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This page was generated on 2025-08-21 11:39 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-18 13:40 -0400 (Mon, 18 Aug 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 merida1

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: 2025-08-19 01:13:23 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 01:15:53 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 150.2 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 RC (2025-06-05 r88288)
* 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 Monterey 12.7.6
* 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 44.297   2.71  36.299
* 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-x86_64/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 RC (2025-06-05 r88288) -- "Great Square Root"
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")
2025-08-19 01:15:12.709772 INFO::Formatting Data.
2025-08-19 01:15:12.716896 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:12.752087 INFO::Removing potential empty rows and columns
2025-08-19 01:15:13.556045 INFO::Found  0  missing values.
2025-08-19 01:15:13.567554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:13.5701 INFO::Done
2025-08-19 01:15:13.571881 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:13.607064 INFO::Starting hierarchical adjustment
2025-08-19 01:15:13.609041 INFO::Found  3  batches.
2025-08-19 01:15:13.610525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:13.613921 INFO::Using default BPPARAM
2025-08-19 01:15:13.615652 INFO::Processing subtree level 1
2025-08-19 01:15:13.8893 INFO::Adjusting the last 1 batches sequentially
2025-08-19 01:15:13.89708 INFO::Done
2025-08-19 01:15:13.898778 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:13.908787 INFO::ASW Batch was 0.0363147959168819 prior to batch effect correction and is now 0.0363147959168819 .
2025-08-19 01:15:13.912117 INFO::Total function execution time is  1.20450520515442  s and adjustment time is  0.288431167602539 s ( 23.95 )
2025-08-19 01:15:13.948713 INFO::Formatting Data.
2025-08-19 01:15:13.950639 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:13.961183 INFO::Removing potential empty rows and columns
2025-08-19 01:15:13.964392 INFO::Found  0  missing values.
2025-08-19 01:15:13.967074 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.
2025-08-19 01:15:13.999453 INFO::Formatting Data.
2025-08-19 01:15:14.001435 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:14.003593 INFO::Removing potential empty rows and columns
2025-08-19 01:15:14.006333 INFO::Found  0  missing values.
2025-08-19 01:15:14.008738 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.
2025-08-19 01:15:14.05184 INFO::Formatting Data.
2025-08-19 01:15:14.053547 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:14.055768 INFO::Removing potential empty rows and columns
2025-08-19 01:15:14.058378 INFO::Found  0  missing values.
2025-08-19 01:15:14.060806 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.
2025-08-19 01:15:14.073153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:14.074726 INFO::Done
2025-08-19 01:15:14.076047 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:14.081648 INFO::Starting hierarchical adjustment
2025-08-19 01:15:14.083719 INFO::Found  2  batches.
2025-08-19 01:15:14.085172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:14.08694 INFO::Using default BPPARAM
2025-08-19 01:15:14.088385 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:14.09095 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 01:15:14.147833 INFO::Done
2025-08-19 01:15:14.149312 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:14.154225 INFO::ASW Batch was 0.0385469128388843 prior to batch effect correction and is now -0.116385591291108 .
2025-08-19 01:15:14.156597 INFO::Total function execution time is  0.10478687286377  s and adjustment time is  0.0645089149475098 s ( 61.56 )
2025-08-19 01:15:14.162919 INFO::Formatting Data.
2025-08-19 01:15:14.164797 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:14.188606 INFO::Formatting Data.
2025-08-19 01:15:14.190525 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:14.246516 INFO::Removing potential empty rows and columns
2025-08-19 01:15:14.248977 INFO::Found  0  missing values.
2025-08-19 01:15:14.256982 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:14.258458 INFO::Done
2025-08-19 01:15:14.25979 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:14.264403 INFO::Starting hierarchical adjustment
2025-08-19 01:15:14.266472 INFO::Found  2  batches.
2025-08-19 01:15:14.267877 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:14.269387 INFO::Using default BPPARAM
2025-08-19 01:15:14.270708 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:14.272934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 01:15:14.312541 INFO::Done
2025-08-19 01:15:14.314125 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:14.319637 INFO::ASW Batch was -0.0611383007197411 prior to batch effect correction and is now -0.115724952367209 .
2025-08-19 01:15:14.321699 INFO::Total function execution time is  0.13316011428833  s and adjustment time is  0.0464088916778564 s ( 34.85 )
2025-08-19 01:15:14.324752 INFO::Formatting Data.
2025-08-19 01:15:14.326528 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:14.329598 INFO::Removing potential empty rows and columns
2025-08-19 01:15:14.332357 INFO::Found  0  missing values.
2025-08-19 01:15:14.340622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:14.342247 INFO::Done
2025-08-19 01:15:14.343811 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:14.348841 INFO::Starting hierarchical adjustment
2025-08-19 01:15:14.350858 INFO::Found  2  batches.
2025-08-19 01:15:14.352394 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:14.354534 INFO::Using default BPPARAM
2025-08-19 01:15:14.355973 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:14.358284 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 01:15:14.403779 INFO::Done
2025-08-19 01:15:14.40542 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:14.410472 INFO::ASW Batch was -0.0611383007197411 prior to batch effect correction and is now -0.115724952367209 .
2025-08-19 01:15:14.412473 INFO::Total function execution time is  0.0877900123596191  s and adjustment time is  0.0533370971679688 s ( 60.76 )
2025-08-19 01:15:21.471687 INFO::Formatting Data.
2025-08-19 01:15:21.473075 INFO::Recognized SummarizedExperiment
2025-08-19 01:15:21.47421 INFO::Typecasting input to dataframe.
2025-08-19 01:15:21.544595 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:21.547 INFO::Removing potential empty rows and columns
2025-08-19 01:15:21.557564 INFO::Found  0  missing values.
2025-08-19 01:15:21.57925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:21.580845 INFO::Done
2025-08-19 01:15:21.582252 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:21.592807 INFO::Starting hierarchical adjustment
2025-08-19 01:15:21.596164 INFO::Found  2  batches.
2025-08-19 01:15:21.597768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:21.600361 INFO::Using default BPPARAM
2025-08-19 01:15:21.60201 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:21.604547 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 01:15:21.780142 INFO::Done
2025-08-19 01:15:21.781618 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:21.792978 INFO::ASW Batch was -0.00550562379146633 prior to batch effect correction and is now -0.0939206725030379 .
2025-08-19 01:15:21.795184 INFO::Total function execution time is  0.324142932891846  s and adjustment time is  0.185873031616211 s ( 57.34 )
2025-08-19 01:15:21.845819 INFO::Formatting Data.
2025-08-19 01:15:21.847472 INFO::Recognized SummarizedExperiment
2025-08-19 01:15:21.84872 INFO::Typecasting input to dataframe.
2025-08-19 01:15:21.875369 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:21.878032 INFO::Removing potential empty rows and columns
2025-08-19 01:15:21.889777 INFO::Found  0  missing values.
2025-08-19 01:15:21.913337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:21.914809 INFO::Done
2025-08-19 01:15:21.916193 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:21.925649 INFO::Starting hierarchical adjustment
2025-08-19 01:15:21.927411 INFO::Found  2  batches.
2025-08-19 01:15:21.928647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:21.930233 INFO::Using default BPPARAM
2025-08-19 01:15:21.931774 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:21.934336 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 01:15:22.019098 INFO::Done
2025-08-19 01:15:22.020543 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:22.029749 INFO::ASW Batch was 0.0190031896420488 prior to batch effect correction and is now 0.0190031896420488 .
2025-08-19 01:15:22.031841 INFO::Total function execution time is  0.185961008071899  s and adjustment time is  0.0919849872589111 s ( 49.46 )
2025-08-19 01:15:22.082144 INFO::Formatting Data.
2025-08-19 01:15:22.083759 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:22.087303 INFO::Removing potential empty rows and columns
2025-08-19 01:15:22.09081 INFO::Found  0  missing values.
2025-08-19 01:15:22.100913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:22.102839 INFO::Done
2025-08-19 01:15:22.104426 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:22.110239 INFO::Starting hierarchical adjustment
2025-08-19 01:15:22.112234 INFO::Found  3  batches.
2025-08-19 01:15:22.113579 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:22.117598 INFO::Using default BPPARAM
2025-08-19 01:15:22.11931 INFO::Processing subtree level 1
2025-08-19 01:15:22.845924 INFO::Adjusting the last 1 batches sequentially
2025-08-19 01:15:22.851804 INFO::Done
2025-08-19 01:15:22.853498 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:22.89082 INFO::ASW Batch was -0.0489593975841503 prior to batch effect correction and is now -0.180263663142379 .
2025-08-19 01:15:22.902032 INFO::Total function execution time is  0.81772780418396  s and adjustment time is  0.739924907684326 s ( 90.49 )
2025-08-19 01:15:23.064305 INFO::Skipping initial DF formatting
2025-08-19 01:15:23.065858 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:23.076016 INFO::Starting hierarchical adjustment
2025-08-19 01:15:23.077986 INFO::Found  5  batches.
2025-08-19 01:15:23.079479 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:23.081074 INFO::Using default BPPARAM
2025-08-19 01:15:23.082705 INFO::Processing subtree level 1
2025-08-19 01:15:23.560353 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:23.57307 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 01:15:23.645302 INFO::Done
2025-08-19 01:15:23.647643 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:23.661574 INFO::ASW Batch was 0.496607792900197 prior to batch effect correction and is now 0.496607792900197 .
2025-08-19 01:15:23.66338 INFO::ASW Label was 0.35881934070159 prior to batch effect correction and is now 0.35881934070159 .
2025-08-19 01:15:23.6681 INFO::Total function execution time is  0.603700876235962  s and adjustment time is  0.567682981491089 s ( 94.03 )
2025-08-19 01:15:23.724857 INFO::Formatting Data.
2025-08-19 01:15:23.726963 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:23.731041 INFO::Removing potential empty rows and columns
2025-08-19 01:15:23.733707 INFO::Found  0  missing values.
2025-08-19 01:15:23.746374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:23.74813 INFO::Done
2025-08-19 01:15:23.74979 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:23.7591 INFO::Starting hierarchical adjustment
2025-08-19 01:15:23.761134 INFO::Found  5  batches.
2025-08-19 01:15:23.762952 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:23.764812 INFO::Using default BPPARAM
2025-08-19 01:15:23.766333 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.

2025-08-19 01:15:24.130467 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:24.144286 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 01:15:24.197394 INFO::Done
2025-08-19 01:15:24.199197 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:24.206711 INFO::ASW Batch was 0.304457279265906 prior to batch effect correction and is now -0.06120885687728 .
2025-08-19 01:15:24.208436 INFO::ASW Label was 0.478786102090638 prior to batch effect correction and is now 0.862264480219498 .
2025-08-19 01:15:24.210682 INFO::Total function execution time is  0.486000061035156  s and adjustment time is  0.436715841293335 s ( 89.86 )
2025-08-19 01:15:24.212967 INFO::Formatting Data.
2025-08-19 01:15:24.214503 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:24.216615 INFO::Removing potential empty rows and columns
2025-08-19 01:15:24.219249 INFO::Found  0  missing values.
2025-08-19 01:15:24.23435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:24.235911 INFO::Done
2025-08-19 01:15:24.237916 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:24.248887 INFO::Starting hierarchical adjustment
2025-08-19 01:15:24.252416 INFO::Found  5  batches.
2025-08-19 01:15:24.254694 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:24.257186 INFO::Using default BPPARAM
2025-08-19 01:15:24.258913 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.

2025-08-19 01:15:24.599135 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:24.611873 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 01:15:24.667803 INFO::Done
2025-08-19 01:15:24.669436 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:24.678557 INFO::ASW Batch was 0.304457279265906 prior to batch effect correction and is now -0.06120885687728 .
2025-08-19 01:15:24.680066 INFO::ASW Label was 0.478786102090638 prior to batch effect correction and is now 0.862264480219498 .
2025-08-19 01:15:24.682459 INFO::Total function execution time is  0.468971014022827  s and adjustment time is  0.415931224822998 s ( 88.69 )
2025-08-19 01:15:24.719205 INFO::Formatting Data.
2025-08-19 01:15:24.721051 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:24.72429 INFO::Removing potential empty rows and columns
2025-08-19 01:15:24.727003 INFO::Found  0  missing values.
2025-08-19 01:15:24.739901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:24.741501 INFO::Done
2025-08-19 01:15:24.742966 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:24.754225 INFO::Starting hierarchical adjustment
2025-08-19 01:15:24.756357 INFO::Found  5  batches.
2025-08-19 01:15:24.758393 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:24.760583 INFO::Using default BPPARAM
2025-08-19 01:15:24.763028 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.

2025-08-19 01:15:25.066146 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:25.082367 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 01:15:25.134538 INFO::Done
2025-08-19 01:15:25.136132 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:25.146682 INFO::ASW Batch was 0.388959472443816 prior to batch effect correction and is now -0.0391990887786933 .
2025-08-19 01:15:25.148473 INFO::ASW Label was 0.341207940860265 prior to batch effect correction and is now 0.790328832063953 .
2025-08-19 01:15:25.151266 INFO::Total function execution time is  0.431408882141113  s and adjustment time is  0.378589868545532 s ( 87.76 )
2025-08-19 01:15:25.154138 INFO::Formatting Data.
2025-08-19 01:15:25.155923 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:25.158227 INFO::Removing potential empty rows and columns
2025-08-19 01:15:25.160941 INFO::Found  0  missing values.
2025-08-19 01:15:25.172709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:25.174198 INFO::Done
2025-08-19 01:15:25.175537 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:25.182747 INFO::Starting hierarchical adjustment
2025-08-19 01:15:25.184737 INFO::Found  5  batches.
2025-08-19 01:15:25.18617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:25.187792 INFO::Using default BPPARAM
2025-08-19 01:15:25.189195 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.

2025-08-19 01:15:25.486395 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:25.499311 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 01:15:25.553815 INFO::Done
2025-08-19 01:15:25.5554 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:25.564034 INFO::ASW Batch was 0.388959472443816 prior to batch effect correction and is now -0.0391990887786933 .
2025-08-19 01:15:25.565743 INFO::ASW Label was 0.341207940860265 prior to batch effect correction and is now 0.790328832063953 .
2025-08-19 01:15:25.569023 INFO::Total function execution time is  0.414233922958374  s and adjustment time is  0.369446039199829 s ( 89.19 )
2025-08-19 01:15:25.607989 INFO::Formatting Data.
2025-08-19 01:15:25.609694 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:25.61224 INFO::Removing potential empty rows and columns
2025-08-19 01:15:25.616146 INFO::Found  0  missing values.
2025-08-19 01:15:25.623614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:25.626197 INFO::Done
2025-08-19 01:15:25.627796 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:25.635261 INFO::Starting hierarchical adjustment
2025-08-19 01:15:25.638168 INFO::Found  2  batches.
2025-08-19 01:15:25.639604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:25.64115 INFO::Using default BPPARAM
2025-08-19 01:15:25.64247 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:25.645 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 01:15:25.685026 INFO::Done
2025-08-19 01:15:25.686868 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:25.694244 INFO::ASW Batch was 0.767390196707185 prior to batch effect correction and is now -0.0270412637775713 .
2025-08-19 01:15:25.695833 INFO::ASW Label was 0.253160081487134 prior to batch effect correction and is now 0.858173309579499 .
2025-08-19 01:15:25.6987 INFO::Total function execution time is  0.090764045715332  s and adjustment time is  0.0473759174346924 s ( 52.2 )
2025-08-19 01:15:25.700642 INFO::Formatting Data.
2025-08-19 01:15:25.702209 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:25.704414 INFO::Removing potential empty rows and columns
2025-08-19 01:15:25.710408 INFO::Found  0  missing values.
2025-08-19 01:15:25.717537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:25.719004 INFO::Done
2025-08-19 01:15:25.72288 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:25.730148 INFO::Starting hierarchical adjustment
2025-08-19 01:15:25.732129 INFO::Found  2  batches.
2025-08-19 01:15:25.73372 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:25.735319 INFO::Using default BPPARAM
2025-08-19 01:15:25.736642 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:25.738927 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-19 01:15:25.780087 INFO::Done
2025-08-19 01:15:25.781627 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:25.788626 INFO::ASW Batch was 0.767390196707185 prior to batch effect correction and is now -0.0270412637775713 .
2025-08-19 01:15:25.790156 INFO::ASW Label was 0.253160081487134 prior to batch effect correction and is now 0.858173309579499 .
2025-08-19 01:15:25.792039 INFO::Total function execution time is  0.0914149284362793  s and adjustment time is  0.0483710765838623 s ( 52.91 )
2025-08-19 01:15:25.8261 INFO::Formatting Data.
2025-08-19 01:15:25.827864 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:25.830859 INFO::Removing potential empty rows and columns
2025-08-19 01:15:25.833103 INFO::Found  0  missing values.
2025-08-19 01:15:25.840771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:25.842457 INFO::Done
2025-08-19 01:15:25.843889 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:25.848443 INFO::Starting hierarchical adjustment
2025-08-19 01:15:25.850459 INFO::Found  2  batches.
2025-08-19 01:15:25.851958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:25.853426 INFO::Using default BPPARAM
2025-08-19 01:15:25.855325 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:25.857846 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 01:15:25.95159 INFO::Done
2025-08-19 01:15:25.953268 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:25.958116 INFO::ASW Batch was 0.0285492747469671 prior to batch effect correction and is now -0.136220171082125 .
2025-08-19 01:15:25.961696 INFO::Total function execution time is  0.135657072067261  s and adjustment time is  0.101493120193481 s ( 74.82 )
2025-08-19 01:15:25.997337 INFO::Formatting Data.
2025-08-19 01:15:25.999123 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:26.001465 INFO::Removing potential empty rows and columns
2025-08-19 01:15:26.009108 INFO::Found  0  missing values.
2025-08-19 01:15:26.012938 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.
2025-08-19 01:15:26.027731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:26.030865 INFO::Done
2025-08-19 01:15:26.032607 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:26.040396 INFO::Starting hierarchical adjustment
2025-08-19 01:15:26.042557 INFO::Found  2  batches.
2025-08-19 01:15:26.04407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:26.045758 INFO::Using default BPPARAM
2025-08-19 01:15:26.047288 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:26.049818 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 01:15:26.097874 INFO::Done
2025-08-19 01:15:26.0995 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:26.10735 INFO::ASW Batch was 0.167387237749174 prior to batch effect correction and is now -0.0225044917686879 .
2025-08-19 01:15:26.108954 INFO::ASW Label was 0.787551172975886 prior to batch effect correction and is now 0.944533173513105 .
2025-08-19 01:15:26.110863 INFO::Total function execution time is  0.113618850708008  s and adjustment time is  0.0557310581207275 s ( 49.05 )
2025-08-19 01:15:26.112728 INFO::Formatting Data.
2025-08-19 01:15:26.114202 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:26.117068 INFO::Removing potential empty rows and columns
2025-08-19 01:15:26.11977 INFO::Found  0  missing values.
2025-08-19 01:15:26.122054 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.
2025-08-19 01:15:26.134921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:26.136273 INFO::Done
2025-08-19 01:15:26.13744 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:26.144842 INFO::Starting hierarchical adjustment
2025-08-19 01:15:26.146766 INFO::Found  2  batches.
2025-08-19 01:15:26.148655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:26.1504 INFO::Using default BPPARAM
2025-08-19 01:15:26.151796 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:26.15413 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 01:15:26.206046 INFO::Done
2025-08-19 01:15:26.207594 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:26.214311 INFO::ASW Batch was 0.167387237749174 prior to batch effect correction and is now -0.0225044917686879 .
2025-08-19 01:15:26.217376 INFO::ASW Label was 0.787551172975886 prior to batch effect correction and is now 0.944533173513105 .
2025-08-19 01:15:26.219438 INFO::Total function execution time is  0.106688022613525  s and adjustment time is  0.0596311092376709 s ( 55.89 )
2025-08-19 01:15:26.840995 INFO::Formatting Data.
2025-08-19 01:15:26.842751 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:26.844897 INFO::Removing potential empty rows and columns
2025-08-19 01:15:26.849027 INFO::Found  0  missing values.
2025-08-19 01:15:26.857809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:26.85943 INFO::Done
2025-08-19 01:15:26.860798 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:26.865727 INFO::Starting hierarchical adjustment
2025-08-19 01:15:26.867594 INFO::Found  3  batches.
2025-08-19 01:15:26.868933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:26.870711 INFO::Using default BPPARAM
2025-08-19 01:15:26.87217 INFO::Processing subtree level 1
2025-08-19 01:15:27.112046 INFO::Adjusting the last 1 batches sequentially
2025-08-19 01:15:27.122049 INFO::Done
2025-08-19 01:15:27.123589 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:27.135435 INFO::ASW Batch was 0.00831723544899209 prior to batch effect correction and is now 0.00831723544899209 .
2025-08-19 01:15:27.145679 INFO::Total function execution time is  0.302910089492798  s and adjustment time is  0.254810094833374 s ( 84.12 )
2025-08-19 01:15:27.149289 INFO::Formatting Data.
2025-08-19 01:15:27.152826 INFO::Typecasting input to dataframe.
2025-08-19 01:15:27.155015 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:27.157938 INFO::Removing potential empty rows and columns
2025-08-19 01:15:27.161292 INFO::Found  0  missing values.
2025-08-19 01:15:27.169195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:27.170689 INFO::Done
2025-08-19 01:15:27.172001 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:27.176594 INFO::Starting hierarchical adjustment
2025-08-19 01:15:27.178435 INFO::Found  3  batches.
2025-08-19 01:15:27.179784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:27.18135 INFO::Using default BPPARAM
2025-08-19 01:15:27.182642 INFO::Processing subtree level 1
2025-08-19 01:15:27.41428 INFO::Adjusting the last 1 batches sequentially
2025-08-19 01:15:27.427334 INFO::Done
2025-08-19 01:15:27.430043 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:27.444791 INFO::ASW Batch was 0.00831723544899209 prior to batch effect correction and is now 0.00831723544899209 .
2025-08-19 01:15:27.451068 INFO::Total function execution time is  0.299608945846558  s and adjustment time is  0.249240159988403 s ( 83.19 )
2025-08-19 01:15:27.488661 INFO::Formatting Data.
2025-08-19 01:15:27.491251 INFO::Typecasting input to dataframe.
2025-08-19 01:15:27.493431 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:27.496565 INFO::Removing potential empty rows and columns
2025-08-19 01:15:27.50263 INFO::Found  0  missing values.
2025-08-19 01:15:27.510946 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:27.512566 INFO::Done
2025-08-19 01:15:27.517391 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:27.523418 INFO::Starting hierarchical adjustment
2025-08-19 01:15:27.525473 INFO::Found  3  batches.
2025-08-19 01:15:27.527592 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:27.529288 INFO::Using default BPPARAM
2025-08-19 01:15:27.530587 INFO::Processing subtree level 1
2025-08-19 01:15:27.780377 INFO::Adjusting the last 1 batches sequentially
2025-08-19 01:15:27.792791 INFO::Done
2025-08-19 01:15:27.794393 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:27.808839 INFO::ASW Batch was -0.124739873012693 prior to batch effect correction and is now -0.124739873012693 .
2025-08-19 01:15:27.813983 INFO::Total function execution time is  0.324522972106934  s and adjustment time is  0.267689943313599 s ( 82.49 )
2025-08-19 01:15:28.227283 INFO::Formatting Data.
2025-08-19 01:15:28.229058 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:28.231727 INFO::Removing potential empty rows and columns
2025-08-19 01:15:28.242687 INFO::Found  1000  missing values.
2025-08-19 01:15:28.304718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:28.30635 INFO::Done
2025-08-19 01:15:28.307713 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:28.32024 INFO::Starting hierarchical adjustment
2025-08-19 01:15:28.322232 INFO::Found  10  batches.
2025-08-19 01:15:28.324129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:28.325784 INFO::Using default BPPARAM
2025-08-19 01:15:28.327265 INFO::Processing subtree level 1
2025-08-19 01:15:28.648295 INFO::Processing subtree level 2
2025-08-19 01:15:29.077613 INFO::Adjusting the last 1 batches sequentially
2025-08-19 01:15:29.096409 INFO::Done
2025-08-19 01:15:29.0981 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:29.121572 INFO::ASW Batch was 0.472951465241813 prior to batch effect correction and is now 0.472951465241813 .
2025-08-19 01:15:29.123291 INFO::ASW Label was 0.334420422546487 prior to batch effect correction and is now 0.334420422546487 .
2025-08-19 01:15:29.12992 INFO::Total function execution time is  0.901563167572021  s and adjustment time is  0.774567127227783 s ( 85.91 )
2025-08-19 01:15:29.133268 INFO::Formatting Data.
2025-08-19 01:15:29.135557 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:29.138975 INFO::Removing potential empty rows and columns
2025-08-19 01:15:29.14847 INFO::Found  1000  missing values.
2025-08-19 01:15:29.218062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:29.219737 INFO::Done
2025-08-19 01:15:29.221211 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:29.233905 INFO::Starting hierarchical adjustment
2025-08-19 01:15:29.236045 INFO::Found  10  batches.
2025-08-19 01:15:30.609072 INFO::Set up parallel execution backend with 2 workers
2025-08-19 01:15:30.610561 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-19 01:15:33.329468 INFO::Adjusting the last 2 batches sequentially
2025-08-19 01:15:33.333237 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-19 01:15:33.390749 INFO::Done
2025-08-19 01:15:33.391966 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:33.40773 INFO::ASW Batch was 0.472951465241813 prior to batch effect correction and is now 0.472951465241813 .
2025-08-19 01:15:33.409171 INFO::ASW Label was 0.334420422546487 prior to batch effect correction and is now 0.334420422546487 .
2025-08-19 01:15:33.410908 INFO::Total function execution time is  4.27785897254944  s and adjustment time is  4.15516805648804 s ( 97.13 )
2025-08-19 01:15:33.828782 INFO::Formatting Data.
2025-08-19 01:15:33.830562 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:33.832952 INFO::Removing potential empty rows and columns
2025-08-19 01:15:33.83663 INFO::Found  0  missing values.
2025-08-19 01:15:33.847056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:33.848427 INFO::Done
2025-08-19 01:15:33.849732 INFO::Acquiring quality metrics before batch effect correction.
2025-08-19 01:15:33.857254 INFO::Starting hierarchical adjustment
2025-08-19 01:15:33.859146 INFO::Found  3  batches.
2025-08-19 01:15:33.860449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-19 01:15:33.862067 INFO::Using default BPPARAM
2025-08-19 01:15:33.863472 INFO::Processing subtree level 1
2025-08-19 01:15:34.164671 INFO::Adjusting the last 1 batches sequentially
2025-08-19 01:15:34.17963 INFO::Done
2025-08-19 01:15:34.182913 INFO::Acquiring quality metrics after batch effect correction.
2025-08-19 01:15:34.199157 INFO::ASW Batch was 0.258608383819731 prior to batch effect correction and is now -0.129514923756116 .
2025-08-19 01:15:34.20132 INFO::ASW Label was -0.198479873014596 prior to batch effect correction and is now 0.0234379665459325 .
2025-08-19 01:15:34.205462 INFO::Total function execution time is  0.376113176345825  s and adjustment time is  0.320809125900269 s ( 85.3 )
2025-08-19 01:15:34.606449 INFO::Formatting Data.
2025-08-19 01:15:34.609903 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:34.613367 INFO::Removing potential empty rows and columns
2025-08-19 01:15:34.616262 INFO::Found  2  missing values.
2025-08-19 01:15:34.624892 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:34.627242 INFO::Done
2025-08-19 01:15:34.721074 INFO::Found NA in Reference column
2025-08-19 01:15:34.751753 INFO::Require at least two references per batch.
2025-08-19 01:15:34.829431 INFO::Formatting Data.
2025-08-19 01:15:34.834877 INFO::Recognized SummarizedExperiment
2025-08-19 01:15:34.837586 INFO::Typecasting input to dataframe.
2025-08-19 01:15:34.877371 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:34.881173 INFO::Removing potential empty rows and columns
2025-08-19 01:15:34.898285 INFO::Found  0  missing values.
2025-08-19 01:15:34.932879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:34.934829 INFO::Done
2025-08-19 01:15:34.998874 INFO::Formatting Data.
2025-08-19 01:15:35.000931 INFO::Recognized SummarizedExperiment
2025-08-19 01:15:35.00253 INFO::Typecasting input to dataframe.
2025-08-19 01:15:35.073895 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:35.077034 INFO::Removing potential empty rows and columns
2025-08-19 01:15:35.094063 INFO::Found  0  missing values.
2025-08-19 01:15:35.1458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:35.14761 INFO::Done
2025-08-19 01:15:35.202369 INFO::Formatting Data.
2025-08-19 01:15:35.205985 INFO::Recognized SummarizedExperiment
2025-08-19 01:15:35.207881 INFO::Typecasting input to dataframe.
2025-08-19 01:15:35.279366 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:35.282204 INFO::Removing potential empty rows and columns
2025-08-19 01:15:35.287042 INFO::Found  0  missing values.
2025-08-19 01:15:35.291475 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.
2025-08-19 01:15:35.316223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:35.324322 INFO::Done
2025-08-19 01:15:35.373973 INFO::Formatting Data.
2025-08-19 01:15:35.376142 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:35.378791 INFO::Removing potential empty rows and columns
2025-08-19 01:15:35.382142 INFO::Found  0  missing values.
2025-08-19 01:15:35.397088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:35.398811 INFO::Done
2025-08-19 01:15:35.438793 INFO::Formatting Data.
2025-08-19 01:15:35.441047 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:35.448429 INFO::Removing potential empty rows and columns
2025-08-19 01:15:35.451659 INFO::Found  0  missing values.
2025-08-19 01:15:35.464648 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:35.466649 INFO::Done
2025-08-19 01:15:35.592624 INFO::Formatting Data.
2025-08-19 01:15:35.599293 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:35.602753 INFO::Removing potential empty rows and columns
2025-08-19 01:15:35.607128 INFO::Found  1  missing values.
2025-08-19 01:15:35.619661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:35.621772 INFO::Done
2025-08-19 01:15:35.772289 INFO::Formatting Data.
2025-08-19 01:15:35.774421 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:35.779366 INFO::Removing potential empty rows and columns
2025-08-19 01:15:35.7822 INFO::Found  2  missing values.
2025-08-19 01:15:35.784717 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.
2025-08-19 01:15:35.791208 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:35.796664 INFO::Done
2025-08-19 01:15:35.825956 INFO::Formatting Data.
2025-08-19 01:15:35.828166 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:35.830951 INFO::Removing potential empty rows and columns
2025-08-19 01:15:35.833567 INFO::Found  2  missing values.
2025-08-19 01:15:35.83795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:35.839726 INFO::Done
2025-08-19 01:15:35.887138 INFO::Formatting Data.
2025-08-19 01:15:35.88903 INFO::Typecasting input to dataframe.
2025-08-19 01:15:35.89191 INFO::Replacing NaNs with NAs.
2025-08-19 01:15:35.894776 INFO::Removing potential empty rows and columns
2025-08-19 01:15:35.9019 INFO::Found  0  missing values.
2025-08-19 01:15:35.913076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-19 01:15:35.91603 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 35.187   7.454  47.243

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT44.297 2.71036.299
compute_asw0.0570.0020.063
count_existing0.0280.0020.032
generate_data_covariables0.0270.0020.030
generate_dataset0.0250.0030.029