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This page was generated on 2025-11-22 11:38 -0500 (Sat, 22 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4829
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4603
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4567
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 167/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.7.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-11-21 13:40 -0500 (Fri, 21 Nov 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: devel
git_last_commit: 2e49878
git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for BERT on lconway

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: 1.7.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
StartedAt: 2025-11-21 19:36:56 -0500 (Fri, 21 Nov 2025)
EndedAt: 2025-11-21 19:38:32 -0500 (Fri, 21 Nov 2025)
EllapsedTime: 96.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 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 29.335  1.602  21.198
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.7.0’
** 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 Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
2025-11-21 19:38:09.335925 INFO::Formatting Data.
2025-11-21 19:38:09.340177 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:09.356441 INFO::Removing potential empty rows and columns
2025-11-21 19:38:09.695263 INFO::Found  0  missing values.
2025-11-21 19:38:09.700277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:09.701278 INFO::Done
2025-11-21 19:38:09.702094 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:09.720316 INFO::Starting hierarchical adjustment
2025-11-21 19:38:09.721318 INFO::Found  3  batches.
2025-11-21 19:38:09.722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:09.723723 INFO::Using default BPPARAM
2025-11-21 19:38:09.724554 INFO::Processing subtree level 1
2025-11-21 19:38:09.91883 INFO::Adjusting the last 1 batches sequentially
2025-11-21 19:38:09.923389 INFO::Done
2025-11-21 19:38:09.925348 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:09.928765 INFO::ASW Batch was 0.00940265522236144 prior to batch effect correction and is now 0.00940265522236144 .
2025-11-21 19:38:09.931174 INFO::Total function execution time is  0.595486879348755  s and adjustment time is  0.202162027359009 s ( 33.95 )
2025-11-21 19:38:09.954101 INFO::Formatting Data.
2025-11-21 19:38:09.955257 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:09.956682 INFO::Removing potential empty rows and columns
2025-11-21 19:38:09.962935 INFO::Found  0  missing values.
2025-11-21 19:38:09.964644 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.
2025-11-21 19:38:09.979191 INFO::Formatting Data.
2025-11-21 19:38:09.981792 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:09.983421 INFO::Removing potential empty rows and columns
2025-11-21 19:38:09.985458 INFO::Found  0  missing values.
2025-11-21 19:38:09.986626 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.
2025-11-21 19:38:10.012544 INFO::Formatting Data.
2025-11-21 19:38:10.013357 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:10.01472 INFO::Removing potential empty rows and columns
2025-11-21 19:38:10.015954 INFO::Found  0  missing values.
2025-11-21 19:38:10.017613 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.
2025-11-21 19:38:10.02354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:10.024463 INFO::Done
2025-11-21 19:38:10.025026 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:10.027334 INFO::Starting hierarchical adjustment
2025-11-21 19:38:10.028098 INFO::Found  2  batches.
2025-11-21 19:38:10.028624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:10.029467 INFO::Using default BPPARAM
2025-11-21 19:38:10.03022 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:10.031665 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 19:38:10.05922 INFO::Done
2025-11-21 19:38:10.061192 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:10.064345 INFO::ASW Batch was 0.0298441836678398 prior to batch effect correction and is now -0.120328099918826 .
2025-11-21 19:38:10.06541 INFO::Total function execution time is  0.0529000759124756  s and adjustment time is  0.0312399864196777 s ( 59.05 )
2025-11-21 19:38:10.069449 INFO::Formatting Data.
2025-11-21 19:38:10.070474 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:10.082172 INFO::Formatting Data.
2025-11-21 19:38:10.082953 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:10.084334 INFO::Removing potential empty rows and columns
2025-11-21 19:38:10.08605 INFO::Found  0  missing values.
2025-11-21 19:38:10.090107 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:10.090977 INFO::Done
2025-11-21 19:38:10.091777 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:10.094357 INFO::Starting hierarchical adjustment
2025-11-21 19:38:10.095064 INFO::Found  2  batches.
2025-11-21 19:38:10.095553 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:10.096486 INFO::Using default BPPARAM
2025-11-21 19:38:10.097277 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:10.098577 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 19:38:10.152605 INFO::Done
2025-11-21 19:38:10.153538 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:10.156201 INFO::ASW Batch was 0.00392467376081469 prior to batch effect correction and is now -0.125055097445998 .
2025-11-21 19:38:10.15733 INFO::Total function execution time is  0.0753118991851807  s and adjustment time is  0.0576169490814209 s ( 76.5 )
2025-11-21 19:38:10.158815 INFO::Formatting Data.
2025-11-21 19:38:10.15971 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:10.160902 INFO::Removing potential empty rows and columns
2025-11-21 19:38:10.162295 INFO::Found  0  missing values.
2025-11-21 19:38:10.165106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:10.165873 INFO::Done
2025-11-21 19:38:10.166637 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:10.169128 INFO::Starting hierarchical adjustment
2025-11-21 19:38:10.170026 INFO::Found  2  batches.
2025-11-21 19:38:10.170697 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:10.171445 INFO::Using default BPPARAM
2025-11-21 19:38:10.172101 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:10.17325 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 19:38:10.193395 INFO::Done
2025-11-21 19:38:10.194242 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:10.196837 INFO::ASW Batch was 0.00392467376081469 prior to batch effect correction and is now -0.125055097445998 .
2025-11-21 19:38:10.197662 INFO::Total function execution time is  0.0388920307159424  s and adjustment time is  0.023500919342041 s ( 60.43 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-21 19:38:13.662637 INFO::Formatting Data.
2025-11-21 19:38:13.663567 INFO::Recognized SummarizedExperiment
2025-11-21 19:38:13.66431 INFO::Typecasting input to dataframe.
2025-11-21 19:38:13.700489 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:13.701597 INFO::Removing potential empty rows and columns
2025-11-21 19:38:13.705852 INFO::Found  0  missing values.
2025-11-21 19:38:13.713257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:13.71388 INFO::Done
2025-11-21 19:38:13.71434 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:13.718761 INFO::Starting hierarchical adjustment
2025-11-21 19:38:13.719696 INFO::Found  2  batches.
2025-11-21 19:38:13.720766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:13.722334 INFO::Using default BPPARAM
2025-11-21 19:38:13.722913 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:13.723886 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 19:38:13.785017 INFO::Done
2025-11-21 19:38:13.786016 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:13.791275 INFO::ASW Batch was -0.007441952483421 prior to batch effect correction and is now -0.0908263257609678 .
2025-11-21 19:38:13.792587 INFO::Total function execution time is  0.130289793014526  s and adjustment time is  0.0655770301818848 s ( 50.33 )
Warning: stack imbalance in '{', 73 then 75
2025-11-21 19:38:13.818444 INFO::Formatting Data.
2025-11-21 19:38:13.819156 INFO::Recognized SummarizedExperiment
2025-11-21 19:38:13.819685 INFO::Typecasting input to dataframe.
2025-11-21 19:38:13.831976 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:13.833814 INFO::Removing potential empty rows and columns
2025-11-21 19:38:13.838607 INFO::Found  0  missing values.
2025-11-21 19:38:13.847715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:13.848334 INFO::Done
2025-11-21 19:38:13.848788 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:13.852082 INFO::Starting hierarchical adjustment
2025-11-21 19:38:13.853087 INFO::Found  2  batches.
2025-11-21 19:38:13.853917 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:13.854648 INFO::Using default BPPARAM
2025-11-21 19:38:13.855215 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:13.856604 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 19:38:13.885245 INFO::Done
2025-11-21 19:38:13.88628 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:13.891667 INFO::ASW Batch was 0.014534968098733 prior to batch effect correction and is now 0.014534968098733 .
2025-11-21 19:38:13.892576 INFO::Total function execution time is  0.0741097927093506  s and adjustment time is  0.0323121547698975 s ( 43.6 )
2025-11-21 19:38:13.918765 INFO::Formatting Data.
2025-11-21 19:38:13.919554 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:13.920468 INFO::Removing potential empty rows and columns
2025-11-21 19:38:13.921766 INFO::Found  0  missing values.
2025-11-21 19:38:13.924784 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:13.925641 INFO::Done
2025-11-21 19:38:13.926339 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:13.928351 INFO::Starting hierarchical adjustment
2025-11-21 19:38:13.929075 INFO::Found  3  batches.
2025-11-21 19:38:13.929712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:13.930561 INFO::Using default BPPARAM
2025-11-21 19:38:13.931305 INFO::Processing subtree level 1
2025-11-21 19:38:14.147924 INFO::Adjusting the last 1 batches sequentially
2025-11-21 19:38:14.156258 INFO::Done
2025-11-21 19:38:14.158386 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:14.166079 INFO::ASW Batch was -0.132271883421099 prior to batch effect correction and is now -0.181752006924298 .
2025-11-21 19:38:14.170087 INFO::Total function execution time is  0.25052809715271  s and adjustment time is  0.227288961410522 s ( 90.72 )
2025-11-21 19:38:14.199495 INFO::Skipping initial DF formatting
2025-11-21 19:38:14.200315 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:14.20575 INFO::Starting hierarchical adjustment
2025-11-21 19:38:14.206991 INFO::Found  5  batches.
2025-11-21 19:38:14.207624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:14.208451 INFO::Using default BPPARAM
2025-11-21 19:38:14.209063 INFO::Processing subtree level 1
2025-11-21 19:38:14.38831 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:14.398819 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 19:38:14.429569 INFO::Done
2025-11-21 19:38:14.431381 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:14.440447 INFO::ASW Batch was 0.518440532103084 prior to batch effect correction and is now 0.518440532103084 .
2025-11-21 19:38:14.44241 INFO::ASW Label was 0.40080625375995 prior to batch effect correction and is now 0.40080625375995 .
2025-11-21 19:38:14.445248 INFO::Total function execution time is  0.24536395072937  s and adjustment time is  0.222774028778076 s ( 90.79 )
2025-11-21 19:38:14.480697 INFO::Formatting Data.
2025-11-21 19:38:14.481859 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:14.483189 INFO::Removing potential empty rows and columns
2025-11-21 19:38:14.484576 INFO::Found  0  missing values.
2025-11-21 19:38:14.490593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:14.49153 INFO::Done
2025-11-21 19:38:14.492323 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:14.496617 INFO::Starting hierarchical adjustment
2025-11-21 19:38:14.497807 INFO::Found  5  batches.
2025-11-21 19:38:14.498742 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:14.499903 INFO::Using default BPPARAM
2025-11-21 19:38:14.502609 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.

2025-11-21 19:38:14.663914 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:14.676989 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 19:38:14.707203 INFO::Done
2025-11-21 19:38:14.708816 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:14.714627 INFO::ASW Batch was 0.40399811469472 prior to batch effect correction and is now -0.103314446689452 .
2025-11-21 19:38:14.715626 INFO::ASW Label was 0.324071228861409 prior to batch effect correction and is now 0.753470161438411 .
2025-11-21 19:38:14.719051 INFO::Total function execution time is  0.237436056137085  s and adjustment time is  0.209563016891479 s ( 88.26 )
2025-11-21 19:38:14.720421 INFO::Formatting Data.
2025-11-21 19:38:14.721088 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:14.721947 INFO::Removing potential empty rows and columns
2025-11-21 19:38:14.722867 INFO::Found  0  missing values.
2025-11-21 19:38:14.729097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:14.730179 INFO::Done
2025-11-21 19:38:14.73111 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:14.735062 INFO::Starting hierarchical adjustment
2025-11-21 19:38:14.736292 INFO::Found  5  batches.
2025-11-21 19:38:14.73707 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:14.737929 INFO::Using default BPPARAM
2025-11-21 19:38:14.738653 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.

2025-11-21 19:38:14.903445 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:14.912285 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 19:38:14.941909 INFO::Done
2025-11-21 19:38:14.94271 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:14.948207 INFO::ASW Batch was 0.40399811469472 prior to batch effect correction and is now -0.103314446689452 .
2025-11-21 19:38:14.94943 INFO::ASW Label was 0.324071228861409 prior to batch effect correction and is now 0.753470161438411 .
2025-11-21 19:38:14.951991 INFO::Total function execution time is  0.231059074401855  s and adjustment time is  0.205641984939575 s ( 89 )
2025-11-21 19:38:14.976947 INFO::Formatting Data.
2025-11-21 19:38:14.97805 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:14.979065 INFO::Removing potential empty rows and columns
2025-11-21 19:38:14.980946 INFO::Found  0  missing values.
2025-11-21 19:38:14.986696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:14.989359 INFO::Done
2025-11-21 19:38:14.990208 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:14.994162 INFO::Starting hierarchical adjustment
2025-11-21 19:38:14.995392 INFO::Found  5  batches.
2025-11-21 19:38:14.996319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:14.996972 INFO::Using default BPPARAM
2025-11-21 19:38:14.997474 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.

2025-11-21 19:38:15.150297 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:15.161986 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 19:38:15.188709 INFO::Done
2025-11-21 19:38:15.190653 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:15.19616 INFO::ASW Batch was 0.527404346170636 prior to batch effect correction and is now -0.10010244950043 .
2025-11-21 19:38:15.197333 INFO::ASW Label was 0.253348447847371 prior to batch effect correction and is now 0.868325162564587 .
2025-11-21 19:38:15.200637 INFO::Total function execution time is  0.222916841506958  s and adjustment time is  0.193691968917847 s ( 86.89 )
2025-11-21 19:38:15.202594 INFO::Formatting Data.
2025-11-21 19:38:15.203519 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:15.204853 INFO::Removing potential empty rows and columns
2025-11-21 19:38:15.206397 INFO::Found  0  missing values.
2025-11-21 19:38:15.211368 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:15.211989 INFO::Done
2025-11-21 19:38:15.212526 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:15.215829 INFO::Starting hierarchical adjustment
2025-11-21 19:38:15.216538 INFO::Found  5  batches.
2025-11-21 19:38:15.217039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:15.217626 INFO::Using default BPPARAM
2025-11-21 19:38:15.218116 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.

2025-11-21 19:38:15.375653 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:15.394342 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 19:38:15.425294 INFO::Done
2025-11-21 19:38:15.426604 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:15.431455 INFO::ASW Batch was 0.527404346170636 prior to batch effect correction and is now -0.10010244950043 .
2025-11-21 19:38:15.433093 INFO::ASW Label was 0.253348447847371 prior to batch effect correction and is now 0.868325162564587 .
2025-11-21 19:38:15.435438 INFO::Total function execution time is  0.232531070709229  s and adjustment time is  0.208817005157471 s ( 89.8 )
2025-11-21 19:38:15.46166 INFO::Formatting Data.
2025-11-21 19:38:15.462777 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:15.463979 INFO::Removing potential empty rows and columns
2025-11-21 19:38:15.465564 INFO::Found  0  missing values.
2025-11-21 19:38:15.469667 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:15.472938 INFO::Done
2025-11-21 19:38:15.473815 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:15.477884 INFO::Starting hierarchical adjustment
2025-11-21 19:38:15.478976 INFO::Found  2  batches.
2025-11-21 19:38:15.479768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:15.480717 INFO::Using default BPPARAM
2025-11-21 19:38:15.48156 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:15.482597 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 19:38:15.502204 INFO::Done
2025-11-21 19:38:15.503228 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:15.508982 INFO::ASW Batch was 0.549186356651276 prior to batch effect correction and is now 0.0339049879078884 .
2025-11-21 19:38:15.511365 INFO::ASW Label was 0.554783925411631 prior to batch effect correction and is now 0.894235257755735 .
2025-11-21 19:38:15.514003 INFO::Total function execution time is  0.0517780780792236  s and adjustment time is  0.0233879089355469 s ( 45.17 )
2025-11-21 19:38:15.516086 INFO::Formatting Data.
2025-11-21 19:38:15.517932 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:15.520357 INFO::Removing potential empty rows and columns
2025-11-21 19:38:15.521878 INFO::Found  0  missing values.
2025-11-21 19:38:15.525695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:15.526539 INFO::Done
2025-11-21 19:38:15.527302 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:15.531442 INFO::Starting hierarchical adjustment
2025-11-21 19:38:15.532627 INFO::Found  2  batches.
2025-11-21 19:38:15.533421 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:15.534169 INFO::Using default BPPARAM
2025-11-21 19:38:15.534881 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:15.536118 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 19:38:15.555513 INFO::Done
2025-11-21 19:38:15.557362 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:15.561518 INFO::ASW Batch was 0.549186356651276 prior to batch effect correction and is now 0.0339049879078884 .
2025-11-21 19:38:15.562328 INFO::ASW Label was 0.554783925411631 prior to batch effect correction and is now 0.894235257755735 .
2025-11-21 19:38:15.56309 INFO::Total function execution time is  0.0471830368041992  s and adjustment time is  0.0231189727783203 s ( 49 )
2025-11-21 19:38:15.584505 INFO::Formatting Data.
2025-11-21 19:38:15.585605 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:15.586725 INFO::Removing potential empty rows and columns
2025-11-21 19:38:15.588133 INFO::Found  0  missing values.
2025-11-21 19:38:15.591806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:15.592393 INFO::Done
2025-11-21 19:38:15.593298 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:15.595836 INFO::Starting hierarchical adjustment
2025-11-21 19:38:15.596546 INFO::Found  2  batches.
2025-11-21 19:38:15.597164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:15.598245 INFO::Using default BPPARAM
2025-11-21 19:38:15.599326 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:15.600779 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 19:38:15.645385 INFO::Done
2025-11-21 19:38:15.646639 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:15.648999 INFO::ASW Batch was -0.0408373105899747 prior to batch effect correction and is now -0.17701648511223 .
2025-11-21 19:38:15.650005 INFO::Total function execution time is  0.0656418800354004  s and adjustment time is  0.0489399433135986 s ( 74.56 )
2025-11-21 19:38:15.67252 INFO::Formatting Data.
2025-11-21 19:38:15.673638 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:15.67491 INFO::Removing potential empty rows and columns
2025-11-21 19:38:15.676312 INFO::Found  0  missing values.
2025-11-21 19:38:15.677921 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.
2025-11-21 19:38:15.684449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:15.690262 INFO::Done
2025-11-21 19:38:15.69138 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:15.695807 INFO::Starting hierarchical adjustment
2025-11-21 19:38:15.697179 INFO::Found  2  batches.
2025-11-21 19:38:15.698199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:15.698904 INFO::Using default BPPARAM
2025-11-21 19:38:15.699446 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:15.700606 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 19:38:15.723646 INFO::Done
2025-11-21 19:38:15.724627 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:15.729218 INFO::ASW Batch was 0.3571858578548 prior to batch effect correction and is now 0.00147596703461715 .
2025-11-21 19:38:15.730072 INFO::ASW Label was 0.697351172134281 prior to batch effect correction and is now 0.911700997507306 .
2025-11-21 19:38:15.731228 INFO::Total function execution time is  0.0588119029998779  s and adjustment time is  0.026792049407959 s ( 45.56 )
2025-11-21 19:38:15.732323 INFO::Formatting Data.
2025-11-21 19:38:15.733173 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:15.734428 INFO::Removing potential empty rows and columns
2025-11-21 19:38:15.735907 INFO::Found  0  missing values.
2025-11-21 19:38:15.737192 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.
2025-11-21 19:38:15.743448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:15.747002 INFO::Done
2025-11-21 19:38:15.747954 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:15.752161 INFO::Starting hierarchical adjustment
2025-11-21 19:38:15.75323 INFO::Found  2  batches.
2025-11-21 19:38:15.753983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:15.754984 INFO::Using default BPPARAM
2025-11-21 19:38:15.755789 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:15.757322 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 19:38:15.780113 INFO::Done
2025-11-21 19:38:15.780851 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:15.784527 INFO::ASW Batch was 0.3571858578548 prior to batch effect correction and is now 0.00147596703461715 .
2025-11-21 19:38:15.785139 INFO::ASW Label was 0.697351172134281 prior to batch effect correction and is now 0.911700997507306 .
2025-11-21 19:38:15.785949 INFO::Total function execution time is  0.0536611080169678  s and adjustment time is  0.0270760059356689 s ( 50.46 )
2025-11-21 19:38:16.0715 INFO::Formatting Data.
2025-11-21 19:38:16.074341 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:16.075678 INFO::Removing potential empty rows and columns
2025-11-21 19:38:16.07733 INFO::Found  0  missing values.
2025-11-21 19:38:16.08082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:16.081424 INFO::Done
2025-11-21 19:38:16.082102 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:16.08451 INFO::Starting hierarchical adjustment
2025-11-21 19:38:16.085363 INFO::Found  3  batches.
2025-11-21 19:38:16.086064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:16.086748 INFO::Using default BPPARAM
2025-11-21 19:38:16.087459 INFO::Processing subtree level 1
2025-11-21 19:38:16.227668 INFO::Adjusting the last 1 batches sequentially
2025-11-21 19:38:16.241009 INFO::Done
2025-11-21 19:38:16.246526 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:16.258341 INFO::ASW Batch was -0.0731761618775792 prior to batch effect correction and is now -0.0731761618775792 .
2025-11-21 19:38:16.262211 INFO::Total function execution time is  0.190034866333008  s and adjustment time is  0.155748128890991 s ( 81.96 )
2025-11-21 19:38:16.263892 INFO::Formatting Data.
2025-11-21 19:38:16.264693 INFO::Typecasting input to dataframe.
2025-11-21 19:38:16.266536 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:16.269089 INFO::Removing potential empty rows and columns
2025-11-21 19:38:16.2721 INFO::Found  0  missing values.
2025-11-21 19:38:16.277353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:16.278103 INFO::Done
2025-11-21 19:38:16.278606 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:16.281215 INFO::Starting hierarchical adjustment
2025-11-21 19:38:16.282676 INFO::Found  3  batches.
2025-11-21 19:38:16.283441 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:16.284338 INFO::Using default BPPARAM
2025-11-21 19:38:16.285037 INFO::Processing subtree level 1
2025-11-21 19:38:16.415271 INFO::Adjusting the last 1 batches sequentially
2025-11-21 19:38:16.430008 INFO::Done
2025-11-21 19:38:16.432587 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:16.439708 INFO::ASW Batch was -0.0731761618775792 prior to batch effect correction and is now -0.0731761618775792 .
2025-11-21 19:38:16.44636 INFO::Total function execution time is  0.181149005889893  s and adjustment time is  0.147395133972168 s ( 81.37 )
2025-11-21 19:38:16.471732 INFO::Formatting Data.
2025-11-21 19:38:16.472836 INFO::Typecasting input to dataframe.
2025-11-21 19:38:16.474195 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:16.475166 INFO::Removing potential empty rows and columns
2025-11-21 19:38:16.476421 INFO::Found  0  missing values.
2025-11-21 19:38:16.485516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:16.486511 INFO::Done
2025-11-21 19:38:16.487362 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:16.490189 INFO::Starting hierarchical adjustment
2025-11-21 19:38:16.491266 INFO::Found  3  batches.
2025-11-21 19:38:16.492061 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:16.492953 INFO::Using default BPPARAM
2025-11-21 19:38:16.493711 INFO::Processing subtree level 1
2025-11-21 19:38:16.634721 INFO::Adjusting the last 1 batches sequentially
2025-11-21 19:38:16.641792 INFO::Done
2025-11-21 19:38:16.643951 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:16.651203 INFO::ASW Batch was -0.066398273074379 prior to batch effect correction and is now -0.066398273074379 .
2025-11-21 19:38:16.655691 INFO::Total function execution time is  0.183202981948853  s and adjustment time is  0.150722026824951 s ( 82.27 )
2025-11-21 19:38:16.89227 INFO::Formatting Data.
2025-11-21 19:38:16.893705 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:16.894901 INFO::Removing potential empty rows and columns
2025-11-21 19:38:16.898481 INFO::Found  1000  missing values.
2025-11-21 19:38:16.923537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:16.92441 INFO::Done
2025-11-21 19:38:16.925224 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:16.93282 INFO::Starting hierarchical adjustment
2025-11-21 19:38:16.934211 INFO::Found  10  batches.
2025-11-21 19:38:16.935292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:16.936277 INFO::Using default BPPARAM
2025-11-21 19:38:16.937256 INFO::Processing subtree level 1
2025-11-21 19:38:17.125204 INFO::Processing subtree level 2
2025-11-21 19:38:17.538865 INFO::Adjusting the last 1 batches sequentially
2025-11-21 19:38:17.543083 INFO::Done
2025-11-21 19:38:17.546664 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:17.582573 INFO::ASW Batch was 0.481188051242821 prior to batch effect correction and is now 0.481188051242821 .
2025-11-21 19:38:17.583946 INFO::ASW Label was 0.345127323817332 prior to batch effect correction and is now 0.345127323817332 .
2025-11-21 19:38:17.590299 INFO::Total function execution time is  0.696448087692261  s and adjustment time is  0.609307050704956 s ( 87.49 )
2025-11-21 19:38:17.593465 INFO::Formatting Data.
2025-11-21 19:38:17.594633 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:17.596502 INFO::Removing potential empty rows and columns
2025-11-21 19:38:17.602717 INFO::Found  1000  missing values.
2025-11-21 19:38:17.695989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:17.697068 INFO::Done
2025-11-21 19:38:17.6979 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:17.706638 INFO::Starting hierarchical adjustment
2025-11-21 19:38:17.707727 INFO::Found  10  batches.
2025-11-21 19:38:18.822796 INFO::Set up parallel execution backend with 2 workers
2025-11-21 19:38:18.823458 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-21 19:38:20.271696 INFO::Adjusting the last 2 batches sequentially
2025-11-21 19:38:20.273515 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 19:38:20.291328 INFO::Done
2025-11-21 19:38:20.291981 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:20.298242 INFO::ASW Batch was 0.481188051242821 prior to batch effect correction and is now 0.481188051242821 .
2025-11-21 19:38:20.299088 INFO::ASW Label was 0.345127323817332 prior to batch effect correction and is now 0.345127323817332 .
2025-11-21 19:38:20.30019 INFO::Total function execution time is  2.70688891410828  s and adjustment time is  2.58390712738037 s ( 95.46 )
2025-11-21 19:38:20.547367 INFO::Formatting Data.
2025-11-21 19:38:20.548764 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:20.550371 INFO::Removing potential empty rows and columns
2025-11-21 19:38:20.552181 INFO::Found  0  missing values.
2025-11-21 19:38:20.556058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:20.556663 INFO::Done
2025-11-21 19:38:20.557231 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 19:38:20.560558 INFO::Starting hierarchical adjustment
2025-11-21 19:38:20.561318 INFO::Found  3  batches.
2025-11-21 19:38:20.561888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 19:38:20.562549 INFO::Using default BPPARAM
2025-11-21 19:38:20.563108 INFO::Processing subtree level 1
2025-11-21 19:38:20.729705 INFO::Adjusting the last 1 batches sequentially
2025-11-21 19:38:20.736094 INFO::Done
2025-11-21 19:38:20.738415 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 19:38:20.746734 INFO::ASW Batch was 0.173803492455232 prior to batch effect correction and is now -0.164857937560975 .
2025-11-21 19:38:20.747769 INFO::ASW Label was -0.147459760407394 prior to batch effect correction and is now -0.0573318237636588 .
2025-11-21 19:38:20.750005 INFO::Total function execution time is  0.20263409614563  s and adjustment time is  0.174848079681396 s ( 86.29 )
2025-11-21 19:38:20.950667 INFO::Formatting Data.
2025-11-21 19:38:20.951462 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:20.952339 INFO::Removing potential empty rows and columns
2025-11-21 19:38:20.953295 INFO::Found  2  missing values.
2025-11-21 19:38:20.956895 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:20.957714 INFO::Done
2025-11-21 19:38:21.008451 INFO::Found NA in Reference column
2025-11-21 19:38:21.024082 INFO::Require at least two references per batch.
2025-11-21 19:38:21.050062 INFO::Formatting Data.
2025-11-21 19:38:21.051225 INFO::Recognized SummarizedExperiment
2025-11-21 19:38:21.051834 INFO::Typecasting input to dataframe.
2025-11-21 19:38:21.062104 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.063411 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.068439 INFO::Found  0  missing values.
2025-11-21 19:38:21.078153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.079232 INFO::Done
2025-11-21 19:38:21.105955 INFO::Formatting Data.
2025-11-21 19:38:21.107168 INFO::Recognized SummarizedExperiment
2025-11-21 19:38:21.10806 INFO::Typecasting input to dataframe.
2025-11-21 19:38:21.133192 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.135202 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.140299 INFO::Found  0  missing values.
2025-11-21 19:38:21.150546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.151325 INFO::Done
2025-11-21 19:38:21.170333 INFO::Formatting Data.
2025-11-21 19:38:21.171121 INFO::Recognized SummarizedExperiment
2025-11-21 19:38:21.171689 INFO::Typecasting input to dataframe.
2025-11-21 19:38:21.191112 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.194774 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.196774 INFO::Found  0  missing values.
2025-11-21 19:38:21.198034 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.
2025-11-21 19:38:21.203582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.20445 INFO::Done
2025-11-21 19:38:21.220874 INFO::Formatting Data.
2025-11-21 19:38:21.222042 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.223365 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.224802 INFO::Found  0  missing values.
2025-11-21 19:38:21.227852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.228375 INFO::Done
2025-11-21 19:38:21.247677 INFO::Formatting Data.
2025-11-21 19:38:21.248776 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.250163 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.251671 INFO::Found  0  missing values.
2025-11-21 19:38:21.254912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.255855 INFO::Done
2025-11-21 19:38:21.309974 INFO::Formatting Data.
2025-11-21 19:38:21.310798 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.312131 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.313912 INFO::Found  1  missing values.
2025-11-21 19:38:21.317779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.318517 INFO::Done
2025-11-21 19:38:21.349351 INFO::Formatting Data.
2025-11-21 19:38:21.350547 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.351842 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.353187 INFO::Found  2  missing values.
2025-11-21 19:38:21.354189 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.
2025-11-21 19:38:21.357415 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.358188 INFO::Done
2025-11-21 19:38:21.376697 INFO::Formatting Data.
2025-11-21 19:38:21.378182 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.379578 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.38104 INFO::Found  2  missing values.
2025-11-21 19:38:21.383162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.383695 INFO::Done
2025-11-21 19:38:21.401573 INFO::Formatting Data.
2025-11-21 19:38:21.40279 INFO::Typecasting input to dataframe.
2025-11-21 19:38:21.404057 INFO::Replacing NaNs with NAs.
2025-11-21 19:38:21.404954 INFO::Removing potential empty rows and columns
2025-11-21 19:38:21.40589 INFO::Found  0  missing values.
2025-11-21 19:38:21.408381 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 19:38:21.408892 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 21.209   4.178  26.216

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT29.335 1.60221.198
compute_asw0.0340.0020.037
count_existing0.0200.0010.021
generate_data_covariables0.0140.0000.015
generate_dataset0.0150.0010.016