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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 163/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.4.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_21
git_last_commit: dedce04
git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on kjohnson1

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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2025-10-14 13:53:10 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 13:54:37 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 87.8 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* 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 29.304  1.609  21.767
* 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/4.5-arm64/Resources/library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.4.0’
** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
2025-10-14 13:54:13.872332 INFO::Formatting Data.
2025-10-14 13:54:13.877624 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:13.893914 INFO::Removing potential empty rows and columns
2025-10-14 13:54:14.264298 INFO::Found  0  missing values.
2025-10-14 13:54:14.268684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:14.269527 INFO::Done
2025-10-14 13:54:14.270294 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:14.292114 INFO::Starting hierarchical adjustment
2025-10-14 13:54:14.293206 INFO::Found  3  batches.
2025-10-14 13:54:14.293828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:14.295448 INFO::Using default BPPARAM
2025-10-14 13:54:14.296119 INFO::Processing subtree level 1
2025-10-14 13:54:14.475357 INFO::Adjusting the last 1 batches sequentially
2025-10-14 13:54:14.480354 INFO::Done
2025-10-14 13:54:14.482734 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:14.489305 INFO::ASW Batch was 0.0543704788595926 prior to batch effect correction and is now 0.0543704788595926 .
2025-10-14 13:54:14.493171 INFO::Total function execution time is  0.62215518951416  s and adjustment time is  0.187326908111572 s ( 30.11 )
2025-10-14 13:54:14.521682 INFO::Formatting Data.
2025-10-14 13:54:14.522728 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:14.52395 INFO::Removing potential empty rows and columns
2025-10-14 13:54:14.525806 INFO::Found  0  missing values.
2025-10-14 13:54:14.527175 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.
2025-10-14 13:54:14.542726 INFO::Formatting Data.
2025-10-14 13:54:14.543862 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:14.545024 INFO::Removing potential empty rows and columns
2025-10-14 13:54:14.546393 INFO::Found  0  missing values.
2025-10-14 13:54:14.548515 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.
2025-10-14 13:54:14.582995 INFO::Formatting Data.
2025-10-14 13:54:14.584136 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:14.585328 INFO::Removing potential empty rows and columns
2025-10-14 13:54:14.586538 INFO::Found  0  missing values.
2025-10-14 13:54:14.5876 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.
2025-10-14 13:54:14.592339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:14.593106 INFO::Done
2025-10-14 13:54:14.593714 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:14.596147 INFO::Starting hierarchical adjustment
2025-10-14 13:54:14.596966 INFO::Found  2  batches.
2025-10-14 13:54:14.597568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:14.598461 INFO::Using default BPPARAM
2025-10-14 13:54:14.599029 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:14.599959 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 13:54:14.641266 INFO::Done
2025-10-14 13:54:14.642335 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:14.645118 INFO::ASW Batch was 0.0146996372594626 prior to batch effect correction and is now -0.106080444993218 .
2025-10-14 13:54:14.646256 INFO::Total function execution time is  0.0634348392486572  s and adjustment time is  0.0443718433380127 s ( 69.95 )
2025-10-14 13:54:14.650335 INFO::Formatting Data.
2025-10-14 13:54:14.651265 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:14.662572 INFO::Formatting Data.
2025-10-14 13:54:14.75845 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:14.759812 INFO::Removing potential empty rows and columns
2025-10-14 13:54:14.760872 INFO::Found  0  missing values.
2025-10-14 13:54:14.763699 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:14.764237 INFO::Done
2025-10-14 13:54:14.764761 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:14.766995 INFO::Starting hierarchical adjustment
2025-10-14 13:54:14.767792 INFO::Found  2  batches.
2025-10-14 13:54:14.768289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:14.768863 INFO::Using default BPPARAM
2025-10-14 13:54:14.769354 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:14.770138 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 13:54:14.785841 INFO::Done
2025-10-14 13:54:14.78661 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:14.788691 INFO::ASW Batch was -0.00529080469398573 prior to batch effect correction and is now -0.119847885358225 .
2025-10-14 13:54:14.789474 INFO::Total function execution time is  0.127022981643677  s and adjustment time is  0.0181341171264648 s ( 14.28 )
2025-10-14 13:54:14.790428 INFO::Formatting Data.
2025-10-14 13:54:14.790987 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:14.791742 INFO::Removing potential empty rows and columns
2025-10-14 13:54:14.792698 INFO::Found  0  missing values.
2025-10-14 13:54:14.795462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:14.796075 INFO::Done
2025-10-14 13:54:14.796636 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:14.798696 INFO::Starting hierarchical adjustment
2025-10-14 13:54:14.799443 INFO::Found  2  batches.
2025-10-14 13:54:14.799935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:14.800512 INFO::Using default BPPARAM
2025-10-14 13:54:14.801009 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:14.801884 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 13:54:14.818455 INFO::Done
2025-10-14 13:54:14.81927 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:14.821495 INFO::ASW Batch was -0.00529080469398573 prior to batch effect correction and is now -0.119847885358225 .
2025-10-14 13:54:14.822336 INFO::Total function execution time is  0.0318930149078369  s and adjustment time is  0.0191168785095215 s ( 59.94 )
2025-10-14 13:54:18.494015 INFO::Formatting Data.
2025-10-14 13:54:18.494917 INFO::Recognized SummarizedExperiment
2025-10-14 13:54:18.495396 INFO::Typecasting input to dataframe.
2025-10-14 13:54:18.532611 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:18.534006 INFO::Removing potential empty rows and columns
2025-10-14 13:54:18.537171 INFO::Found  0  missing values.
2025-10-14 13:54:18.54392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:18.544691 INFO::Done
2025-10-14 13:54:18.545174 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:18.548952 INFO::Starting hierarchical adjustment
2025-10-14 13:54:18.549684 INFO::Found  2  batches.
2025-10-14 13:54:18.550692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:18.553823 INFO::Using default BPPARAM
2025-10-14 13:54:18.554363 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:18.555731 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 13:54:18.613515 INFO::Done
2025-10-14 13:54:18.614393 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:18.619449 INFO::ASW Batch was -0.00886992517558624 prior to batch effect correction and is now -0.0882001342673965 .
2025-10-14 13:54:18.620419 INFO::Total function execution time is  0.126716136932373  s and adjustment time is  0.063878059387207 s ( 50.41 )
2025-10-14 13:54:18.641125 INFO::Formatting Data.
2025-10-14 13:54:18.642052 INFO::Recognized SummarizedExperiment
2025-10-14 13:54:18.642545 INFO::Typecasting input to dataframe.
2025-10-14 13:54:18.653172 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:18.654525 INFO::Removing potential empty rows and columns
2025-10-14 13:54:18.657977 INFO::Found  0  missing values.
2025-10-14 13:54:18.665014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:18.665763 INFO::Done
2025-10-14 13:54:18.666314 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:18.670511 INFO::Starting hierarchical adjustment
2025-10-14 13:54:18.671383 INFO::Found  2  batches.
2025-10-14 13:54:18.671876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:18.672437 INFO::Using default BPPARAM
2025-10-14 13:54:18.672914 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:18.673951 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 13:54:18.700257 INFO::Done
2025-10-14 13:54:18.701156 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:18.705145 INFO::ASW Batch was -0.00775797734612624 prior to batch effect correction and is now -0.00775797734612624 .
2025-10-14 13:54:18.706151 INFO::Total function execution time is  0.0650429725646973  s and adjustment time is  0.0289750099182129 s ( 44.55 )
2025-10-14 13:54:18.730677 INFO::Formatting Data.
2025-10-14 13:54:18.731604 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:18.732489 INFO::Removing potential empty rows and columns
2025-10-14 13:54:18.733466 INFO::Found  0  missing values.
2025-10-14 13:54:18.736329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:18.737002 INFO::Done
2025-10-14 13:54:18.737503 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:18.739918 INFO::Starting hierarchical adjustment
2025-10-14 13:54:18.740921 INFO::Found  3  batches.
2025-10-14 13:54:18.741459 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:18.742039 INFO::Using default BPPARAM
2025-10-14 13:54:18.742515 INFO::Processing subtree level 1
2025-10-14 13:54:19.202947 INFO::Adjusting the last 1 batches sequentially
2025-10-14 13:54:19.21024 INFO::Done
2025-10-14 13:54:19.21186 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:19.219182 INFO::ASW Batch was -0.0216556467763792 prior to batch effect correction and is now -0.187694662460347 .
2025-10-14 13:54:19.220661 INFO::Total function execution time is  0.49000096321106  s and adjustment time is  0.469504833221436 s ( 95.82 )
2025-10-14 13:54:19.38144 INFO::Skipping initial DF formatting
2025-10-14 13:54:19.382813 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:19.387882 INFO::Starting hierarchical adjustment
2025-10-14 13:54:19.388949 INFO::Found  5  batches.
2025-10-14 13:54:19.389638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:19.390432 INFO::Using default BPPARAM
2025-10-14 13:54:19.390996 INFO::Processing subtree level 1
2025-10-14 13:54:19.659475 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:19.666254 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 13:54:19.71612 INFO::Done
2025-10-14 13:54:19.717624 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:19.726467 INFO::ASW Batch was 0.572014552484389 prior to batch effect correction and is now 0.572014552484389 .
2025-10-14 13:54:19.727561 INFO::ASW Label was 0.353857673074908 prior to batch effect correction and is now 0.353857673074908 .
2025-10-14 13:54:19.729274 INFO::Total function execution time is  0.347982883453369  s and adjustment time is  0.327229022979736 s ( 94.04 )
2025-10-14 13:54:19.760604 INFO::Formatting Data.
2025-10-14 13:54:19.761696 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:19.763014 INFO::Removing potential empty rows and columns
2025-10-14 13:54:19.764518 INFO::Found  0  missing values.
2025-10-14 13:54:19.772662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:19.774085 INFO::Done
2025-10-14 13:54:19.77505 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:19.781125 INFO::Starting hierarchical adjustment
2025-10-14 13:54:19.782659 INFO::Found  5  batches.
2025-10-14 13:54:19.784049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:19.785243 INFO::Using default BPPARAM
2025-10-14 13:54:19.785961 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.

2025-10-14 13:54:20.009825 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:20.01883 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 13:54:20.052981 INFO::Done
2025-10-14 13:54:20.054057 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:20.060344 INFO::ASW Batch was 0.432718872527242 prior to batch effect correction and is now -0.0491183513015683 .
2025-10-14 13:54:20.061596 INFO::ASW Label was 0.320930552882537 prior to batch effect correction and is now 0.730597156532247 .
2025-10-14 13:54:20.066189 INFO::Total function execution time is  0.305517911911011  s and adjustment time is  0.270516157150269 s ( 88.54 )
2025-10-14 13:54:20.06809 INFO::Formatting Data.
2025-10-14 13:54:20.069241 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:20.070694 INFO::Removing potential empty rows and columns
2025-10-14 13:54:20.073294 INFO::Found  0  missing values.
2025-10-14 13:54:20.080086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:20.080994 INFO::Done
2025-10-14 13:54:20.081667 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:20.086798 INFO::Starting hierarchical adjustment
2025-10-14 13:54:20.088074 INFO::Found  5  batches.
2025-10-14 13:54:20.089079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:20.09044 INFO::Using default BPPARAM
2025-10-14 13:54:20.091239 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.

2025-10-14 13:54:20.327337 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:20.333279 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 13:54:20.366217 INFO::Done
2025-10-14 13:54:20.367312 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:20.373902 INFO::ASW Batch was 0.432718872527242 prior to batch effect correction and is now -0.0491183513015683 .
2025-10-14 13:54:20.374741 INFO::ASW Label was 0.320930552882537 prior to batch effect correction and is now 0.730597156532247 .
2025-10-14 13:54:20.375917 INFO::Total function execution time is  0.307788133621216  s and adjustment time is  0.27835488319397 s ( 90.44 )
2025-10-14 13:54:20.399118 INFO::Formatting Data.
2025-10-14 13:54:20.400272 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:20.401587 INFO::Removing potential empty rows and columns
2025-10-14 13:54:20.402928 INFO::Found  0  missing values.
2025-10-14 13:54:20.409644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:20.411086 INFO::Done
2025-10-14 13:54:20.412029 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:20.416461 INFO::Starting hierarchical adjustment
2025-10-14 13:54:20.417592 INFO::Found  5  batches.
2025-10-14 13:54:20.418303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:20.419335 INFO::Using default BPPARAM
2025-10-14 13:54:20.420246 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.

2025-10-14 13:54:20.633356 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:20.640296 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 13:54:20.674828 INFO::Done
2025-10-14 13:54:20.67614 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:20.683339 INFO::ASW Batch was 0.519144780185479 prior to batch effect correction and is now -0.0925536036139191 .
2025-10-14 13:54:20.684311 INFO::ASW Label was 0.190705434753759 prior to batch effect correction and is now 0.810266681716434 .
2025-10-14 13:54:20.685872 INFO::Total function execution time is  0.286725044250488  s and adjustment time is  0.257378816604614 s ( 89.77 )
2025-10-14 13:54:20.687025 INFO::Formatting Data.
2025-10-14 13:54:20.687759 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:20.689037 INFO::Removing potential empty rows and columns
2025-10-14 13:54:20.690393 INFO::Found  0  missing values.
2025-10-14 13:54:20.695303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:20.696184 INFO::Done
2025-10-14 13:54:20.696861 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:20.700636 INFO::Starting hierarchical adjustment
2025-10-14 13:54:20.701787 INFO::Found  5  batches.
2025-10-14 13:54:20.702461 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:20.70339 INFO::Using default BPPARAM
2025-10-14 13:54:20.704126 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.

2025-10-14 13:54:20.901639 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:20.908027 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 13:54:20.942692 INFO::Done
2025-10-14 13:54:20.943827 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:20.950039 INFO::ASW Batch was 0.519144780185479 prior to batch effect correction and is now -0.0925536036139191 .
2025-10-14 13:54:20.950855 INFO::ASW Label was 0.190705434753759 prior to batch effect correction and is now 0.810266681716434 .
2025-10-14 13:54:20.952109 INFO::Total function execution time is  0.264936923980713  s and adjustment time is  0.241091966629028 s ( 91 )
2025-10-14 13:54:20.981235 INFO::Formatting Data.
2025-10-14 13:54:20.982316 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:20.983643 INFO::Removing potential empty rows and columns
2025-10-14 13:54:20.985365 INFO::Found  0  missing values.
2025-10-14 13:54:20.988927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:20.989695 INFO::Done
2025-10-14 13:54:20.990353 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:20.99406 INFO::Starting hierarchical adjustment
2025-10-14 13:54:20.994988 INFO::Found  2  batches.
2025-10-14 13:54:20.99561 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:20.996456 INFO::Using default BPPARAM
2025-10-14 13:54:20.997093 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:20.998204 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 13:54:21.018253 INFO::Done
2025-10-14 13:54:21.019219 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:21.022868 INFO::ASW Batch was 0.33981631489206 prior to batch effect correction and is now 0.116867957941292 .
2025-10-14 13:54:21.0237 INFO::ASW Label was 0.613400560208594 prior to batch effect correction and is now 0.866381418764912 .
2025-10-14 13:54:21.024638 INFO::Total function execution time is  0.0436170101165771  s and adjustment time is  0.0233609676361084 s ( 53.56 )
2025-10-14 13:54:21.02558 INFO::Formatting Data.
2025-10-14 13:54:21.026447 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:21.027687 INFO::Removing potential empty rows and columns
2025-10-14 13:54:21.028923 INFO::Found  0  missing values.
2025-10-14 13:54:21.032337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:21.033111 INFO::Done
2025-10-14 13:54:21.033813 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:21.037536 INFO::Starting hierarchical adjustment
2025-10-14 13:54:21.038491 INFO::Found  2  batches.
2025-10-14 13:54:21.039214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:21.039953 INFO::Using default BPPARAM
2025-10-14 13:54:21.040783 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:21.042044 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-14 13:54:21.067748 INFO::Done
2025-10-14 13:54:21.071283 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:21.077441 INFO::ASW Batch was 0.33981631489206 prior to batch effect correction and is now 0.116867957941292 .
2025-10-14 13:54:21.079027 INFO::ASW Label was 0.613400560208594 prior to batch effect correction and is now 0.866381418764912 .
2025-10-14 13:54:21.080132 INFO::Total function execution time is  0.0545241832733154  s and adjustment time is  0.0293669700622559 s ( 53.86 )
2025-10-14 13:54:21.097545 INFO::Formatting Data.
2025-10-14 13:54:21.098498 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:21.099541 INFO::Removing potential empty rows and columns
2025-10-14 13:54:21.10061 INFO::Found  0  missing values.
2025-10-14 13:54:21.103542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:21.104313 INFO::Done
2025-10-14 13:54:21.105035 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:21.107836 INFO::Starting hierarchical adjustment
2025-10-14 13:54:21.108772 INFO::Found  2  batches.
2025-10-14 13:54:21.109545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:21.110251 INFO::Using default BPPARAM
2025-10-14 13:54:21.11084 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:21.111781 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 13:54:21.155599 INFO::Done
2025-10-14 13:54:21.156508 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:21.158869 INFO::ASW Batch was -0.152026359678438 prior to batch effect correction and is now -0.177780913388337 .
2025-10-14 13:54:21.159865 INFO::Total function execution time is  0.0624339580535889  s and adjustment time is  0.0469779968261719 s ( 75.24 )
2025-10-14 13:54:21.174969 INFO::Formatting Data.
2025-10-14 13:54:21.176125 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:21.177144 INFO::Removing potential empty rows and columns
2025-10-14 13:54:21.178236 INFO::Found  0  missing values.
2025-10-14 13:54:21.179783 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.
2025-10-14 13:54:21.184483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:21.185065 INFO::Done
2025-10-14 13:54:21.185586 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:21.189113 INFO::Starting hierarchical adjustment
2025-10-14 13:54:21.190294 INFO::Found  2  batches.
2025-10-14 13:54:21.190939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:21.191583 INFO::Using default BPPARAM
2025-10-14 13:54:21.192237 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:21.194005 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 13:54:21.213289 INFO::Done
2025-10-14 13:54:21.21417 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:21.217271 INFO::ASW Batch was 0.485315926856903 prior to batch effect correction and is now 0.140132589455429 .
2025-10-14 13:54:21.217973 INFO::ASW Label was 0.62759143602919 prior to batch effect correction and is now 0.825982952998953 .
2025-10-14 13:54:21.218836 INFO::Total function execution time is  0.0440192222595215  s and adjustment time is  0.023190975189209 s ( 52.68 )
2025-10-14 13:54:21.219587 INFO::Formatting Data.
2025-10-14 13:54:21.220172 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:21.221087 INFO::Removing potential empty rows and columns
2025-10-14 13:54:21.222102 INFO::Found  0  missing values.
2025-10-14 13:54:21.222975 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.
2025-10-14 13:54:21.227282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:21.227882 INFO::Done
2025-10-14 13:54:21.228971 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:21.231788 INFO::Starting hierarchical adjustment
2025-10-14 13:54:21.23249 INFO::Found  2  batches.
2025-10-14 13:54:21.232983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:21.234239 INFO::Using default BPPARAM
2025-10-14 13:54:21.235143 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:21.236336 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 13:54:21.255466 INFO::Done
2025-10-14 13:54:21.25633 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:21.259692 INFO::ASW Batch was 0.485315926856903 prior to batch effect correction and is now 0.140132589455429 .
2025-10-14 13:54:21.260378 INFO::ASW Label was 0.62759143602919 prior to batch effect correction and is now 0.825982952998953 .
2025-10-14 13:54:21.261166 INFO::Total function execution time is  0.0415699481964111  s and adjustment time is  0.023043155670166 s ( 55.43 )
2025-10-14 13:54:21.505285 INFO::Formatting Data.
2025-10-14 13:54:21.506247 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:21.507128 INFO::Removing potential empty rows and columns
2025-10-14 13:54:21.508202 INFO::Found  0  missing values.
2025-10-14 13:54:21.51096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:21.511593 INFO::Done
2025-10-14 13:54:21.512099 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:21.514192 INFO::Starting hierarchical adjustment
2025-10-14 13:54:21.515022 INFO::Found  3  batches.
2025-10-14 13:54:21.515537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:21.516128 INFO::Using default BPPARAM
2025-10-14 13:54:21.516622 INFO::Processing subtree level 1
2025-10-14 13:54:21.656169 INFO::Adjusting the last 1 batches sequentially
2025-10-14 13:54:21.660725 INFO::Done
2025-10-14 13:54:21.661727 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:21.668036 INFO::ASW Batch was -0.039924218666593 prior to batch effect correction and is now -0.039924218666593 .
2025-10-14 13:54:21.669491 INFO::Total function execution time is  0.164205074310303  s and adjustment time is  0.145982027053833 s ( 88.9 )
2025-10-14 13:54:21.670664 INFO::Formatting Data.
2025-10-14 13:54:21.671426 INFO::Typecasting input to dataframe.
2025-10-14 13:54:21.672171 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:21.673154 INFO::Removing potential empty rows and columns
2025-10-14 13:54:21.674394 INFO::Found  0  missing values.
2025-10-14 13:54:21.677267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:21.677817 INFO::Done
2025-10-14 13:54:21.678324 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:21.680377 INFO::Starting hierarchical adjustment
2025-10-14 13:54:21.681688 INFO::Found  3  batches.
2025-10-14 13:54:21.683438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:21.684288 INFO::Using default BPPARAM
2025-10-14 13:54:21.684838 INFO::Processing subtree level 1
2025-10-14 13:54:21.831689 INFO::Adjusting the last 1 batches sequentially
2025-10-14 13:54:21.836394 INFO::Done
2025-10-14 13:54:21.837887 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:21.844344 INFO::ASW Batch was -0.039924218666593 prior to batch effect correction and is now -0.039924218666593 .
2025-10-14 13:54:21.845789 INFO::Total function execution time is  0.174986124038696  s and adjustment time is  0.155389785766602 s ( 88.8 )
2025-10-14 13:54:21.866306 INFO::Formatting Data.
2025-10-14 13:54:21.867227 INFO::Typecasting input to dataframe.
2025-10-14 13:54:21.868424 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:21.869384 INFO::Removing potential empty rows and columns
2025-10-14 13:54:21.870685 INFO::Found  0  missing values.
2025-10-14 13:54:21.874856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:21.876094 INFO::Done
2025-10-14 13:54:21.876879 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:21.879418 INFO::Starting hierarchical adjustment
2025-10-14 13:54:21.880255 INFO::Found  3  batches.
2025-10-14 13:54:21.880797 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:21.881557 INFO::Using default BPPARAM
2025-10-14 13:54:21.882181 INFO::Processing subtree level 1
2025-10-14 13:54:22.028829 INFO::Adjusting the last 1 batches sequentially
2025-10-14 13:54:22.035531 INFO::Done
2025-10-14 13:54:22.036628 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:22.043775 INFO::ASW Batch was -0.0781737052962013 prior to batch effect correction and is now -0.0781737052962013 .
2025-10-14 13:54:22.045394 INFO::Total function execution time is  0.179110050201416  s and adjustment time is  0.155413866043091 s ( 86.77 )
2025-10-14 13:54:22.272264 INFO::Formatting Data.
2025-10-14 13:54:22.273174 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:22.274386 INFO::Removing potential empty rows and columns
2025-10-14 13:54:22.278084 INFO::Found  1000  missing values.
2025-10-14 13:54:22.298858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:22.300095 INFO::Done
2025-10-14 13:54:22.300702 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:22.307224 INFO::Starting hierarchical adjustment
2025-10-14 13:54:22.308319 INFO::Found  10  batches.
2025-10-14 13:54:22.308842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:22.309615 INFO::Using default BPPARAM
2025-10-14 13:54:22.310106 INFO::Processing subtree level 1
2025-10-14 13:54:22.494206 INFO::Processing subtree level 2
2025-10-14 13:54:22.715146 INFO::Adjusting the last 1 batches sequentially
2025-10-14 13:54:22.721945 INFO::Done
2025-10-14 13:54:22.726708 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:22.737376 INFO::ASW Batch was 0.474474516156196 prior to batch effect correction and is now 0.474474516156196 .
2025-10-14 13:54:22.73847 INFO::ASW Label was 0.34372159171973 prior to batch effect correction and is now 0.34372159171973 .
2025-10-14 13:54:22.740181 INFO::Total function execution time is  0.467817068099976  s and adjustment time is  0.413249015808105 s ( 88.34 )
2025-10-14 13:54:22.741755 INFO::Formatting Data.
2025-10-14 13:54:22.742549 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:22.74397 INFO::Removing potential empty rows and columns
2025-10-14 13:54:22.747383 INFO::Found  1000  missing values.
2025-10-14 13:54:22.765104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:22.765984 INFO::Done
2025-10-14 13:54:22.766567 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:22.774248 INFO::Starting hierarchical adjustment
2025-10-14 13:54:22.775271 INFO::Found  10  batches.
2025-10-14 13:54:24.297764 INFO::Set up parallel execution backend with 2 workers
2025-10-14 13:54:24.298665 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-14 13:54:26.024545 INFO::Adjusting the last 2 batches sequentially
2025-10-14 13:54:26.026754 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-14 13:54:26.04442 INFO::Done
2025-10-14 13:54:26.045198 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:26.050879 INFO::ASW Batch was 0.474474516156196 prior to batch effect correction and is now 0.474474516156196 .
2025-10-14 13:54:26.051566 INFO::ASW Label was 0.34372159171973 prior to batch effect correction and is now 0.34372159171973 .
2025-10-14 13:54:26.052304 INFO::Total function execution time is  3.31066513061523  s and adjustment time is  3.26929807662964 s ( 98.75 )
2025-10-14 13:54:26.286018 INFO::Formatting Data.
2025-10-14 13:54:26.287102 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:26.288196 INFO::Removing potential empty rows and columns
2025-10-14 13:54:26.289577 INFO::Found  0  missing values.
2025-10-14 13:54:26.294134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:26.294992 INFO::Done
2025-10-14 13:54:26.295661 INFO::Acquiring quality metrics before batch effect correction.
2025-10-14 13:54:26.299229 INFO::Starting hierarchical adjustment
2025-10-14 13:54:26.300182 INFO::Found  3  batches.
2025-10-14 13:54:26.300747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-14 13:54:26.301587 INFO::Using default BPPARAM
2025-10-14 13:54:26.302146 INFO::Processing subtree level 1
2025-10-14 13:54:26.494146 INFO::Adjusting the last 1 batches sequentially
2025-10-14 13:54:26.500137 INFO::Done
2025-10-14 13:54:26.500972 INFO::Acquiring quality metrics after batch effect correction.
2025-10-14 13:54:26.508733 INFO::ASW Batch was 0.160712920586245 prior to batch effect correction and is now -0.13872600140096 .
2025-10-14 13:54:26.510172 INFO::ASW Label was -0.194118189816157 prior to batch effect correction and is now 0.0401142421100139 .
2025-10-14 13:54:26.511767 INFO::Total function execution time is  0.225795984268188  s and adjustment time is  0.200137853622437 s ( 88.64 )
2025-10-14 13:54:26.696417 INFO::Formatting Data.
2025-10-14 13:54:26.698013 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:26.699499 INFO::Removing potential empty rows and columns
2025-10-14 13:54:26.7009 INFO::Found  2  missing values.
2025-10-14 13:54:26.704153 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:26.704834 INFO::Done
2025-10-14 13:54:26.741677 INFO::Found NA in Reference column
2025-10-14 13:54:26.755434 INFO::Require at least two references per batch.
2025-10-14 13:54:26.786866 INFO::Formatting Data.
2025-10-14 13:54:26.787884 INFO::Recognized SummarizedExperiment
2025-10-14 13:54:26.78851 INFO::Typecasting input to dataframe.
2025-10-14 13:54:26.803603 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:26.805176 INFO::Removing potential empty rows and columns
2025-10-14 13:54:26.810007 INFO::Found  0  missing values.
2025-10-14 13:54:26.819238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:26.820173 INFO::Done
2025-10-14 13:54:26.839357 INFO::Formatting Data.
2025-10-14 13:54:26.840319 INFO::Recognized SummarizedExperiment
2025-10-14 13:54:26.84095 INFO::Typecasting input to dataframe.
2025-10-14 13:54:26.864579 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:26.866834 INFO::Removing potential empty rows and columns
2025-10-14 13:54:26.87206 INFO::Found  0  missing values.
2025-10-14 13:54:26.886165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:26.887062 INFO::Done
2025-10-14 13:54:26.905478 INFO::Formatting Data.
2025-10-14 13:54:26.906401 INFO::Recognized SummarizedExperiment
2025-10-14 13:54:26.906946 INFO::Typecasting input to dataframe.
2025-10-14 13:54:26.926223 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:26.927405 INFO::Removing potential empty rows and columns
2025-10-14 13:54:26.928586 INFO::Found  0  missing values.
2025-10-14 13:54:26.92955 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.
2025-10-14 13:54:26.934171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:26.934866 INFO::Done
2025-10-14 13:54:26.947497 INFO::Formatting Data.
2025-10-14 13:54:26.94844 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:26.949463 INFO::Removing potential empty rows and columns
2025-10-14 13:54:26.950614 INFO::Found  0  missing values.
2025-10-14 13:54:26.953688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:26.954365 INFO::Done
2025-10-14 13:54:26.970937 INFO::Formatting Data.
2025-10-14 13:54:26.971925 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:26.972899 INFO::Removing potential empty rows and columns
2025-10-14 13:54:26.973984 INFO::Found  0  missing values.
2025-10-14 13:54:26.977251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:26.977873 INFO::Done
2025-10-14 13:54:27.018189 INFO::Formatting Data.
2025-10-14 13:54:27.019264 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:27.020604 INFO::Removing potential empty rows and columns
2025-10-14 13:54:27.022538 INFO::Found  1  missing values.
2025-10-14 13:54:27.025955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:27.026869 INFO::Done
2025-10-14 13:54:27.053995 INFO::Formatting Data.
2025-10-14 13:54:27.055187 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:27.056315 INFO::Removing potential empty rows and columns
2025-10-14 13:54:27.057495 INFO::Found  2  missing values.
2025-10-14 13:54:27.059016 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.
2025-10-14 13:54:27.062301 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:27.06302 INFO::Done
2025-10-14 13:54:27.075893 INFO::Formatting Data.
2025-10-14 13:54:27.076915 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:27.077942 INFO::Removing potential empty rows and columns
2025-10-14 13:54:27.078972 INFO::Found  2  missing values.
2025-10-14 13:54:27.08081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:27.081539 INFO::Done
2025-10-14 13:54:27.098909 INFO::Formatting Data.
2025-10-14 13:54:27.100605 INFO::Typecasting input to dataframe.
2025-10-14 13:54:27.101733 INFO::Replacing NaNs with NAs.
2025-10-14 13:54:27.103108 INFO::Removing potential empty rows and columns
2025-10-14 13:54:27.104733 INFO::Found  0  missing values.
2025-10-14 13:54:27.10869 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-14 13:54:27.109399 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 20.475   6.332  27.541

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT29.304 1.60921.767
compute_asw0.0300.0020.031
count_existing0.0160.0010.017
generate_data_covariables0.0140.0020.015
generate_dataset0.0140.0020.015