Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-12-15 12:07 -0500 (Mon, 15 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4882
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4607
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4671
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 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_22
git_last_commit: 49dbe48
git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on kjohnson1

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

raw results


Summary

Package: BERT
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2025-12-12 16:21:36 -0500 (Fri, 12 Dec 2025)
EndedAt: 2025-12-12 16:23:42 -0500 (Fri, 12 Dec 2025)
EllapsedTime: 125.2 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 29.839  1.176  34.396
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.6.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-12-12 16:23:10.710914 INFO::Formatting Data.
2025-12-12 16:23:10.715995 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:10.727757 INFO::Removing potential empty rows and columns
2025-12-12 16:23:11.179004 INFO::Found  0  missing values.
2025-12-12 16:23:11.18244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:11.183095 INFO::Done
2025-12-12 16:23:11.183622 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:11.227076 INFO::Starting hierarchical adjustment
2025-12-12 16:23:11.228278 INFO::Found  3  batches.
2025-12-12 16:23:11.228911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:11.230373 INFO::Using default BPPARAM
2025-12-12 16:23:11.230979 INFO::Processing subtree level 1
2025-12-12 16:23:11.361309 INFO::Adjusting the last 1 batches sequentially
2025-12-12 16:23:11.364183 INFO::Done
2025-12-12 16:23:11.365191 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:11.369277 INFO::ASW Batch was -0.0341532001392257 prior to batch effect correction and is now -0.0341532001392257 .
2025-12-12 16:23:11.370923 INFO::Total function execution time is  0.660784006118774  s and adjustment time is  0.136152982711792 s ( 20.6 )
2025-12-12 16:23:11.400417 INFO::Formatting Data.
2025-12-12 16:23:11.401543 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:11.402736 INFO::Removing potential empty rows and columns
2025-12-12 16:23:11.413337 INFO::Found  0  missing values.
2025-12-12 16:23:11.415558 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.
2025-12-12 16:23:11.430504 INFO::Formatting Data.
2025-12-12 16:23:11.431467 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:11.432476 INFO::Removing potential empty rows and columns
2025-12-12 16:23:11.433829 INFO::Found  0  missing values.
2025-12-12 16:23:11.434877 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.
2025-12-12 16:23:11.474741 INFO::Formatting Data.
2025-12-12 16:23:11.475684 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:11.476682 INFO::Removing potential empty rows and columns
2025-12-12 16:23:11.477777 INFO::Found  0  missing values.
2025-12-12 16:23:11.478733 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.
2025-12-12 16:23:11.483263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:11.483921 INFO::Done
2025-12-12 16:23:11.484444 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:11.493348 INFO::Starting hierarchical adjustment
2025-12-12 16:23:11.494879 INFO::Found  2  batches.
2025-12-12 16:23:11.49544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:11.496205 INFO::Using default BPPARAM
2025-12-12 16:23:11.496767 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:11.498684 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 16:23:11.540265 INFO::Done
2025-12-12 16:23:11.541075 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:11.543722 INFO::ASW Batch was -0.000183964566684631 prior to batch effect correction and is now -0.107299470670902 .
2025-12-12 16:23:11.544778 INFO::Total function execution time is  0.0701761245727539  s and adjustment time is  0.0456221103668213 s ( 65.01 )
2025-12-12 16:23:11.549089 INFO::Formatting Data.
2025-12-12 16:23:11.549881 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:11.560256 INFO::Formatting Data.
2025-12-12 16:23:11.561232 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:11.56217 INFO::Removing potential empty rows and columns
2025-12-12 16:23:11.563376 INFO::Found  0  missing values.
2025-12-12 16:23:11.569541 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:11.570419 INFO::Done
2025-12-12 16:23:11.575899 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:11.64382 INFO::Starting hierarchical adjustment
2025-12-12 16:23:11.644953 INFO::Found  2  batches.
2025-12-12 16:23:11.645509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:11.646099 INFO::Using default BPPARAM
2025-12-12 16:23:11.646572 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:11.647521 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 16:23:11.666743 INFO::Done
2025-12-12 16:23:11.667541 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:11.672842 INFO::ASW Batch was 0.0163731289910079 prior to batch effect correction and is now -0.119131677570481 .
2025-12-12 16:23:11.674534 INFO::Total function execution time is  0.114322185516357  s and adjustment time is  0.0219581127166748 s ( 19.21 )
2025-12-12 16:23:11.680023 INFO::Formatting Data.
2025-12-12 16:23:11.681028 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:11.68201 INFO::Removing potential empty rows and columns
2025-12-12 16:23:11.683055 INFO::Found  0  missing values.
2025-12-12 16:23:11.693258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:11.699173 INFO::Done
2025-12-12 16:23:11.699882 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:11.702241 INFO::Starting hierarchical adjustment
2025-12-12 16:23:11.70297 INFO::Found  2  batches.
2025-12-12 16:23:11.703466 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:11.704022 INFO::Using default BPPARAM
2025-12-12 16:23:11.70449 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:11.705313 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 16:23:11.723325 INFO::Done
2025-12-12 16:23:11.724189 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:11.726487 INFO::ASW Batch was 0.0163731289910079 prior to batch effect correction and is now -0.119131677570481 .
2025-12-12 16:23:11.727447 INFO::Total function execution time is  0.0514900684356689  s and adjustment time is  0.020427942276001 s ( 39.67 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-12 16:23:17.196193 INFO::Formatting Data.
2025-12-12 16:23:17.196986 INFO::Recognized SummarizedExperiment
2025-12-12 16:23:17.197469 INFO::Typecasting input to dataframe.
2025-12-12 16:23:17.240868 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:17.242313 INFO::Removing potential empty rows and columns
2025-12-12 16:23:17.246054 INFO::Found  0  missing values.
2025-12-12 16:23:17.273424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:17.27431 INFO::Done
2025-12-12 16:23:17.27487 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:17.278829 INFO::Starting hierarchical adjustment
2025-12-12 16:23:17.279607 INFO::Found  2  batches.
2025-12-12 16:23:17.2801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:17.281357 INFO::Using default BPPARAM
2025-12-12 16:23:17.281849 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:17.282832 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 16:23:17.452265 INFO::Done
2025-12-12 16:23:17.453104 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:17.45697 INFO::ASW Batch was 0.0221254957171534 prior to batch effect correction and is now -0.0937623824205273 .
2025-12-12 16:23:17.457892 INFO::Total function execution time is  0.262044906616211  s and adjustment time is  0.172739028930664 s ( 65.92 )
Warning: stack imbalance in '{', 73 then 75
2025-12-12 16:23:17.483016 INFO::Formatting Data.
2025-12-12 16:23:17.48388 INFO::Recognized SummarizedExperiment
2025-12-12 16:23:17.484391 INFO::Typecasting input to dataframe.
2025-12-12 16:23:17.500269 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:17.501583 INFO::Removing potential empty rows and columns
2025-12-12 16:23:17.506607 INFO::Found  0  missing values.
2025-12-12 16:23:17.514022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:17.514842 INFO::Done
2025-12-12 16:23:17.515628 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:17.520408 INFO::Starting hierarchical adjustment
2025-12-12 16:23:17.524305 INFO::Found  2  batches.
2025-12-12 16:23:17.525005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:17.525634 INFO::Using default BPPARAM
2025-12-12 16:23:17.526122 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:17.527413 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 16:23:17.561984 INFO::Done
2025-12-12 16:23:17.571836 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:17.581251 INFO::ASW Batch was 0.0247905836331344 prior to batch effect correction and is now 0.0247905836331344 .
2025-12-12 16:23:17.582353 INFO::Total function execution time is  0.0993590354919434  s and adjustment time is  0.0380699634552002 s ( 38.32 )
2025-12-12 16:23:17.619749 INFO::Formatting Data.
2025-12-12 16:23:17.620616 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:17.621542 INFO::Removing potential empty rows and columns
2025-12-12 16:23:17.622565 INFO::Found  0  missing values.
2025-12-12 16:23:17.627253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:17.628305 INFO::Done
2025-12-12 16:23:17.62892 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:17.63114 INFO::Starting hierarchical adjustment
2025-12-12 16:23:17.631843 INFO::Found  3  batches.
2025-12-12 16:23:17.632315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:17.632874 INFO::Using default BPPARAM
2025-12-12 16:23:17.633314 INFO::Processing subtree level 1
2025-12-12 16:23:17.849222 INFO::Adjusting the last 1 batches sequentially
2025-12-12 16:23:17.862739 INFO::Done
2025-12-12 16:23:17.86368 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:17.872633 INFO::ASW Batch was 0.0751377764478663 prior to batch effect correction and is now -0.167379658294874 .
2025-12-12 16:23:17.874437 INFO::Total function execution time is  0.254719972610474  s and adjustment time is  0.230933904647827 s ( 90.66 )
2025-12-12 16:23:17.907392 INFO::Skipping initial DF formatting
2025-12-12 16:23:17.908501 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:17.913085 INFO::Starting hierarchical adjustment
2025-12-12 16:23:17.913989 INFO::Found  5  batches.
2025-12-12 16:23:17.914543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:17.915252 INFO::Using default BPPARAM
2025-12-12 16:23:17.915751 INFO::Processing subtree level 1
2025-12-12 16:23:18.362407 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:18.36892 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 16:23:18.401255 INFO::Done
2025-12-12 16:23:18.402509 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:18.408503 INFO::ASW Batch was 0.548172531859672 prior to batch effect correction and is now 0.548172531859672 .
2025-12-12 16:23:18.409664 INFO::ASW Label was 0.346192361792442 prior to batch effect correction and is now 0.346192361792442 .
2025-12-12 16:23:18.410718 INFO::Total function execution time is  0.503432989120483  s and adjustment time is  0.48735785484314 s ( 96.81 )
2025-12-12 16:23:18.517846 INFO::Formatting Data.
2025-12-12 16:23:18.518859 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:18.519845 INFO::Removing potential empty rows and columns
2025-12-12 16:23:18.520916 INFO::Found  0  missing values.
2025-12-12 16:23:18.525335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:18.526062 INFO::Done
2025-12-12 16:23:18.526599 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:18.538231 INFO::Starting hierarchical adjustment
2025-12-12 16:23:18.539287 INFO::Found  5  batches.
2025-12-12 16:23:18.539899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:18.540612 INFO::Using default BPPARAM
2025-12-12 16:23:18.541119 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.

2025-12-12 16:23:18.780618 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:18.793683 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 16:23:18.849358 INFO::Done
2025-12-12 16:23:18.851058 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:18.85727 INFO::ASW Batch was 0.346606757561621 prior to batch effect correction and is now -0.0723186757573598 .
2025-12-12 16:23:18.858188 INFO::ASW Label was 0.363360585491363 prior to batch effect correction and is now 0.834473449377581 .
2025-12-12 16:23:18.859375 INFO::Total function execution time is  0.34158205986023  s and adjustment time is  0.310177087783813 s ( 90.81 )
2025-12-12 16:23:18.860393 INFO::Formatting Data.
2025-12-12 16:23:18.861082 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:18.863071 INFO::Removing potential empty rows and columns
2025-12-12 16:23:18.86438 INFO::Found  0  missing values.
2025-12-12 16:23:18.869986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:18.870889 INFO::Done
2025-12-12 16:23:18.871574 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:18.875367 INFO::Starting hierarchical adjustment
2025-12-12 16:23:18.876552 INFO::Found  5  batches.
2025-12-12 16:23:18.877247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:18.878155 INFO::Using default BPPARAM
2025-12-12 16:23:18.87903 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.

2025-12-12 16:23:19.037927 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:19.050279 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 16:23:19.093695 INFO::Done
2025-12-12 16:23:19.095092 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:19.101433 INFO::ASW Batch was 0.346606757561621 prior to batch effect correction and is now -0.0723186757573598 .
2025-12-12 16:23:19.102297 INFO::ASW Label was 0.363360585491363 prior to batch effect correction and is now 0.834473449377581 .
2025-12-12 16:23:19.104308 INFO::Total function execution time is  0.24301290512085  s and adjustment time is  0.2173011302948 s ( 89.42 )
2025-12-12 16:23:19.126754 INFO::Formatting Data.
2025-12-12 16:23:19.127817 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:19.128865 INFO::Removing potential empty rows and columns
2025-12-12 16:23:19.129976 INFO::Found  0  missing values.
2025-12-12 16:23:19.133981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:19.134587 INFO::Done
2025-12-12 16:23:19.135115 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:19.138384 INFO::Starting hierarchical adjustment
2025-12-12 16:23:19.139151 INFO::Found  5  batches.
2025-12-12 16:23:19.139663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:19.140712 INFO::Using default BPPARAM
2025-12-12 16:23:19.141257 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.

2025-12-12 16:23:19.318162 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:19.333196 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 16:23:19.373242 INFO::Done
2025-12-12 16:23:19.374975 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:19.380389 INFO::ASW Batch was 0.401635440634618 prior to batch effect correction and is now -0.106565968603704 .
2025-12-12 16:23:19.381118 INFO::ASW Label was 0.352429819497041 prior to batch effect correction and is now 0.811984489062845 .
2025-12-12 16:23:19.38205 INFO::Total function execution time is  0.255490064620972  s and adjustment time is  0.234163999557495 s ( 91.65 )
2025-12-12 16:23:19.383568 INFO::Formatting Data.
2025-12-12 16:23:19.38418 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:19.385111 INFO::Removing potential empty rows and columns
2025-12-12 16:23:19.38618 INFO::Found  0  missing values.
2025-12-12 16:23:19.390215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:19.390855 INFO::Done
2025-12-12 16:23:19.391381 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:19.39452 INFO::Starting hierarchical adjustment
2025-12-12 16:23:19.395342 INFO::Found  5  batches.
2025-12-12 16:23:19.395899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:19.396624 INFO::Using default BPPARAM
2025-12-12 16:23:19.397499 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.

2025-12-12 16:23:19.589042 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:19.598118 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 16:23:19.62818 INFO::Done
2025-12-12 16:23:19.629647 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:19.634744 INFO::ASW Batch was 0.401635440634618 prior to batch effect correction and is now -0.106565968603704 .
2025-12-12 16:23:19.635469 INFO::ASW Label was 0.352429819497041 prior to batch effect correction and is now 0.811984489062845 .
2025-12-12 16:23:19.641951 INFO::Total function execution time is  0.257983922958374  s and adjustment time is  0.232937097549438 s ( 90.29 )
2025-12-12 16:23:19.667136 INFO::Formatting Data.
2025-12-12 16:23:19.66805 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:19.669031 INFO::Removing potential empty rows and columns
2025-12-12 16:23:19.670172 INFO::Found  0  missing values.
2025-12-12 16:23:19.672995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:19.673622 INFO::Done
2025-12-12 16:23:19.674126 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:19.677339 INFO::Starting hierarchical adjustment
2025-12-12 16:23:19.678142 INFO::Found  2  batches.
2025-12-12 16:23:19.678678 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:19.680588 INFO::Using default BPPARAM
2025-12-12 16:23:19.68131 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:19.682759 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 16:23:19.699417 INFO::Done
2025-12-12 16:23:19.700204 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:19.703341 INFO::ASW Batch was 0.512916904741595 prior to batch effect correction and is now 0.0763359408282576 .
2025-12-12 16:23:19.704957 INFO::ASW Label was 0.580770153228179 prior to batch effect correction and is now 0.836443199525016 .
2025-12-12 16:23:19.706173 INFO::Total function execution time is  0.0391879081726074  s and adjustment time is  0.0213968753814697 s ( 54.6 )
2025-12-12 16:23:19.707051 INFO::Formatting Data.
2025-12-12 16:23:19.707686 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:19.708913 INFO::Removing potential empty rows and columns
2025-12-12 16:23:19.710215 INFO::Found  0  missing values.
2025-12-12 16:23:19.717214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:19.717846 INFO::Done
2025-12-12 16:23:19.71835 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:19.721471 INFO::Starting hierarchical adjustment
2025-12-12 16:23:19.722207 INFO::Found  2  batches.
2025-12-12 16:23:19.72271 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:19.723297 INFO::Using default BPPARAM
2025-12-12 16:23:19.723756 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:19.72537 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 16:23:19.744425 INFO::Done
2025-12-12 16:23:19.761234 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:19.765432 INFO::ASW Batch was 0.512916904741595 prior to batch effect correction and is now 0.0763359408282576 .
2025-12-12 16:23:19.766124 INFO::ASW Label was 0.580770153228179 prior to batch effect correction and is now 0.836443199525016 .
2025-12-12 16:23:19.766999 INFO::Total function execution time is  0.0599181652069092  s and adjustment time is  0.0223190784454346 s ( 37.25 )
2025-12-12 16:23:19.780427 INFO::Formatting Data.
2025-12-12 16:23:19.781275 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:19.782156 INFO::Removing potential empty rows and columns
2025-12-12 16:23:19.783028 INFO::Found  0  missing values.
2025-12-12 16:23:19.784956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:19.785504 INFO::Done
2025-12-12 16:23:19.785989 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:19.787908 INFO::Starting hierarchical adjustment
2025-12-12 16:23:19.788662 INFO::Found  2  batches.
2025-12-12 16:23:19.789183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:19.789791 INFO::Using default BPPARAM
2025-12-12 16:23:19.790293 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:19.791172 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 16:23:19.853102 INFO::Done
2025-12-12 16:23:19.853984 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:19.856104 INFO::ASW Batch was 0.0611055949035373 prior to batch effect correction and is now 0.00434729678544634 .
2025-12-12 16:23:19.856973 INFO::Total function execution time is  0.0766868591308594  s and adjustment time is  0.064532995223999 s ( 84.15 )
2025-12-12 16:23:19.870392 INFO::Formatting Data.
2025-12-12 16:23:19.871245 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:19.872217 INFO::Removing potential empty rows and columns
2025-12-12 16:23:19.873215 INFO::Found  0  missing values.
2025-12-12 16:23:19.874537 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.
2025-12-12 16:23:19.885012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:19.887774 INFO::Done
2025-12-12 16:23:19.888629 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:19.904722 INFO::Starting hierarchical adjustment
2025-12-12 16:23:19.905775 INFO::Found  2  batches.
2025-12-12 16:23:19.906325 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:19.906935 INFO::Using default BPPARAM
2025-12-12 16:23:19.907411 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:19.908343 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 16:23:19.931975 INFO::Done
2025-12-12 16:23:19.932808 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:19.935787 INFO::ASW Batch was 0.167748285303359 prior to batch effect correction and is now -0.0185689522221064 .
2025-12-12 16:23:19.936371 INFO::ASW Label was 0.833503145578577 prior to batch effect correction and is now 0.936926210845694 .
2025-12-12 16:23:19.937112 INFO::Total function execution time is  0.0668609142303467  s and adjustment time is  0.0263030529022217 s ( 39.34 )
2025-12-12 16:23:19.937849 INFO::Formatting Data.
2025-12-12 16:23:19.938393 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:19.939325 INFO::Removing potential empty rows and columns
2025-12-12 16:23:19.940441 INFO::Found  0  missing values.
2025-12-12 16:23:19.943994 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.
2025-12-12 16:23:19.949004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:19.949755 INFO::Done
2025-12-12 16:23:19.950292 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:19.953356 INFO::Starting hierarchical adjustment
2025-12-12 16:23:19.954143 INFO::Found  2  batches.
2025-12-12 16:23:19.954641 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:19.95522 INFO::Using default BPPARAM
2025-12-12 16:23:19.955685 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:19.96425 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 16:23:19.989615 INFO::Done
2025-12-12 16:23:19.990513 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:19.993617 INFO::ASW Batch was 0.167748285303359 prior to batch effect correction and is now -0.0185689522221064 .
2025-12-12 16:23:19.994313 INFO::ASW Label was 0.833503145578577 prior to batch effect correction and is now 0.936926210845694 .
2025-12-12 16:23:19.995107 INFO::Total function execution time is  0.0572309494018555  s and adjustment time is  0.0355610847473145 s ( 62.14 )
2025-12-12 16:23:20.415609 INFO::Formatting Data.
2025-12-12 16:23:20.417068 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:20.418209 INFO::Removing potential empty rows and columns
2025-12-12 16:23:20.420345 INFO::Found  0  missing values.
2025-12-12 16:23:20.42574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:20.426707 INFO::Done
2025-12-12 16:23:20.427208 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:20.436197 INFO::Starting hierarchical adjustment
2025-12-12 16:23:20.440196 INFO::Found  3  batches.
2025-12-12 16:23:20.441341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:20.442071 INFO::Using default BPPARAM
2025-12-12 16:23:20.44258 INFO::Processing subtree level 1
2025-12-12 16:23:20.561519 INFO::Adjusting the last 1 batches sequentially
2025-12-12 16:23:20.567089 INFO::Done
2025-12-12 16:23:20.56827 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:20.577349 INFO::ASW Batch was -0.0954517262625538 prior to batch effect correction and is now -0.0954517262625538 .
2025-12-12 16:23:20.579996 INFO::Total function execution time is  0.16496205329895  s and adjustment time is  0.127259016036987 s ( 77.14 )
2025-12-12 16:23:20.581294 INFO::Formatting Data.
2025-12-12 16:23:20.582387 INFO::Typecasting input to dataframe.
2025-12-12 16:23:20.583227 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:20.584751 INFO::Removing potential empty rows and columns
2025-12-12 16:23:20.586026 INFO::Found  0  missing values.
2025-12-12 16:23:20.592326 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:20.594025 INFO::Done
2025-12-12 16:23:20.59457 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:20.597419 INFO::Starting hierarchical adjustment
2025-12-12 16:23:20.598305 INFO::Found  3  batches.
2025-12-12 16:23:20.59888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:20.599539 INFO::Using default BPPARAM
2025-12-12 16:23:20.600061 INFO::Processing subtree level 1
2025-12-12 16:23:20.718388 INFO::Adjusting the last 1 batches sequentially
2025-12-12 16:23:20.722111 INFO::Done
2025-12-12 16:23:20.723416 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:20.729283 INFO::ASW Batch was -0.0954517262625538 prior to batch effect correction and is now -0.0954517262625538 .
2025-12-12 16:23:20.731984 INFO::Total function execution time is  0.15054202079773  s and adjustment time is  0.123963832855225 s ( 82.35 )
2025-12-12 16:23:20.757009 INFO::Formatting Data.
2025-12-12 16:23:20.758408 INFO::Typecasting input to dataframe.
2025-12-12 16:23:20.759496 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:20.760597 INFO::Removing potential empty rows and columns
2025-12-12 16:23:20.761978 INFO::Found  0  missing values.
2025-12-12 16:23:20.765023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:20.765667 INFO::Done
2025-12-12 16:23:20.7662 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:20.768305 INFO::Starting hierarchical adjustment
2025-12-12 16:23:20.769005 INFO::Found  3  batches.
2025-12-12 16:23:20.769495 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:20.77012 INFO::Using default BPPARAM
2025-12-12 16:23:20.770599 INFO::Processing subtree level 1
2025-12-12 16:23:20.869994 INFO::Adjusting the last 1 batches sequentially
2025-12-12 16:23:20.881068 INFO::Done
2025-12-12 16:23:20.890527 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:20.899118 INFO::ASW Batch was -0.0355995471430438 prior to batch effect correction and is now -0.0355995471430438 .
2025-12-12 16:23:20.901675 INFO::Total function execution time is  0.143992900848389  s and adjustment time is  0.112108945846558 s ( 77.86 )
2025-12-12 16:23:21.095402 INFO::Formatting Data.
2025-12-12 16:23:21.096335 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:21.097472 INFO::Removing potential empty rows and columns
2025-12-12 16:23:21.1003 INFO::Found  1000  missing values.
2025-12-12 16:23:21.120947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:21.12599 INFO::Done
2025-12-12 16:23:21.126562 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:21.132875 INFO::Starting hierarchical adjustment
2025-12-12 16:23:21.133826 INFO::Found  10  batches.
2025-12-12 16:23:21.134428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:21.135105 INFO::Using default BPPARAM
2025-12-12 16:23:21.135599 INFO::Processing subtree level 1
2025-12-12 16:23:21.310714 INFO::Processing subtree level 2
2025-12-12 16:23:21.507697 INFO::Adjusting the last 1 batches sequentially
2025-12-12 16:23:21.513329 INFO::Done
2025-12-12 16:23:21.514422 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:21.524208 INFO::ASW Batch was 0.469697841876111 prior to batch effect correction and is now 0.469697841876111 .
2025-12-12 16:23:21.525349 INFO::ASW Label was 0.384160464634517 prior to batch effect correction and is now 0.384160464634517 .
2025-12-12 16:23:21.526882 INFO::Total function execution time is  0.431368112564087  s and adjustment time is  0.379596948623657 s ( 88 )
2025-12-12 16:23:21.528198 INFO::Formatting Data.
2025-12-12 16:23:21.528914 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:21.530294 INFO::Removing potential empty rows and columns
2025-12-12 16:23:21.533199 INFO::Found  1000  missing values.
2025-12-12 16:23:21.550542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:21.551397 INFO::Done
2025-12-12 16:23:21.552258 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:21.559337 INFO::Starting hierarchical adjustment
2025-12-12 16:23:21.560642 INFO::Found  10  batches.
2025-12-12 16:23:23.395845 INFO::Set up parallel execution backend with 2 workers
2025-12-12 16:23:23.396756 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-12 16:23:25.472733 INFO::Adjusting the last 2 batches sequentially
2025-12-12 16:23:25.474359 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 16:23:25.526304 INFO::Done
2025-12-12 16:23:25.527594 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:25.563861 INFO::ASW Batch was 0.469697841876111 prior to batch effect correction and is now 0.469697841876111 .
2025-12-12 16:23:25.569985 INFO::ASW Label was 0.384160464634517 prior to batch effect correction and is now 0.384160464634517 .
2025-12-12 16:23:25.572302 INFO::Total function execution time is  4.04396080970764  s and adjustment time is  3.96486401557922 s ( 98.04 )
2025-12-12 16:23:25.77609 INFO::Formatting Data.
2025-12-12 16:23:25.777128 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:25.778186 INFO::Removing potential empty rows and columns
2025-12-12 16:23:25.779412 INFO::Found  0  missing values.
2025-12-12 16:23:25.783339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:25.784043 INFO::Done
2025-12-12 16:23:25.784589 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 16:23:25.787625 INFO::Starting hierarchical adjustment
2025-12-12 16:23:25.788394 INFO::Found  3  batches.
2025-12-12 16:23:25.788895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 16:23:25.789541 INFO::Using default BPPARAM
2025-12-12 16:23:25.790039 INFO::Processing subtree level 1
2025-12-12 16:23:25.940739 INFO::Adjusting the last 1 batches sequentially
2025-12-12 16:23:25.94648 INFO::Done
2025-12-12 16:23:25.947721 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 16:23:25.957911 INFO::ASW Batch was 0.187003407334573 prior to batch effect correction and is now -0.172937726158978 .
2025-12-12 16:23:25.958915 INFO::ASW Label was -0.153129068415379 prior to batch effect correction and is now 0.192179038270074 .
2025-12-12 16:23:25.960055 INFO::Total function execution time is  0.184123992919922  s and adjustment time is  0.158179044723511 s ( 85.91 )
2025-12-12 16:23:26.217367 INFO::Formatting Data.
2025-12-12 16:23:26.218497 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.219583 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.226968 INFO::Found  2  missing values.
2025-12-12 16:23:26.230606 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.231234 INFO::Done
2025-12-12 16:23:26.26592 INFO::Found NA in Reference column
2025-12-12 16:23:26.277741 INFO::Require at least two references per batch.
2025-12-12 16:23:26.302647 INFO::Formatting Data.
2025-12-12 16:23:26.303586 INFO::Recognized SummarizedExperiment
2025-12-12 16:23:26.30415 INFO::Typecasting input to dataframe.
2025-12-12 16:23:26.387751 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.396355 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.401656 INFO::Found  0  missing values.
2025-12-12 16:23:26.411054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.41198 INFO::Done
2025-12-12 16:23:26.453775 INFO::Formatting Data.
2025-12-12 16:23:26.455307 INFO::Recognized SummarizedExperiment
2025-12-12 16:23:26.455913 INFO::Typecasting input to dataframe.
2025-12-12 16:23:26.48634 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.487892 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.491606 INFO::Found  0  missing values.
2025-12-12 16:23:26.508658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.509944 INFO::Done
2025-12-12 16:23:26.543595 INFO::Formatting Data.
2025-12-12 16:23:26.54452 INFO::Recognized SummarizedExperiment
2025-12-12 16:23:26.545059 INFO::Typecasting input to dataframe.
2025-12-12 16:23:26.581342 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.582624 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.585247 INFO::Found  0  missing values.
2025-12-12 16:23:26.586876 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.
2025-12-12 16:23:26.597032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.597842 INFO::Done
2025-12-12 16:23:26.610685 INFO::Formatting Data.
2025-12-12 16:23:26.61162 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.612515 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.618754 INFO::Found  0  missing values.
2025-12-12 16:23:26.621773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.622394 INFO::Done
2025-12-12 16:23:26.636316 INFO::Formatting Data.
2025-12-12 16:23:26.637614 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.638779 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.640426 INFO::Found  0  missing values.
2025-12-12 16:23:26.643242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.643852 INFO::Done
2025-12-12 16:23:26.715462 INFO::Formatting Data.
2025-12-12 16:23:26.717468 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.719002 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.722948 INFO::Found  1  missing values.
2025-12-12 16:23:26.726304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.727004 INFO::Done
2025-12-12 16:23:26.791462 INFO::Formatting Data.
2025-12-12 16:23:26.792526 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.793464 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.794436 INFO::Found  2  missing values.
2025-12-12 16:23:26.795359 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.
2025-12-12 16:23:26.799373 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.800152 INFO::Done
2025-12-12 16:23:26.831392 INFO::Formatting Data.
2025-12-12 16:23:26.833275 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.835004 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.836373 INFO::Found  2  missing values.
2025-12-12 16:23:26.838268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.838879 INFO::Done
2025-12-12 16:23:26.856529 INFO::Formatting Data.
2025-12-12 16:23:26.857489 INFO::Typecasting input to dataframe.
2025-12-12 16:23:26.858282 INFO::Replacing NaNs with NAs.
2025-12-12 16:23:26.859165 INFO::Removing potential empty rows and columns
2025-12-12 16:23:26.860165 INFO::Found  0  missing values.
2025-12-12 16:23:26.862917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 16:23:26.863545 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 21.310   3.956  38.007

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT29.839 1.17634.396
compute_asw0.0330.0020.086
count_existing0.0160.0010.016
generate_data_covariables0.0150.0010.015
generate_dataset0.0140.0010.014