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This page was generated on 2025-10-28 12:03 -0400 (Tue, 28 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.5.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-10-27 13:45 -0400 (Mon, 27 Oct 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: devel
git_last_commit: 3fb455b
git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for BERT on lconway

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

raw results


Summary

Package: BERT
Version: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2025-10-27 20:06:42 -0400 (Mon, 27 Oct 2025)
EndedAt: 2025-10-27 20:08:06 -0400 (Mon, 27 Oct 2025)
EllapsedTime: 83.6 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.5.0’
* 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 26.945  1.442  19.253
* 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 ‘1.5.0’
** 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 (2025-09-10 r88807) -- "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")
2025-10-27 20:07:44.882469 INFO::Formatting Data.
2025-10-27 20:07:44.886887 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:44.899733 INFO::Removing potential empty rows and columns
2025-10-27 20:07:45.1863 INFO::Found  0  missing values.
2025-10-27 20:07:45.190717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:45.191743 INFO::Done
2025-10-27 20:07:45.19262 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:45.209726 INFO::Starting hierarchical adjustment
2025-10-27 20:07:45.210881 INFO::Found  3  batches.
2025-10-27 20:07:45.211627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:45.213023 INFO::Using default BPPARAM
2025-10-27 20:07:45.213743 INFO::Processing subtree level 1
2025-10-27 20:07:45.372183 INFO::Adjusting the last 1 batches sequentially
2025-10-27 20:07:45.379427 INFO::Done
2025-10-27 20:07:45.380446 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:45.390573 INFO::ASW Batch was -0.0755531173849358 prior to batch effect correction and is now -0.0755531173849358 .
2025-10-27 20:07:45.392596 INFO::Total function execution time is  0.510963916778564  s and adjustment time is  0.168726205825806 s ( 33.02 )
2025-10-27 20:07:45.415917 INFO::Formatting Data.
2025-10-27 20:07:45.417031 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:45.419043 INFO::Removing potential empty rows and columns
2025-10-27 20:07:45.421248 INFO::Found  0  missing values.
2025-10-27 20:07:45.422721 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.
2025-10-27 20:07:45.437595 INFO::Formatting Data.
2025-10-27 20:07:45.438722 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:45.439963 INFO::Removing potential empty rows and columns
2025-10-27 20:07:45.440945 INFO::Found  0  missing values.
2025-10-27 20:07:45.441821 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.
2025-10-27 20:07:45.46234 INFO::Formatting Data.
2025-10-27 20:07:45.463177 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:45.464119 INFO::Removing potential empty rows and columns
2025-10-27 20:07:45.465287 INFO::Found  0  missing values.
2025-10-27 20:07:45.466709 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.
2025-10-27 20:07:45.471534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:45.47242 INFO::Done
2025-10-27 20:07:45.473082 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:45.475318 INFO::Starting hierarchical adjustment
2025-10-27 20:07:45.475992 INFO::Found  2  batches.
2025-10-27 20:07:45.476499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:45.477092 INFO::Using default BPPARAM
2025-10-27 20:07:45.477577 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:45.478459 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-27 20:07:45.501075 INFO::Done
2025-10-27 20:07:45.50189 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:45.504049 INFO::ASW Batch was -0.0318484511492611 prior to batch effect correction and is now -0.0885762990878542 .
2025-10-27 20:07:45.505106 INFO::Total function execution time is  0.0427830219268799  s and adjustment time is  0.0251839160919189 s ( 58.86 )
2025-10-27 20:07:45.507718 INFO::Formatting Data.
2025-10-27 20:07:45.508305 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:45.516794 INFO::Formatting Data.
2025-10-27 20:07:45.517807 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:45.51902 INFO::Removing potential empty rows and columns
2025-10-27 20:07:45.520425 INFO::Found  0  missing values.
2025-10-27 20:07:45.524026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:45.524879 INFO::Done
2025-10-27 20:07:45.525623 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:45.528585 INFO::Starting hierarchical adjustment
2025-10-27 20:07:45.52971 INFO::Found  2  batches.
2025-10-27 20:07:45.530465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:45.531179 INFO::Using default BPPARAM
2025-10-27 20:07:45.531879 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:45.533109 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-27 20:07:45.58664 INFO::Done
2025-10-27 20:07:45.587631 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:45.590383 INFO::ASW Batch was 0.0539874127503018 prior to batch effect correction and is now -0.131931832690378 .
2025-10-27 20:07:45.591461 INFO::Total function execution time is  0.074692964553833  s and adjustment time is  0.0571448802947998 s ( 76.51 )
2025-10-27 20:07:45.592543 INFO::Formatting Data.
2025-10-27 20:07:45.593105 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:45.59388 INFO::Removing potential empty rows and columns
2025-10-27 20:07:45.59477 INFO::Found  0  missing values.
2025-10-27 20:07:45.597432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:45.597917 INFO::Done
2025-10-27 20:07:45.598367 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:45.60006 INFO::Starting hierarchical adjustment
2025-10-27 20:07:45.600672 INFO::Found  2  batches.
2025-10-27 20:07:45.601121 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:45.601627 INFO::Using default BPPARAM
2025-10-27 20:07:45.602086 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:45.603165 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-27 20:07:45.617035 INFO::Done
2025-10-27 20:07:45.617932 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:45.620343 INFO::ASW Batch was 0.0539874127503018 prior to batch effect correction and is now -0.131931832690378 .
2025-10-27 20:07:45.621078 INFO::Total function execution time is  0.0285608768463135  s and adjustment time is  0.0164101123809814 s ( 57.46 )
2025-10-27 20:07:48.706526 INFO::Formatting Data.
2025-10-27 20:07:48.707595 INFO::Recognized SummarizedExperiment
2025-10-27 20:07:48.708407 INFO::Typecasting input to dataframe.
2025-10-27 20:07:48.737675 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:48.73921 INFO::Removing potential empty rows and columns
2025-10-27 20:07:48.744224 INFO::Found  0  missing values.
2025-10-27 20:07:48.752629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:48.753294 INFO::Done
2025-10-27 20:07:48.753773 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:48.756782 INFO::Starting hierarchical adjustment
2025-10-27 20:07:48.757448 INFO::Found  2  batches.
2025-10-27 20:07:48.757903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:48.758813 INFO::Using default BPPARAM
2025-10-27 20:07:48.759275 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:48.760141 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-27 20:07:48.816418 INFO::Done
2025-10-27 20:07:48.817076 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:48.82033 INFO::ASW Batch was -0.010791207250449 prior to batch effect correction and is now -0.0836908156171496 .
2025-10-27 20:07:48.821131 INFO::Total function execution time is  0.11507511138916  s and adjustment time is  0.059074878692627 s ( 51.34 )
2025-10-27 20:07:48.842397 INFO::Formatting Data.
2025-10-27 20:07:48.843075 INFO::Recognized SummarizedExperiment
2025-10-27 20:07:48.843585 INFO::Typecasting input to dataframe.
2025-10-27 20:07:48.853236 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:48.855031 INFO::Removing potential empty rows and columns
2025-10-27 20:07:48.860328 INFO::Found  0  missing values.
2025-10-27 20:07:48.867215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:48.867966 INFO::Done
2025-10-27 20:07:48.868873 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:48.872527 INFO::Starting hierarchical adjustment
2025-10-27 20:07:48.873283 INFO::Found  2  batches.
2025-10-27 20:07:48.87379 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:48.874313 INFO::Using default BPPARAM
2025-10-27 20:07:48.874771 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:48.875972 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-27 20:07:48.904566 INFO::Done
2025-10-27 20:07:48.905227 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:48.909271 INFO::ASW Batch was -0.0155322224712632 prior to batch effect correction and is now -0.0155322224712632 .
2025-10-27 20:07:48.910142 INFO::Total function execution time is  0.0677249431610107  s and adjustment time is  0.031404972076416 s ( 46.37 )
2025-10-27 20:07:48.937049 INFO::Formatting Data.
2025-10-27 20:07:48.938194 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:48.939478 INFO::Removing potential empty rows and columns
2025-10-27 20:07:48.940889 INFO::Found  0  missing values.
2025-10-27 20:07:48.9442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:48.945064 INFO::Done
2025-10-27 20:07:48.94585 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:48.948595 INFO::Starting hierarchical adjustment
2025-10-27 20:07:48.949641 INFO::Found  3  batches.
2025-10-27 20:07:48.950284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:48.950859 INFO::Using default BPPARAM
2025-10-27 20:07:48.951357 INFO::Processing subtree level 1
2025-10-27 20:07:49.166864 INFO::Adjusting the last 1 batches sequentially
2025-10-27 20:07:49.172452 INFO::Done
2025-10-27 20:07:49.174042 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:49.183638 INFO::ASW Batch was -0.136382375351894 prior to batch effect correction and is now -0.18098153815982 .
2025-10-27 20:07:49.185901 INFO::Total function execution time is  0.248219966888428  s and adjustment time is  0.223159074783325 s ( 89.9 )
2025-10-27 20:07:49.208989 INFO::Skipping initial DF formatting
2025-10-27 20:07:49.210523 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:49.216624 INFO::Starting hierarchical adjustment
2025-10-27 20:07:49.218663 INFO::Found  5  batches.
2025-10-27 20:07:49.219669 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:49.220664 INFO::Using default BPPARAM
2025-10-27 20:07:49.221379 INFO::Processing subtree level 1
2025-10-27 20:07:49.581688 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:49.585322 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-27 20:07:49.643585 INFO::Done
2025-10-27 20:07:49.644881 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:49.660146 INFO::ASW Batch was 0.509889758171955 prior to batch effect correction and is now 0.509889758171955 .
2025-10-27 20:07:49.662543 INFO::ASW Label was 0.418961193729961 prior to batch effect correction and is now 0.418961193729961 .
2025-10-27 20:07:49.665449 INFO::Total function execution time is  0.455985069274902  s and adjustment time is  0.425943851470947 s ( 93.41 )
2025-10-27 20:07:49.769144 INFO::Formatting Data.
2025-10-27 20:07:49.770389 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:49.771895 INFO::Removing potential empty rows and columns
2025-10-27 20:07:49.773033 INFO::Found  0  missing values.
2025-10-27 20:07:49.776921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:49.777529 INFO::Done
2025-10-27 20:07:49.778119 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:49.782783 INFO::Starting hierarchical adjustment
2025-10-27 20:07:49.784114 INFO::Found  5  batches.
2025-10-27 20:07:49.785098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:49.78605 INFO::Using default BPPARAM
2025-10-27 20:07:49.786813 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.

2025-10-27 20:07:50.019394 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:50.029847 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-27 20:07:50.061662 INFO::Done
2025-10-27 20:07:50.063441 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:50.06851 INFO::ASW Batch was 0.379398149425545 prior to batch effect correction and is now -0.0991376280002416 .
2025-10-27 20:07:50.06979 INFO::ASW Label was 0.252304859989442 prior to batch effect correction and is now 0.866498611041987 .
2025-10-27 20:07:50.071392 INFO::Total function execution time is  0.302296876907349  s and adjustment time is  0.277734994888306 s ( 91.87 )
2025-10-27 20:07:50.072857 INFO::Formatting Data.
2025-10-27 20:07:50.074006 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:50.075514 INFO::Removing potential empty rows and columns
2025-10-27 20:07:50.077345 INFO::Found  0  missing values.
2025-10-27 20:07:50.081938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:50.082577 INFO::Done
2025-10-27 20:07:50.083285 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:50.086702 INFO::Starting hierarchical adjustment
2025-10-27 20:07:50.087476 INFO::Found  5  batches.
2025-10-27 20:07:50.087997 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:50.088656 INFO::Using default BPPARAM
2025-10-27 20:07:50.089535 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.

2025-10-27 20:07:50.262996 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:50.288456 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-27 20:07:50.325717 INFO::Done
2025-10-27 20:07:50.3266 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:50.33276 INFO::ASW Batch was 0.379398149425545 prior to batch effect correction and is now -0.0991376280002416 .
2025-10-27 20:07:50.333948 INFO::ASW Label was 0.252304859989442 prior to batch effect correction and is now 0.866498611041987 .
2025-10-27 20:07:50.335292 INFO::Total function execution time is  0.262535810470581  s and adjustment time is  0.238367080688477 s ( 90.79 )
2025-10-27 20:07:50.359401 INFO::Formatting Data.
2025-10-27 20:07:50.360326 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:50.36207 INFO::Removing potential empty rows and columns
2025-10-27 20:07:50.363185 INFO::Found  0  missing values.
2025-10-27 20:07:50.367853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:50.368576 INFO::Done
2025-10-27 20:07:50.369203 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:50.373814 INFO::Starting hierarchical adjustment
2025-10-27 20:07:50.374795 INFO::Found  5  batches.
2025-10-27 20:07:50.375404 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:50.375995 INFO::Using default BPPARAM
2025-10-27 20:07:50.376509 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.

2025-10-27 20:07:50.568108 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:50.578281 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-27 20:07:50.617409 INFO::Done
2025-10-27 20:07:50.618952 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:50.624818 INFO::ASW Batch was 0.43105627979248 prior to batch effect correction and is now -0.0698478890849404 .
2025-10-27 20:07:50.626371 INFO::ASW Label was 0.245968871814696 prior to batch effect correction and is now 0.795989427175656 .
2025-10-27 20:07:50.627398 INFO::Total function execution time is  0.268078088760376  s and adjustment time is  0.242799043655396 s ( 90.57 )
2025-10-27 20:07:50.628415 INFO::Formatting Data.
2025-10-27 20:07:50.629118 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:50.630542 INFO::Removing potential empty rows and columns
2025-10-27 20:07:50.631655 INFO::Found  0  missing values.
2025-10-27 20:07:50.637687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:50.638686 INFO::Done
2025-10-27 20:07:50.639473 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:50.644372 INFO::Starting hierarchical adjustment
2025-10-27 20:07:50.645843 INFO::Found  5  batches.
2025-10-27 20:07:50.646449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:50.647061 INFO::Using default BPPARAM
2025-10-27 20:07:50.648827 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.

2025-10-27 20:07:50.851586 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:50.857884 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-27 20:07:50.893302 INFO::Done
2025-10-27 20:07:50.894903 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:50.901779 INFO::ASW Batch was 0.43105627979248 prior to batch effect correction and is now -0.0698478890849404 .
2025-10-27 20:07:50.903286 INFO::ASW Label was 0.245968871814696 prior to batch effect correction and is now 0.795989427175656 .
2025-10-27 20:07:50.905085 INFO::Total function execution time is  0.276514053344727  s and adjustment time is  0.247959852218628 s ( 89.67 )
2025-10-27 20:07:50.93085 INFO::Formatting Data.
2025-10-27 20:07:50.932254 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:50.933768 INFO::Removing potential empty rows and columns
2025-10-27 20:07:50.935366 INFO::Found  0  missing values.
2025-10-27 20:07:50.940154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:50.941187 INFO::Done
2025-10-27 20:07:50.942065 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:50.946803 INFO::Starting hierarchical adjustment
2025-10-27 20:07:50.948141 INFO::Found  2  batches.
2025-10-27 20:07:50.949073 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:50.950278 INFO::Using default BPPARAM
2025-10-27 20:07:50.951135 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:50.952592 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-27 20:07:50.971722 INFO::Done
2025-10-27 20:07:50.972814 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:50.977226 INFO::ASW Batch was 0.558738948367519 prior to batch effect correction and is now 0.0551499834092487 .
2025-10-27 20:07:50.978191 INFO::ASW Label was 0.577620291100153 prior to batch effect correction and is now 0.904013183320379 .
2025-10-27 20:07:50.979485 INFO::Total function execution time is  0.0487849712371826  s and adjustment time is  0.0238349437713623 s ( 48.86 )
2025-10-27 20:07:50.980712 INFO::Formatting Data.
2025-10-27 20:07:50.981648 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:50.982923 INFO::Removing potential empty rows and columns
2025-10-27 20:07:50.984335 INFO::Found  0  missing values.
2025-10-27 20:07:50.986948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:50.987579 INFO::Done
2025-10-27 20:07:50.988241 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:50.992365 INFO::Starting hierarchical adjustment
2025-10-27 20:07:50.99329 INFO::Found  2  batches.
2025-10-27 20:07:50.993828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:50.994421 INFO::Using default BPPARAM
2025-10-27 20:07:50.994935 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:50.995867 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-27 20:07:51.01205 INFO::Done
2025-10-27 20:07:51.013182 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:51.016701 INFO::ASW Batch was 0.558738948367519 prior to batch effect correction and is now 0.0551499834092487 .
2025-10-27 20:07:51.017354 INFO::ASW Label was 0.577620291100153 prior to batch effect correction and is now 0.904013183320379 .
2025-10-27 20:07:51.018205 INFO::Total function execution time is  0.0376050472259521  s and adjustment time is  0.0188319683074951 s ( 50.08 )
2025-10-27 20:07:51.036533 INFO::Formatting Data.
2025-10-27 20:07:51.037434 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:51.038381 INFO::Removing potential empty rows and columns
2025-10-27 20:07:51.039292 INFO::Found  0  missing values.
2025-10-27 20:07:51.041736 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:51.042268 INFO::Done
2025-10-27 20:07:51.042782 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:51.044703 INFO::Starting hierarchical adjustment
2025-10-27 20:07:51.045385 INFO::Found  2  batches.
2025-10-27 20:07:51.04589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:51.046471 INFO::Using default BPPARAM
2025-10-27 20:07:51.046973 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:51.04799 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-27 20:07:51.085544 INFO::Done
2025-10-27 20:07:51.08674 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:51.089705 INFO::ASW Batch was -0.0159174462780221 prior to batch effect correction and is now -0.119685992070611 .
2025-10-27 20:07:51.090599 INFO::Total function execution time is  0.054175853729248  s and adjustment time is  0.0402038097381592 s ( 74.21 )
2025-10-27 20:07:51.109464 INFO::Formatting Data.
2025-10-27 20:07:51.110332 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:51.111508 INFO::Removing potential empty rows and columns
2025-10-27 20:07:51.112963 INFO::Found  0  missing values.
2025-10-27 20:07:51.114609 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.
2025-10-27 20:07:51.120055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:51.120996 INFO::Done
2025-10-27 20:07:51.121806 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:51.126123 INFO::Starting hierarchical adjustment
2025-10-27 20:07:51.127237 INFO::Found  2  batches.
2025-10-27 20:07:51.128031 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:51.128912 INFO::Using default BPPARAM
2025-10-27 20:07:51.129617 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:51.130574 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-27 20:07:51.153908 INFO::Done
2025-10-27 20:07:51.154656 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:51.158447 INFO::ASW Batch was 0.710000617777877 prior to batch effect correction and is now -0.0334791369408203 .
2025-10-27 20:07:51.159364 INFO::ASW Label was 0.306600832670818 prior to batch effect correction and is now 0.894388518671901 .
2025-10-27 20:07:51.160465 INFO::Total function execution time is  0.051063060760498  s and adjustment time is  0.0268850326538086 s ( 52.65 )
2025-10-27 20:07:51.161528 INFO::Formatting Data.
2025-10-27 20:07:51.162379 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:51.163646 INFO::Removing potential empty rows and columns
2025-10-27 20:07:51.164988 INFO::Found  0  missing values.
2025-10-27 20:07:51.166445 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.
2025-10-27 20:07:51.171998 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:51.172954 INFO::Done
2025-10-27 20:07:51.173956 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:51.17811 INFO::Starting hierarchical adjustment
2025-10-27 20:07:51.179466 INFO::Found  2  batches.
2025-10-27 20:07:51.18022 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:51.181072 INFO::Using default BPPARAM
2025-10-27 20:07:51.182197 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:51.183634 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-27 20:07:51.202185 INFO::Done
2025-10-27 20:07:51.202984 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:51.206356 INFO::ASW Batch was 0.710000617777877 prior to batch effect correction and is now -0.0334791369408203 .
2025-10-27 20:07:51.207024 INFO::ASW Label was 0.306600832670818 prior to batch effect correction and is now 0.894388518671901 .
2025-10-27 20:07:51.207832 INFO::Total function execution time is  0.0463809967041016  s and adjustment time is  0.0230660438537598 s ( 49.73 )
2025-10-27 20:07:51.488693 INFO::Formatting Data.
2025-10-27 20:07:51.490018 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:51.49154 INFO::Removing potential empty rows and columns
2025-10-27 20:07:51.493242 INFO::Found  0  missing values.
2025-10-27 20:07:51.49715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:51.498002 INFO::Done
2025-10-27 20:07:51.498892 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:51.501577 INFO::Starting hierarchical adjustment
2025-10-27 20:07:51.5027 INFO::Found  3  batches.
2025-10-27 20:07:51.503472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:51.504329 INFO::Using default BPPARAM
2025-10-27 20:07:51.505035 INFO::Processing subtree level 1
2025-10-27 20:07:51.633931 INFO::Adjusting the last 1 batches sequentially
2025-10-27 20:07:51.647239 INFO::Done
2025-10-27 20:07:51.649538 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:51.660275 INFO::ASW Batch was -0.0231959765515166 prior to batch effect correction and is now -0.0231959765515166 .
2025-10-27 20:07:51.663776 INFO::Total function execution time is  0.175141096115112  s and adjustment time is  0.144771099090576 s ( 82.66 )
2025-10-27 20:07:51.666372 INFO::Formatting Data.
2025-10-27 20:07:51.667462 INFO::Typecasting input to dataframe.
2025-10-27 20:07:51.669572 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:51.671157 INFO::Removing potential empty rows and columns
2025-10-27 20:07:51.675612 INFO::Found  0  missing values.
2025-10-27 20:07:51.683689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:51.684794 INFO::Done
2025-10-27 20:07:51.688813 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:51.694297 INFO::Starting hierarchical adjustment
2025-10-27 20:07:51.696403 INFO::Found  3  batches.
2025-10-27 20:07:51.697552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:51.698576 INFO::Using default BPPARAM
2025-10-27 20:07:51.701282 INFO::Processing subtree level 1
2025-10-27 20:07:51.840299 INFO::Adjusting the last 1 batches sequentially
2025-10-27 20:07:51.86687 INFO::Done
2025-10-27 20:07:51.870405 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:51.885881 INFO::ASW Batch was -0.0231959765515166 prior to batch effect correction and is now -0.0231959765515166 .
2025-10-27 20:07:51.892919 INFO::Total function execution time is  0.225504875183105  s and adjustment time is  0.170677900314331 s ( 75.69 )
2025-10-27 20:07:51.933173 INFO::Formatting Data.
2025-10-27 20:07:51.934425 INFO::Typecasting input to dataframe.
2025-10-27 20:07:51.935824 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:51.937269 INFO::Removing potential empty rows and columns
2025-10-27 20:07:51.939559 INFO::Found  0  missing values.
2025-10-27 20:07:51.944323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:51.945223 INFO::Done
2025-10-27 20:07:51.94601 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:51.948829 INFO::Starting hierarchical adjustment
2025-10-27 20:07:51.949866 INFO::Found  3  batches.
2025-10-27 20:07:51.950588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:51.951609 INFO::Using default BPPARAM
2025-10-27 20:07:51.953361 INFO::Processing subtree level 1
2025-10-27 20:07:52.10366 INFO::Adjusting the last 1 batches sequentially
2025-10-27 20:07:52.121985 INFO::Done
2025-10-27 20:07:52.128506 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:52.14377 INFO::ASW Batch was -0.0387275914659312 prior to batch effect correction and is now -0.0387275914659312 .
2025-10-27 20:07:52.146344 INFO::Total function execution time is  0.21320915222168  s and adjustment time is  0.172260999679565 s ( 80.79 )
2025-10-27 20:07:52.401248 INFO::Formatting Data.
2025-10-27 20:07:52.40248 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:52.404427 INFO::Removing potential empty rows and columns
2025-10-27 20:07:52.408894 INFO::Found  1000  missing values.
2025-10-27 20:07:52.433437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:52.434685 INFO::Done
2025-10-27 20:07:52.435785 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:52.443627 INFO::Starting hierarchical adjustment
2025-10-27 20:07:52.445071 INFO::Found  10  batches.
2025-10-27 20:07:52.445844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:52.44648 INFO::Using default BPPARAM
2025-10-27 20:07:52.447806 INFO::Processing subtree level 1
2025-10-27 20:07:52.620153 INFO::Processing subtree level 2
2025-10-27 20:07:52.856848 INFO::Adjusting the last 1 batches sequentially
2025-10-27 20:07:52.87294 INFO::Done
2025-10-27 20:07:52.875778 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:52.895806 INFO::ASW Batch was 0.46570525932455 prior to batch effect correction and is now 0.46570525932455 .
2025-10-27 20:07:52.896818 INFO::ASW Label was 0.354077442105464 prior to batch effect correction and is now 0.354077442105464 .
2025-10-27 20:07:52.902431 INFO::Total function execution time is  0.499338865280151  s and adjustment time is  0.428153991699219 s ( 85.74 )
2025-10-27 20:07:52.904836 INFO::Formatting Data.
2025-10-27 20:07:52.906521 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:52.910113 INFO::Removing potential empty rows and columns
2025-10-27 20:07:52.915172 INFO::Found  1000  missing values.
2025-10-27 20:07:52.939901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:52.940949 INFO::Done
2025-10-27 20:07:52.941883 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:52.949067 INFO::Starting hierarchical adjustment
2025-10-27 20:07:52.950287 INFO::Found  10  batches.
2025-10-27 20:07:54.110217 INFO::Set up parallel execution backend with 2 workers
2025-10-27 20:07:54.111184 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-27 20:07:55.446393 INFO::Adjusting the last 2 batches sequentially
2025-10-27 20:07:55.447539 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-27 20:07:55.463849 INFO::Done
2025-10-27 20:07:55.464514 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:55.470365 INFO::ASW Batch was 0.46570525932455 prior to batch effect correction and is now 0.46570525932455 .
2025-10-27 20:07:55.471318 INFO::ASW Label was 0.354077442105464 prior to batch effect correction and is now 0.354077442105464 .
2025-10-27 20:07:55.472417 INFO::Total function execution time is  2.56766200065613  s and adjustment time is  2.51382684707642 s ( 97.9 )
2025-10-27 20:07:55.721449 INFO::Formatting Data.
2025-10-27 20:07:55.722896 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:55.724468 INFO::Removing potential empty rows and columns
2025-10-27 20:07:55.725718 INFO::Found  0  missing values.
2025-10-27 20:07:55.730853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:55.731913 INFO::Done
2025-10-27 20:07:55.732691 INFO::Acquiring quality metrics before batch effect correction.
2025-10-27 20:07:55.736037 INFO::Starting hierarchical adjustment
2025-10-27 20:07:55.737105 INFO::Found  3  batches.
2025-10-27 20:07:55.737702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-27 20:07:55.738616 INFO::Using default BPPARAM
2025-10-27 20:07:55.739905 INFO::Processing subtree level 1
2025-10-27 20:07:55.913132 INFO::Adjusting the last 1 batches sequentially
2025-10-27 20:07:55.925842 INFO::Done
2025-10-27 20:07:55.929173 INFO::Acquiring quality metrics after batch effect correction.
2025-10-27 20:07:55.939353 INFO::ASW Batch was 0.17321530267494 prior to batch effect correction and is now -0.159955794820518 .
2025-10-27 20:07:55.941841 INFO::ASW Label was -0.179347051035522 prior to batch effect correction and is now -0.0244034667588757 .
2025-10-27 20:07:55.945018 INFO::Total function execution time is  0.223459005355835  s and adjustment time is  0.188905000686646 s ( 84.54 )
2025-10-27 20:07:56.137088 INFO::Formatting Data.
2025-10-27 20:07:56.137844 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.138686 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.139907 INFO::Found  2  missing values.
2025-10-27 20:07:56.143641 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.144601 INFO::Done
2025-10-27 20:07:56.190175 INFO::Found NA in Reference column
2025-10-27 20:07:56.206314 INFO::Require at least two references per batch.
2025-10-27 20:07:56.237089 INFO::Formatting Data.
2025-10-27 20:07:56.237888 INFO::Recognized SummarizedExperiment
2025-10-27 20:07:56.238434 INFO::Typecasting input to dataframe.
2025-10-27 20:07:56.250388 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.251645 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.255119 INFO::Found  0  missing values.
2025-10-27 20:07:56.264825 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.265959 INFO::Done
2025-10-27 20:07:56.286681 INFO::Formatting Data.
2025-10-27 20:07:56.287483 INFO::Recognized SummarizedExperiment
2025-10-27 20:07:56.287997 INFO::Typecasting input to dataframe.
2025-10-27 20:07:56.309534 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.310957 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.314394 INFO::Found  0  missing values.
2025-10-27 20:07:56.326331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.327282 INFO::Done
2025-10-27 20:07:56.347154 INFO::Formatting Data.
2025-10-27 20:07:56.347951 INFO::Recognized SummarizedExperiment
2025-10-27 20:07:56.348654 INFO::Typecasting input to dataframe.
2025-10-27 20:07:56.367461 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.368519 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.369807 INFO::Found  0  missing values.
2025-10-27 20:07:56.370739 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.
2025-10-27 20:07:56.3752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.37604 INFO::Done
2025-10-27 20:07:56.390475 INFO::Formatting Data.
2025-10-27 20:07:56.39158 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.392513 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.393391 INFO::Found  0  missing values.
2025-10-27 20:07:56.396017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.396804 INFO::Done
2025-10-27 20:07:56.414302 INFO::Formatting Data.
2025-10-27 20:07:56.415128 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.416427 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.417494 INFO::Found  0  missing values.
2025-10-27 20:07:56.420677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.42142 INFO::Done
2025-10-27 20:07:56.466475 INFO::Formatting Data.
2025-10-27 20:07:56.467624 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.469078 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.470657 INFO::Found  1  missing values.
2025-10-27 20:07:56.474249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.474907 INFO::Done
2025-10-27 20:07:56.503923 INFO::Formatting Data.
2025-10-27 20:07:56.504821 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.506084 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.507403 INFO::Found  2  missing values.
2025-10-27 20:07:56.508672 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.
2025-10-27 20:07:56.511719 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.512502 INFO::Done
2025-10-27 20:07:56.527105 INFO::Formatting Data.
2025-10-27 20:07:56.527933 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.528832 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.530051 INFO::Found  2  missing values.
2025-10-27 20:07:56.532483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.533279 INFO::Done
2025-10-27 20:07:56.551501 INFO::Formatting Data.
2025-10-27 20:07:56.552663 INFO::Typecasting input to dataframe.
2025-10-27 20:07:56.553934 INFO::Replacing NaNs with NAs.
2025-10-27 20:07:56.555259 INFO::Removing potential empty rows and columns
2025-10-27 20:07:56.556427 INFO::Found  0  missing values.
2025-10-27 20:07:56.558886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-27 20:07:56.5594 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 20.094   4.379  24.773

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT26.945 1.44219.253
compute_asw0.0300.0020.032
count_existing0.0160.0020.018
generate_data_covariables0.0100.0000.011
generate_dataset0.0140.0010.016