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This page was generated on 2026-02-18 11:57 -0500 (Wed, 18 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4890
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Package 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-02-16 13:45 -0500 (Mon, 16 Feb 2026)
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
See other builds for BERT in R Universe.

CHECK results for BERT on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
StartedAt: 2026-02-16 21:30:24 -0500 (Mon, 16 Feb 2026)
EndedAt: 2026-02-16 21:31:53 -0500 (Mon, 16 Feb 2026)
EllapsedTime: 89.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 24.488  1.538  17.727
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
2026-02-16 21:31:16.540561 INFO::Formatting Data.
2026-02-16 21:31:16.5424 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:16.557205 INFO::Removing potential empty rows and columns
2026-02-16 21:31:16.85779 INFO::Found  0  missing values.
2026-02-16 21:31:16.862894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:16.863915 INFO::Done
2026-02-16 21:31:16.864743 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:16.87802 INFO::Starting hierarchical adjustment
2026-02-16 21:31:16.878986 INFO::Found  3  batches.
2026-02-16 21:31:16.879596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:16.880938 INFO::Using default BPPARAM
2026-02-16 21:31:16.881602 INFO::Processing subtree level 1
2026-02-16 21:31:16.991682 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:31:16.993664 INFO::Done
2026-02-16 21:31:16.994413 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:16.997383 INFO::ASW Batch was -0.0777398378627811 prior to batch effect correction and is now -0.0777398378627811 .
2026-02-16 21:31:16.998626 INFO::Total function execution time is  0.458928346633911  s and adjustment time is  0.114863157272339 s ( 25.03 )
2026-02-16 21:31:17.01502 INFO::Formatting Data.
2026-02-16 21:31:17.015906 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:17.016881 INFO::Removing potential empty rows and columns
2026-02-16 21:31:17.018074 INFO::Found  0  missing values.
2026-02-16 21:31:17.019063 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.
2026-02-16 21:31:17.029959 INFO::Formatting Data.
2026-02-16 21:31:17.030724 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:17.031671 INFO::Removing potential empty rows and columns
2026-02-16 21:31:17.032807 INFO::Found  0  missing values.
2026-02-16 21:31:17.033784 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.
2026-02-16 21:31:17.060524 INFO::Formatting Data.
2026-02-16 21:31:17.06167 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:17.06278 INFO::Removing potential empty rows and columns
2026-02-16 21:31:17.064001 INFO::Found  0  missing values.
2026-02-16 21:31:17.065078 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.
2026-02-16 21:31:17.070212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:17.070837 INFO::Done
2026-02-16 21:31:17.071429 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:17.074247 INFO::Starting hierarchical adjustment
2026-02-16 21:31:17.074983 INFO::Found  2  batches.
2026-02-16 21:31:17.075504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:17.07622 INFO::Using default BPPARAM
2026-02-16 21:31:17.076786 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:17.07779 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:31:17.10132 INFO::Done
2026-02-16 21:31:17.102061 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:17.104475 INFO::ASW Batch was -0.0530122157849423 prior to batch effect correction and is now -0.117769808192149 .
2026-02-16 21:31:17.1054 INFO::Total function execution time is  0.0450835227966309  s and adjustment time is  0.0263848304748535 s ( 58.52 )
2026-02-16 21:31:17.108432 INFO::Formatting Data.
2026-02-16 21:31:17.109107 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:17.118802 INFO::Formatting Data.
2026-02-16 21:31:17.119609 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:17.120588 INFO::Removing potential empty rows and columns
2026-02-16 21:31:17.12171 INFO::Found  0  missing values.
2026-02-16 21:31:17.124934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:17.125535 INFO::Done
2026-02-16 21:31:17.126102 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:17.162817 INFO::Starting hierarchical adjustment
2026-02-16 21:31:17.165526 INFO::Found  2  batches.
2026-02-16 21:31:17.166136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:17.166735 INFO::Using default BPPARAM
2026-02-16 21:31:17.167256 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:17.168172 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:31:17.182319 INFO::Done
2026-02-16 21:31:17.18295 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:17.184836 INFO::ASW Batch was -0.0613058464722439 prior to batch effect correction and is now -0.11813985671615 .
2026-02-16 21:31:17.185571 INFO::Total function execution time is  0.0668485164642334  s and adjustment time is  0.0169930458068848 s ( 25.42 )
2026-02-16 21:31:17.186534 INFO::Formatting Data.
2026-02-16 21:31:17.187096 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:17.187911 INFO::Removing potential empty rows and columns
2026-02-16 21:31:17.188839 INFO::Found  0  missing values.
2026-02-16 21:31:17.191475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:17.191993 INFO::Done
2026-02-16 21:31:17.192486 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:17.19435 INFO::Starting hierarchical adjustment
2026-02-16 21:31:17.19504 INFO::Found  2  batches.
2026-02-16 21:31:17.195548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:17.196162 INFO::Using default BPPARAM
2026-02-16 21:31:17.196682 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:17.197554 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:31:17.21195 INFO::Done
2026-02-16 21:31:17.21258 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:17.214527 INFO::ASW Batch was -0.0613058464722439 prior to batch effect correction and is now -0.11813985671615 .
2026-02-16 21:31:17.215276 INFO::Total function execution time is  0.0287430286407471  s and adjustment time is  0.0170340538024902 s ( 59.26 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-16 21:31:20.236089 INFO::Formatting Data.
2026-02-16 21:31:20.236764 INFO::Recognized SummarizedExperiment
2026-02-16 21:31:20.237234 INFO::Typecasting input to dataframe.
2026-02-16 21:31:20.265356 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:20.266628 INFO::Removing potential empty rows and columns
2026-02-16 21:31:20.270409 INFO::Found  0  missing values.
2026-02-16 21:31:20.277625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:20.278223 INFO::Done
2026-02-16 21:31:20.278757 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:20.282298 INFO::Starting hierarchical adjustment
2026-02-16 21:31:20.28302 INFO::Found  2  batches.
2026-02-16 21:31:20.283545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:20.284611 INFO::Using default BPPARAM
2026-02-16 21:31:20.285138 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:20.286102 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:31:20.341759 INFO::Done
2026-02-16 21:31:20.342457 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:20.346029 INFO::ASW Batch was -0.015069625411637 prior to batch effect correction and is now -0.0945649380772906 .
2026-02-16 21:31:20.346878 INFO::Total function execution time is  0.111040353775024  s and adjustment time is  0.058863639831543 s ( 53.01 )
Warning: stack imbalance in '{', 73 then 75
2026-02-16 21:31:20.365565 INFO::Formatting Data.
2026-02-16 21:31:20.366289 INFO::Recognized SummarizedExperiment
2026-02-16 21:31:20.366823 INFO::Typecasting input to dataframe.
2026-02-16 21:31:20.37609 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:20.377299 INFO::Removing potential empty rows and columns
2026-02-16 21:31:20.381027 INFO::Found  0  missing values.
2026-02-16 21:31:20.38818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:20.388847 INFO::Done
2026-02-16 21:31:20.389378 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:20.39295 INFO::Starting hierarchical adjustment
2026-02-16 21:31:20.393674 INFO::Found  2  batches.
2026-02-16 21:31:20.394199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:20.3948 INFO::Using default BPPARAM
2026-02-16 21:31:20.395308 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:20.396261 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:31:20.42106 INFO::Done
2026-02-16 21:31:20.421762 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:20.425399 INFO::ASW Batch was 0.00154637914670977 prior to batch effect correction and is now 0.00154637914670977 .
2026-02-16 21:31:20.426286 INFO::Total function execution time is  0.0606980323791504  s and adjustment time is  0.0275108814239502 s ( 45.32 )
2026-02-16 21:31:20.444818 INFO::Formatting Data.
2026-02-16 21:31:20.445693 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:20.446639 INFO::Removing potential empty rows and columns
2026-02-16 21:31:20.447671 INFO::Found  0  missing values.
2026-02-16 21:31:20.450667 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:20.451199 INFO::Done
2026-02-16 21:31:20.451715 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:20.453729 INFO::Starting hierarchical adjustment
2026-02-16 21:31:20.454429 INFO::Found  3  batches.
2026-02-16 21:31:20.454958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:20.45556 INFO::Using default BPPARAM
2026-02-16 21:31:20.456075 INFO::Processing subtree level 1
2026-02-16 21:31:20.587556 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:31:20.589277 INFO::Done
2026-02-16 21:31:20.589952 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:20.592361 INFO::ASW Batch was -0.0188910039359157 prior to batch effect correction and is now -0.173114648097719 .
2026-02-16 21:31:20.593329 INFO::Total function execution time is  0.148674488067627  s and adjustment time is  0.13497519493103 s ( 90.79 )
2026-02-16 21:31:20.607834 INFO::Skipping initial DF formatting
2026-02-16 21:31:20.608565 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:20.612648 INFO::Starting hierarchical adjustment
2026-02-16 21:31:20.61344 INFO::Found  5  batches.
2026-02-16 21:31:20.614014 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:20.614646 INFO::Using default BPPARAM
2026-02-16 21:31:20.615179 INFO::Processing subtree level 1
2026-02-16 21:31:20.83148 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:20.83307 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:31:20.853111 INFO::Done
2026-02-16 21:31:20.853875 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:20.858228 INFO::ASW Batch was 0.494699595805401 prior to batch effect correction and is now 0.494699595805401 .
2026-02-16 21:31:20.858875 INFO::ASW Label was 0.393615510752541 prior to batch effect correction and is now 0.393615510752541 .
2026-02-16 21:31:20.859738 INFO::Total function execution time is  0.252010822296143  s and adjustment time is  0.239792346954346 s ( 95.15 )
2026-02-16 21:31:20.923493 INFO::Formatting Data.
2026-02-16 21:31:20.924241 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:20.925169 INFO::Removing potential empty rows and columns
2026-02-16 21:31:20.926145 INFO::Found  0  missing values.
2026-02-16 21:31:20.93007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:20.93065 INFO::Done
2026-02-16 21:31:20.931147 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:20.934042 INFO::Starting hierarchical adjustment
2026-02-16 21:31:20.934766 INFO::Found  5  batches.
2026-02-16 21:31:20.935295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:20.935906 INFO::Using default BPPARAM
2026-02-16 21:31:20.936415 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.

2026-02-16 21:31:21.068741 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.070386 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:31:21.087743 INFO::Done
2026-02-16 21:31:21.088447 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.091998 INFO::ASW Batch was 0.300241564407245 prior to batch effect correction and is now -0.0687669092422013 .
2026-02-16 21:31:21.092648 INFO::ASW Label was 0.403469065210292 prior to batch effect correction and is now 0.858530600216848 .
2026-02-16 21:31:21.093458 INFO::Total function execution time is  0.170030832290649  s and adjustment time is  0.15312123298645 s ( 90.05 )
2026-02-16 21:31:21.094405 INFO::Formatting Data.
2026-02-16 21:31:21.095077 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:21.096032 INFO::Removing potential empty rows and columns
2026-02-16 21:31:21.097158 INFO::Found  0  missing values.
2026-02-16 21:31:21.101558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:21.102122 INFO::Done
2026-02-16 21:31:21.102699 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:21.105973 INFO::Starting hierarchical adjustment
2026-02-16 21:31:21.106741 INFO::Found  5  batches.
2026-02-16 21:31:21.107287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:21.107946 INFO::Using default BPPARAM
2026-02-16 21:31:21.108484 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.

2026-02-16 21:31:21.229956 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.231493 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:31:21.24718 INFO::Done
2026-02-16 21:31:21.247883 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.251098 INFO::ASW Batch was 0.300241564407245 prior to batch effect correction and is now -0.0687669092422013 .
2026-02-16 21:31:21.251699 INFO::ASW Label was 0.403469065210292 prior to batch effect correction and is now 0.858530600216848 .
2026-02-16 21:31:21.252517 INFO::Total function execution time is  0.158104419708252  s and adjustment time is  0.140611171722412 s ( 88.94 )
2026-02-16 21:31:21.265863 INFO::Formatting Data.
2026-02-16 21:31:21.266649 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:21.267849 INFO::Removing potential empty rows and columns
2026-02-16 21:31:21.268861 INFO::Found  0  missing values.
2026-02-16 21:31:21.272823 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:21.273363 INFO::Done
2026-02-16 21:31:21.273898 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:21.276908 INFO::Starting hierarchical adjustment
2026-02-16 21:31:21.277616 INFO::Found  5  batches.
2026-02-16 21:31:21.278126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:21.278779 INFO::Using default BPPARAM
2026-02-16 21:31:21.279344 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.

2026-02-16 21:31:21.398085 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.399734 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:31:21.415968 INFO::Done
2026-02-16 21:31:21.416759 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.420189 INFO::ASW Batch was 0.378329433360749 prior to batch effect correction and is now -0.0610007364093638 .
2026-02-16 21:31:21.420839 INFO::ASW Label was 0.479453682827524 prior to batch effect correction and is now 0.764445089148299 .
2026-02-16 21:31:21.42167 INFO::Total function execution time is  0.1558678150177  s and adjustment time is  0.138446092605591 s ( 88.82 )
2026-02-16 21:31:21.422536 INFO::Formatting Data.
2026-02-16 21:31:21.42318 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:21.424121 INFO::Removing potential empty rows and columns
2026-02-16 21:31:21.425168 INFO::Found  0  missing values.
2026-02-16 21:31:21.429388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:21.429969 INFO::Done
2026-02-16 21:31:21.430503 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:21.433637 INFO::Starting hierarchical adjustment
2026-02-16 21:31:21.434375 INFO::Found  5  batches.
2026-02-16 21:31:21.434927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:21.43557 INFO::Using default BPPARAM
2026-02-16 21:31:21.436102 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.

2026-02-16 21:31:21.557921 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.559599 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:31:21.578138 INFO::Done
2026-02-16 21:31:21.578939 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.582919 INFO::ASW Batch was 0.378329433360749 prior to batch effect correction and is now -0.0610007364093638 .
2026-02-16 21:31:21.583616 INFO::ASW Label was 0.479453682827524 prior to batch effect correction and is now 0.764445089148299 .
2026-02-16 21:31:21.58449 INFO::Total function execution time is  0.161968469619751  s and adjustment time is  0.143876075744629 s ( 88.83 )
2026-02-16 21:31:21.598473 INFO::Formatting Data.
2026-02-16 21:31:21.599236 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:21.600145 INFO::Removing potential empty rows and columns
2026-02-16 21:31:21.601144 INFO::Found  0  missing values.
2026-02-16 21:31:21.603787 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:21.604307 INFO::Done
2026-02-16 21:31:21.60482 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:21.607684 INFO::Starting hierarchical adjustment
2026-02-16 21:31:21.608378 INFO::Found  2  batches.
2026-02-16 21:31:21.608903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:21.609498 INFO::Using default BPPARAM
2026-02-16 21:31:21.610027 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.610926 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:31:21.625448 INFO::Done
2026-02-16 21:31:21.62611 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.62895 INFO::ASW Batch was 0.518566429830157 prior to batch effect correction and is now 0.0290402964309708 .
2026-02-16 21:31:21.629526 INFO::ASW Label was 0.48970204636044 prior to batch effect correction and is now 0.895477938025991 .
2026-02-16 21:31:21.630297 INFO::Total function execution time is  0.0318934917449951  s and adjustment time is  0.0171866416931152 s ( 53.89 )
2026-02-16 21:31:21.631056 INFO::Formatting Data.
2026-02-16 21:31:21.631664 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:21.632495 INFO::Removing potential empty rows and columns
2026-02-16 21:31:21.633473 INFO::Found  0  missing values.
2026-02-16 21:31:21.636085 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:21.636614 INFO::Done
2026-02-16 21:31:21.637105 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:21.639917 INFO::Starting hierarchical adjustment
2026-02-16 21:31:21.640615 INFO::Found  2  batches.
2026-02-16 21:31:21.641125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:21.648668 INFO::Using default BPPARAM
2026-02-16 21:31:21.649293 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.650251 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:31:21.665884 INFO::Done
2026-02-16 21:31:21.666582 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.669827 INFO::ASW Batch was 0.518566429830157 prior to batch effect correction and is now 0.0290402964309708 .
2026-02-16 21:31:21.67044 INFO::ASW Label was 0.48970204636044 prior to batch effect correction and is now 0.895477938025991 .
2026-02-16 21:31:21.67126 INFO::Total function execution time is  0.040189266204834  s and adjustment time is  0.0254037380218506 s ( 63.21 )
2026-02-16 21:31:21.682933 INFO::Formatting Data.
2026-02-16 21:31:21.683746 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:21.684691 INFO::Removing potential empty rows and columns
2026-02-16 21:31:21.685675 INFO::Found  0  missing values.
2026-02-16 21:31:21.68788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:21.688429 INFO::Done
2026-02-16 21:31:21.688962 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:21.690975 INFO::Starting hierarchical adjustment
2026-02-16 21:31:21.691689 INFO::Found  2  batches.
2026-02-16 21:31:21.692214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:21.692819 INFO::Using default BPPARAM
2026-02-16 21:31:21.693335 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.69424 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:31:21.725167 INFO::Done
2026-02-16 21:31:21.725823 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.727717 INFO::ASW Batch was -0.0135110793690506 prior to batch effect correction and is now -0.113947475171766 .
2026-02-16 21:31:21.728503 INFO::Total function execution time is  0.0456724166870117  s and adjustment time is  0.0336248874664307 s ( 73.62 )
2026-02-16 21:31:21.740246 INFO::Formatting Data.
2026-02-16 21:31:21.741016 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:21.741889 INFO::Removing potential empty rows and columns
2026-02-16 21:31:21.742869 INFO::Found  0  missing values.
2026-02-16 21:31:21.743997 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.
2026-02-16 21:31:21.748488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:21.749033 INFO::Done
2026-02-16 21:31:21.749544 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:21.752404 INFO::Starting hierarchical adjustment
2026-02-16 21:31:21.753109 INFO::Found  2  batches.
2026-02-16 21:31:21.75362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:21.75418 INFO::Using default BPPARAM
2026-02-16 21:31:21.754693 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.755579 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:31:21.77119 INFO::Done
2026-02-16 21:31:21.771874 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.774682 INFO::ASW Batch was 0.675057919128008 prior to batch effect correction and is now -0.00843543070465507 .
2026-02-16 21:31:21.775254 INFO::ASW Label was 0.367798597559548 prior to batch effect correction and is now 0.869363487717905 .
2026-02-16 21:31:21.775993 INFO::Total function execution time is  0.0358498096466064  s and adjustment time is  0.0181944370269775 s ( 50.75 )
2026-02-16 21:31:21.776771 INFO::Formatting Data.
2026-02-16 21:31:21.777364 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:21.778221 INFO::Removing potential empty rows and columns
2026-02-16 21:31:21.779209 INFO::Found  0  missing values.
2026-02-16 21:31:21.780076 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.
2026-02-16 21:31:21.784261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:21.784779 INFO::Done
2026-02-16 21:31:21.785262 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:21.787972 INFO::Starting hierarchical adjustment
2026-02-16 21:31:21.788659 INFO::Found  2  batches.
2026-02-16 21:31:21.789158 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:21.789731 INFO::Using default BPPARAM
2026-02-16 21:31:21.790218 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:21.791084 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:31:21.806781 INFO::Done
2026-02-16 21:31:21.807433 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:21.810275 INFO::ASW Batch was 0.675057919128008 prior to batch effect correction and is now -0.00843543070465507 .
2026-02-16 21:31:21.810894 INFO::ASW Label was 0.367798597559548 prior to batch effect correction and is now 0.869363487717905 .
2026-02-16 21:31:21.811666 INFO::Total function execution time is  0.0348997116088867  s and adjustment time is  0.018251895904541 s ( 52.3 )
2026-02-16 21:31:22.011914 INFO::Formatting Data.
2026-02-16 21:31:22.012868 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:22.013839 INFO::Removing potential empty rows and columns
2026-02-16 21:31:22.014902 INFO::Found  0  missing values.
2026-02-16 21:31:22.017948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:22.018496 INFO::Done
2026-02-16 21:31:22.019027 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:22.021089 INFO::Starting hierarchical adjustment
2026-02-16 21:31:22.021798 INFO::Found  3  batches.
2026-02-16 21:31:22.022323 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:22.022937 INFO::Using default BPPARAM
2026-02-16 21:31:22.023448 INFO::Processing subtree level 1
2026-02-16 21:31:22.106997 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:31:22.108793 INFO::Done
2026-02-16 21:31:22.109454 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:22.111984 INFO::ASW Batch was -0.0546930510550111 prior to batch effect correction and is now -0.0546930510550111 .
2026-02-16 21:31:22.112952 INFO::Total function execution time is  0.101089239120483  s and adjustment time is  0.0871224403381348 s ( 86.18 )
2026-02-16 21:31:22.114031 INFO::Formatting Data.
2026-02-16 21:31:22.114703 INFO::Typecasting input to dataframe.
2026-02-16 21:31:22.115519 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:22.116461 INFO::Removing potential empty rows and columns
2026-02-16 21:31:22.117606 INFO::Found  0  missing values.
2026-02-16 21:31:22.120781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:22.121334 INFO::Done
2026-02-16 21:31:22.121872 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:22.123987 INFO::Starting hierarchical adjustment
2026-02-16 21:31:22.124721 INFO::Found  3  batches.
2026-02-16 21:31:22.125258 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:22.125887 INFO::Using default BPPARAM
2026-02-16 21:31:22.126422 INFO::Processing subtree level 1
2026-02-16 21:31:22.210252 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:31:22.21207 INFO::Done
2026-02-16 21:31:22.212751 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:22.215291 INFO::ASW Batch was -0.0546930510550111 prior to batch effect correction and is now -0.0546930510550111 .
2026-02-16 21:31:22.216255 INFO::Total function execution time is  0.102191686630249  s and adjustment time is  0.0874857902526855 s ( 85.61 )
2026-02-16 21:31:22.229728 INFO::Formatting Data.
2026-02-16 21:31:22.230555 INFO::Typecasting input to dataframe.
2026-02-16 21:31:22.231416 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:22.232353 INFO::Removing potential empty rows and columns
2026-02-16 21:31:22.233495 INFO::Found  0  missing values.
2026-02-16 21:31:22.236566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:22.237101 INFO::Done
2026-02-16 21:31:22.237689 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:22.239738 INFO::Starting hierarchical adjustment
2026-02-16 21:31:22.240435 INFO::Found  3  batches.
2026-02-16 21:31:22.240975 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:22.241616 INFO::Using default BPPARAM
2026-02-16 21:31:22.242145 INFO::Processing subtree level 1
2026-02-16 21:31:22.324913 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:31:22.326701 INFO::Done
2026-02-16 21:31:22.327356 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:22.329911 INFO::ASW Batch was -0.0730666472576961 prior to batch effect correction and is now -0.0730666472576961 .
2026-02-16 21:31:22.330862 INFO::Total function execution time is  0.101209878921509  s and adjustment time is  0.0863819122314453 s ( 85.35 )
2026-02-16 21:31:22.462066 INFO::Formatting Data.
2026-02-16 21:31:22.462846 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:22.464013 INFO::Removing potential empty rows and columns
2026-02-16 21:31:22.466759 INFO::Found  1000  missing values.
2026-02-16 21:31:22.485559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:22.486279 INFO::Done
2026-02-16 21:31:22.486833 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:22.492265 INFO::Starting hierarchical adjustment
2026-02-16 21:31:22.493048 INFO::Found  10  batches.
2026-02-16 21:31:22.493584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:22.494195 INFO::Using default BPPARAM
2026-02-16 21:31:22.494735 INFO::Processing subtree level 1
2026-02-16 21:31:22.615709 INFO::Processing subtree level 2
2026-02-16 21:31:22.761497 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:31:22.764258 INFO::Done
2026-02-16 21:31:22.765326 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:22.774412 INFO::ASW Batch was 0.47006045350568 prior to batch effect correction and is now 0.47006045350568 .
2026-02-16 21:31:22.775594 INFO::ASW Label was 0.344175795310944 prior to batch effect correction and is now 0.344175795310944 .
2026-02-16 21:31:22.776979 INFO::Total function execution time is  0.314886331558228  s and adjustment time is  0.271263837814331 s ( 86.15 )
2026-02-16 21:31:22.778296 INFO::Formatting Data.
2026-02-16 21:31:22.779318 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:22.781165 INFO::Removing potential empty rows and columns
2026-02-16 21:31:22.785826 INFO::Found  1000  missing values.
2026-02-16 21:31:22.818191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:22.819264 INFO::Done
2026-02-16 21:31:22.820147 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:22.828636 INFO::Starting hierarchical adjustment
2026-02-16 21:31:22.829857 INFO::Found  10  batches.
2026-02-16 21:31:23.744236 INFO::Set up parallel execution backend with 2 workers
2026-02-16 21:31:23.74643 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-16 21:31:24.866497 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:31:24.86813 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:31:24.883459 INFO::Done
2026-02-16 21:31:24.884077 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:24.888405 INFO::ASW Batch was 0.47006045350568 prior to batch effect correction and is now 0.47006045350568 .
2026-02-16 21:31:24.888955 INFO::ASW Label was 0.344175795310944 prior to batch effect correction and is now 0.344175795310944 .
2026-02-16 21:31:24.889644 INFO::Total function execution time is  2.11147332191467  s and adjustment time is  2.05390167236328 s ( 97.27 )
2026-02-16 21:31:25.022846 INFO::Formatting Data.
2026-02-16 21:31:25.023612 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.024487 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.025518 INFO::Found  0  missing values.
2026-02-16 21:31:25.028944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.02945 INFO::Done
2026-02-16 21:31:25.029954 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:31:25.032549 INFO::Starting hierarchical adjustment
2026-02-16 21:31:25.033209 INFO::Found  3  batches.
2026-02-16 21:31:25.033712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:31:25.034275 INFO::Using default BPPARAM
2026-02-16 21:31:25.034768 INFO::Processing subtree level 1
2026-02-16 21:31:25.133924 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:31:25.135592 INFO::Done
2026-02-16 21:31:25.13618 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:31:25.139178 INFO::ASW Batch was 0.251770010390091 prior to batch effect correction and is now -0.160735325983311 .
2026-02-16 21:31:25.139757 INFO::ASW Label was -0.205199601755788 prior to batch effect correction and is now -0.001043551575707 .
2026-02-16 21:31:25.140601 INFO::Total function execution time is  0.117821931838989  s and adjustment time is  0.102488994598389 s ( 86.99 )
2026-02-16 21:31:25.254601 INFO::Formatting Data.
2026-02-16 21:31:25.255339 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.256178 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.257137 INFO::Found  2  missing values.
2026-02-16 21:31:25.259751 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.260249 INFO::Done
2026-02-16 21:31:25.286956 INFO::Found NA in Reference column
2026-02-16 21:31:25.296028 INFO::Require at least two references per batch.
2026-02-16 21:31:25.315381 INFO::Formatting Data.
2026-02-16 21:31:25.316119 INFO::Recognized SummarizedExperiment
2026-02-16 21:31:25.316636 INFO::Typecasting input to dataframe.
2026-02-16 21:31:25.325751 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.326842 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.330107 INFO::Found  0  missing values.
2026-02-16 21:31:25.336426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.336972 INFO::Done
2026-02-16 21:31:25.351757 INFO::Formatting Data.
2026-02-16 21:31:25.352446 INFO::Recognized SummarizedExperiment
2026-02-16 21:31:25.352961 INFO::Typecasting input to dataframe.
2026-02-16 21:31:25.36936 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.370616 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.373976 INFO::Found  0  missing values.
2026-02-16 21:31:25.383896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.384468 INFO::Done
2026-02-16 21:31:25.398947 INFO::Formatting Data.
2026-02-16 21:31:25.399629 INFO::Recognized SummarizedExperiment
2026-02-16 21:31:25.400114 INFO::Typecasting input to dataframe.
2026-02-16 21:31:25.415159 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.416068 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.417044 INFO::Found  0  missing values.
2026-02-16 21:31:25.41788 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.
2026-02-16 21:31:25.42189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.422382 INFO::Done
2026-02-16 21:31:25.431388 INFO::Formatting Data.
2026-02-16 21:31:25.432063 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.432841 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.433818 INFO::Found  0  missing values.
2026-02-16 21:31:25.436406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.436899 INFO::Done
2026-02-16 21:31:25.447128 INFO::Formatting Data.
2026-02-16 21:31:25.44794 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.448873 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.4498 INFO::Found  0  missing values.
2026-02-16 21:31:25.452467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.45299 INFO::Done
2026-02-16 21:31:25.480293 INFO::Formatting Data.
2026-02-16 21:31:25.481117 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.482111 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.483213 INFO::Found  1  missing values.
2026-02-16 21:31:25.485685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.486198 INFO::Done
2026-02-16 21:31:25.503834 INFO::Formatting Data.
2026-02-16 21:31:25.504567 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.505363 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.506243 INFO::Found  2  missing values.
2026-02-16 21:31:25.507092 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.
2026-02-16 21:31:25.509201 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.509705 INFO::Done
2026-02-16 21:31:25.519079 INFO::Formatting Data.
2026-02-16 21:31:25.519852 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.520679 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.521565 INFO::Found  2  missing values.
2026-02-16 21:31:25.530004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.530678 INFO::Done
2026-02-16 21:31:25.541729 INFO::Formatting Data.
2026-02-16 21:31:25.5425 INFO::Typecasting input to dataframe.
2026-02-16 21:31:25.543312 INFO::Replacing NaNs with NAs.
2026-02-16 21:31:25.544191 INFO::Removing potential empty rows and columns
2026-02-16 21:31:25.545244 INFO::Found  0  missing values.
2026-02-16 21:31:25.5483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:31:25.548858 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.475   3.142  20.494

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT24.488 1.53817.727
compute_asw0.0230.0030.025
count_existing0.0120.0020.015
generate_data_covariables0.0110.0010.012
generate_dataset0.0110.0010.012