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This page was generated on 2026-03-13 11:57 -0400 (Fri, 13 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4892
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Package 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-03-12 13:45 -0400 (Thu, 12 Mar 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 -0400 (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: 2026-03-12 21:52:02 -0400 (Thu, 12 Mar 2026)
EndedAt: 2026-03-12 21:53:31 -0400 (Thu, 12 Mar 2026)
EllapsedTime: 89.1 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 24.269  1.287  17.803
* 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")
2026-03-12 21:52:54.453856 INFO::Formatting Data.
2026-03-12 21:52:54.45516 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:54.46619 INFO::Removing potential empty rows and columns
2026-03-12 21:52:54.704091 INFO::Found  0  missing values.
2026-03-12 21:52:54.707356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:54.708038 INFO::Done
2026-03-12 21:52:54.7086 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:54.719319 INFO::Starting hierarchical adjustment
2026-03-12 21:52:54.720187 INFO::Found  3  batches.
2026-03-12 21:52:54.720739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:54.721843 INFO::Using default BPPARAM
2026-03-12 21:52:54.722399 INFO::Processing subtree level 1
2026-03-12 21:52:54.822151 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:52:54.824129 INFO::Done
2026-03-12 21:52:54.824906 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:54.827776 INFO::ASW Batch was -0.088127951302399 prior to batch effect correction and is now -0.088127951302399 .
2026-03-12 21:52:54.828941 INFO::Total function execution time is  0.375661134719849  s and adjustment time is  0.104096174240112 s ( 27.71 )
2026-03-12 21:52:54.843702 INFO::Formatting Data.
2026-03-12 21:52:54.844558 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:54.845552 INFO::Removing potential empty rows and columns
2026-03-12 21:52:54.84675 INFO::Found  0  missing values.
2026-03-12 21:52:54.847767 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.
2026-03-12 21:52:54.859198 INFO::Formatting Data.
2026-03-12 21:52:54.859978 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:54.86089 INFO::Removing potential empty rows and columns
2026-03-12 21:52:54.862031 INFO::Found  0  missing values.
2026-03-12 21:52:54.862992 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.
2026-03-12 21:52:54.879622 INFO::Formatting Data.
2026-03-12 21:52:54.880454 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:54.881406 INFO::Removing potential empty rows and columns
2026-03-12 21:52:54.882483 INFO::Found  0  missing values.
2026-03-12 21:52:54.883423 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.
2026-03-12 21:52:54.888065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:54.88866 INFO::Done
2026-03-12 21:52:54.889182 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:54.891243 INFO::Starting hierarchical adjustment
2026-03-12 21:52:54.891963 INFO::Found  2  batches.
2026-03-12 21:52:54.892514 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:54.893159 INFO::Using default BPPARAM
2026-03-12 21:52:54.893698 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:54.894638 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:52:54.916945 INFO::Done
2026-03-12 21:52:54.917724 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:54.920226 INFO::ASW Batch was -0.067438817980134 prior to batch effect correction and is now -0.116733363076674 .
2026-03-12 21:52:54.921146 INFO::Total function execution time is  0.0415933132171631  s and adjustment time is  0.0250935554504395 s ( 60.33 )
2026-03-12 21:52:54.924376 INFO::Formatting Data.
2026-03-12 21:52:54.925073 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:54.934705 INFO::Formatting Data.
2026-03-12 21:52:54.935813 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:54.936803 INFO::Removing potential empty rows and columns
2026-03-12 21:52:54.937959 INFO::Found  0  missing values.
2026-03-12 21:52:54.941111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:54.941692 INFO::Done
2026-03-12 21:52:54.94224 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:54.967014 INFO::Starting hierarchical adjustment
2026-03-12 21:52:54.968296 INFO::Found  2  batches.
2026-03-12 21:52:54.968833 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:54.969378 INFO::Using default BPPARAM
2026-03-12 21:52:54.969928 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:54.97087 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:52:54.984611 INFO::Done
2026-03-12 21:52:54.985227 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:54.987194 INFO::ASW Batch was 0.00698190058037742 prior to batch effect correction and is now -0.103257633390075 .
2026-03-12 21:52:54.98793 INFO::Total function execution time is  0.0533173084259033  s and adjustment time is  0.0164651870727539 s ( 30.88 )
2026-03-12 21:52:54.988888 INFO::Formatting Data.
2026-03-12 21:52:54.989451 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:54.990243 INFO::Removing potential empty rows and columns
2026-03-12 21:52:54.991182 INFO::Found  0  missing values.
2026-03-12 21:52:54.993777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:54.994341 INFO::Done
2026-03-12 21:52:54.994841 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:54.99668 INFO::Starting hierarchical adjustment
2026-03-12 21:52:54.997335 INFO::Found  2  batches.
2026-03-12 21:52:54.997835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:54.99839 INFO::Using default BPPARAM
2026-03-12 21:52:54.998895 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:54.999729 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:52:55.013523 INFO::Done
2026-03-12 21:52:55.014169 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:55.016089 INFO::ASW Batch was 0.00698190058037742 prior to batch effect correction and is now -0.103257633390075 .
2026-03-12 21:52:55.01684 INFO::Total function execution time is  0.027940034866333  s and adjustment time is  0.0162925720214844 s ( 58.31 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-12 21:52:57.851735 INFO::Formatting Data.
2026-03-12 21:52:57.85239 INFO::Recognized SummarizedExperiment
2026-03-12 21:52:57.852881 INFO::Typecasting input to dataframe.
2026-03-12 21:52:57.882352 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:57.883684 INFO::Removing potential empty rows and columns
2026-03-12 21:52:57.887648 INFO::Found  0  missing values.
2026-03-12 21:52:57.895127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:57.895952 INFO::Done
2026-03-12 21:52:57.896523 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:57.900185 INFO::Starting hierarchical adjustment
2026-03-12 21:52:57.900944 INFO::Found  2  batches.
2026-03-12 21:52:57.901471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:57.902613 INFO::Using default BPPARAM
2026-03-12 21:52:57.903171 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:57.904173 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:52:57.961675 INFO::Done
2026-03-12 21:52:57.962392 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:57.96608 INFO::ASW Batch was -0.00423185920152632 prior to batch effect correction and is now -0.0903969087578946 .
2026-03-12 21:52:57.966974 INFO::Total function execution time is  0.115521192550659  s and adjustment time is  0.0608408451080322 s ( 52.67 )
Warning: stack imbalance in '{', 73 then 75
2026-03-12 21:52:57.986371 INFO::Formatting Data.
2026-03-12 21:52:57.987183 INFO::Recognized SummarizedExperiment
2026-03-12 21:52:57.987755 INFO::Typecasting input to dataframe.
2026-03-12 21:52:57.997601 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:57.998854 INFO::Removing potential empty rows and columns
2026-03-12 21:52:58.002848 INFO::Found  0  missing values.
2026-03-12 21:52:58.010226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:58.010936 INFO::Done
2026-03-12 21:52:58.011479 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:58.015216 INFO::Starting hierarchical adjustment
2026-03-12 21:52:58.015986 INFO::Found  2  batches.
2026-03-12 21:52:58.016534 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:58.017146 INFO::Using default BPPARAM
2026-03-12 21:52:58.017703 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:58.018723 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:52:58.044705 INFO::Done
2026-03-12 21:52:58.045475 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:58.04925 INFO::ASW Batch was 0.0121165576952365 prior to batch effect correction and is now 0.0121165576952365 .
2026-03-12 21:52:58.050282 INFO::Total function execution time is  0.0638885498046875  s and adjustment time is  0.0288252830505371 s ( 45.12 )
2026-03-12 21:52:58.069626 INFO::Formatting Data.
2026-03-12 21:52:58.070476 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:58.071446 INFO::Removing potential empty rows and columns
2026-03-12 21:52:58.072562 INFO::Found  0  missing values.
2026-03-12 21:52:58.075702 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:58.076254 INFO::Done
2026-03-12 21:52:58.076797 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:58.078918 INFO::Starting hierarchical adjustment
2026-03-12 21:52:58.079654 INFO::Found  3  batches.
2026-03-12 21:52:58.080188 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:58.080824 INFO::Using default BPPARAM
2026-03-12 21:52:58.081351 INFO::Processing subtree level 1
2026-03-12 21:52:58.225836 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:52:58.22792 INFO::Done
2026-03-12 21:52:58.228642 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:58.231393 INFO::ASW Batch was -0.069677176669928 prior to batch effect correction and is now -0.164601972999551 .
2026-03-12 21:52:58.232419 INFO::Total function execution time is  0.16289496421814  s and adjustment time is  0.148404598236084 s ( 91.1 )
2026-03-12 21:52:58.247976 INFO::Skipping initial DF formatting
2026-03-12 21:52:58.248854 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:58.253181 INFO::Starting hierarchical adjustment
2026-03-12 21:52:58.254044 INFO::Found  5  batches.
2026-03-12 21:52:58.254637 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:58.255303 INFO::Using default BPPARAM
2026-03-12 21:52:58.255872 INFO::Processing subtree level 1
2026-03-12 21:52:58.504956 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:58.50696 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:52:58.528176 INFO::Done
2026-03-12 21:52:58.528999 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:58.534257 INFO::ASW Batch was 0.535425125130695 prior to batch effect correction and is now 0.535425125130695 .
2026-03-12 21:52:58.534956 INFO::ASW Label was 0.340685578888155 prior to batch effect correction and is now 0.340685578888155 .
2026-03-12 21:52:58.535874 INFO::Total function execution time is  0.28797459602356  s and adjustment time is  0.274265289306641 s ( 95.24 )
2026-03-12 21:52:58.603456 INFO::Formatting Data.
2026-03-12 21:52:58.604308 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:58.605245 INFO::Removing potential empty rows and columns
2026-03-12 21:52:58.606292 INFO::Found  0  missing values.
2026-03-12 21:52:58.61036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:58.610941 INFO::Done
2026-03-12 21:52:58.611442 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:58.614495 INFO::Starting hierarchical adjustment
2026-03-12 21:52:58.61522 INFO::Found  5  batches.
2026-03-12 21:52:58.615771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:58.616386 INFO::Using default BPPARAM
2026-03-12 21:52:58.616911 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.

2026-03-12 21:52:58.778564 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:58.781104 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:52:58.808074 INFO::Done
2026-03-12 21:52:58.809268 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:58.814625 INFO::ASW Batch was 0.615743542036495 prior to batch effect correction and is now -0.0475838842603542 .
2026-03-12 21:52:58.815617 INFO::ASW Label was 0.159978385592072 prior to batch effect correction and is now 0.707959868445277 .
2026-03-12 21:52:58.816909 INFO::Total function execution time is  0.213467359542847  s and adjustment time is  0.192894697189331 s ( 90.36 )
2026-03-12 21:52:58.818242 INFO::Formatting Data.
2026-03-12 21:52:58.819232 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:58.820636 INFO::Removing potential empty rows and columns
2026-03-12 21:52:58.82222 INFO::Found  0  missing values.
2026-03-12 21:52:58.829531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:58.830474 INFO::Done
2026-03-12 21:52:58.831316 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:58.836152 INFO::Starting hierarchical adjustment
2026-03-12 21:52:58.837337 INFO::Found  5  batches.
2026-03-12 21:52:58.838255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:58.839278 INFO::Using default BPPARAM
2026-03-12 21:52:58.840165 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.

2026-03-12 21:52:58.981143 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:58.982776 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:52:58.999233 INFO::Done
2026-03-12 21:52:58.999994 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.003356 INFO::ASW Batch was 0.615743542036495 prior to batch effect correction and is now -0.0475838842603542 .
2026-03-12 21:52:59.003978 INFO::ASW Label was 0.159978385592072 prior to batch effect correction and is now 0.707959868445277 .
2026-03-12 21:52:59.004802 INFO::Total function execution time is  0.186646223068237  s and adjustment time is  0.162184238433838 s ( 86.89 )
2026-03-12 21:52:59.018467 INFO::Formatting Data.
2026-03-12 21:52:59.019276 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.020189 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.021375 INFO::Found  0  missing values.
2026-03-12 21:52:59.025717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.026263 INFO::Done
2026-03-12 21:52:59.026774 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.02983 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.030571 INFO::Found  5  batches.
2026-03-12 21:52:59.031098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.031722 INFO::Using default BPPARAM
2026-03-12 21:52:59.032233 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.

2026-03-12 21:52:59.163777 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:59.165461 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:52:59.182043 INFO::Done
2026-03-12 21:52:59.182814 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.186182 INFO::ASW Batch was 0.558340109833546 prior to batch effect correction and is now 0.00365971586327343 .
2026-03-12 21:52:59.186825 INFO::ASW Label was 0.164636768096236 prior to batch effect correction and is now 0.68490028414142 .
2026-03-12 21:52:59.187622 INFO::Total function execution time is  0.169232606887817  s and adjustment time is  0.151598453521729 s ( 89.58 )
2026-03-12 21:52:59.188408 INFO::Formatting Data.
2026-03-12 21:52:59.189036 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.189903 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.19088 INFO::Found  0  missing values.
2026-03-12 21:52:59.194812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.195331 INFO::Done
2026-03-12 21:52:59.195851 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.198785 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.199468 INFO::Found  5  batches.
2026-03-12 21:52:59.199989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.200603 INFO::Using default BPPARAM
2026-03-12 21:52:59.201115 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.

2026-03-12 21:52:59.330311 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:59.331987 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:52:59.348832 INFO::Done
2026-03-12 21:52:59.349571 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.353261 INFO::ASW Batch was 0.558340109833546 prior to batch effect correction and is now 0.00365971586327343 .
2026-03-12 21:52:59.35404 INFO::ASW Label was 0.164636768096236 prior to batch effect correction and is now 0.68490028414142 .
2026-03-12 21:52:59.355207 INFO::Total function execution time is  0.166756391525269  s and adjustment time is  0.149475574493408 s ( 89.64 )
2026-03-12 21:52:59.368838 INFO::Formatting Data.
2026-03-12 21:52:59.369632 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.370572 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.371583 INFO::Found  0  missing values.
2026-03-12 21:52:59.374216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.374746 INFO::Done
2026-03-12 21:52:59.375239 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.378134 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.378857 INFO::Found  2  batches.
2026-03-12 21:52:59.379365 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.379987 INFO::Using default BPPARAM
2026-03-12 21:52:59.380492 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:59.381382 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:52:59.395477 INFO::Done
2026-03-12 21:52:59.39612 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.398938 INFO::ASW Batch was 0.456665630934717 prior to batch effect correction and is now -0.00562374765244145 .
2026-03-12 21:52:59.3995 INFO::ASW Label was 0.610655149770486 prior to batch effect correction and is now 0.907223304956475 .
2026-03-12 21:52:59.40024 INFO::Total function execution time is  0.0314922332763672  s and adjustment time is  0.0167582035064697 s ( 53.21 )
2026-03-12 21:52:59.400985 INFO::Formatting Data.
2026-03-12 21:52:59.401593 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.402408 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.403347 INFO::Found  0  missing values.
2026-03-12 21:52:59.405898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.406424 INFO::Done
2026-03-12 21:52:59.406941 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.409846 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.410565 INFO::Found  2  batches.
2026-03-12 21:52:59.411082 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.411694 INFO::Using default BPPARAM
2026-03-12 21:52:59.412211 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:59.41314 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-12 21:52:59.427755 INFO::Done
2026-03-12 21:52:59.42837 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.431236 INFO::ASW Batch was 0.456665630934717 prior to batch effect correction and is now -0.00562374765244145 .
2026-03-12 21:52:59.431828 INFO::ASW Label was 0.610655149770486 prior to batch effect correction and is now 0.907223304956475 .
2026-03-12 21:52:59.432592 INFO::Total function execution time is  0.0315966606140137  s and adjustment time is  0.0173335075378418 s ( 54.86 )
2026-03-12 21:52:59.443664 INFO::Formatting Data.
2026-03-12 21:52:59.444403 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.445272 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.446179 INFO::Found  0  missing values.
2026-03-12 21:52:59.448359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.448898 INFO::Done
2026-03-12 21:52:59.449395 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.451291 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.451977 INFO::Found  2  batches.
2026-03-12 21:52:59.452474 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.453077 INFO::Using default BPPARAM
2026-03-12 21:52:59.453598 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:59.454435 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:52:59.483853 INFO::Done
2026-03-12 21:52:59.484532 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.486418 INFO::ASW Batch was -0.0385239425246272 prior to batch effect correction and is now -0.100600941248994 .
2026-03-12 21:52:59.487203 INFO::Total function execution time is  0.043637752532959  s and adjustment time is  0.0319910049438477 s ( 73.31 )
2026-03-12 21:52:59.498524 INFO::Formatting Data.
2026-03-12 21:52:59.499253 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.500109 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.501034 INFO::Found  0  missing values.
2026-03-12 21:52:59.50209 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.
2026-03-12 21:52:59.506337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.506876 INFO::Done
2026-03-12 21:52:59.507356 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.510104 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.510775 INFO::Found  2  batches.
2026-03-12 21:52:59.511272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.511838 INFO::Using default BPPARAM
2026-03-12 21:52:59.512329 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:59.513196 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:52:59.528654 INFO::Done
2026-03-12 21:52:59.529351 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.532375 INFO::ASW Batch was 0.498567657731793 prior to batch effect correction and is now -0.0350106395220974 .
2026-03-12 21:52:59.532994 INFO::ASW Label was 0.524287296625328 prior to batch effect correction and is now 0.910679895678127 .
2026-03-12 21:52:59.533778 INFO::Total function execution time is  0.0353405475616455  s and adjustment time is  0.0179743766784668 s ( 50.86 )
2026-03-12 21:52:59.534581 INFO::Formatting Data.
2026-03-12 21:52:59.535191 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.536118 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.537147 INFO::Found  0  missing values.
2026-03-12 21:52:59.538045 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.
2026-03-12 21:52:59.542449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.543001 INFO::Done
2026-03-12 21:52:59.5435 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.546319 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.54702 INFO::Found  2  batches.
2026-03-12 21:52:59.547529 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.548113 INFO::Using default BPPARAM
2026-03-12 21:52:59.54863 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:52:59.549534 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:52:59.565325 INFO::Done
2026-03-12 21:52:59.566019 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.568897 INFO::ASW Batch was 0.498567657731793 prior to batch effect correction and is now -0.0350106395220974 .
2026-03-12 21:52:59.569477 INFO::ASW Label was 0.524287296625328 prior to batch effect correction and is now 0.910679895678127 .
2026-03-12 21:52:59.570244 INFO::Total function execution time is  0.0357036590576172  s and adjustment time is  0.0184171199798584 s ( 51.58 )
2026-03-12 21:52:59.770484 INFO::Formatting Data.
2026-03-12 21:52:59.771391 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.772367 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.773463 INFO::Found  0  missing values.
2026-03-12 21:52:59.776565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.777103 INFO::Done
2026-03-12 21:52:59.777622 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.779723 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.780431 INFO::Found  3  batches.
2026-03-12 21:52:59.780961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.781565 INFO::Using default BPPARAM
2026-03-12 21:52:59.782076 INFO::Processing subtree level 1
2026-03-12 21:52:59.870013 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:52:59.871792 INFO::Done
2026-03-12 21:52:59.872437 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.874926 INFO::ASW Batch was -0.0270935154587755 prior to batch effect correction and is now -0.0270935154587755 .
2026-03-12 21:52:59.875883 INFO::Total function execution time is  0.105504751205444  s and adjustment time is  0.0914900302886963 s ( 86.72 )
2026-03-12 21:52:59.876954 INFO::Formatting Data.
2026-03-12 21:52:59.8776 INFO::Typecasting input to dataframe.
2026-03-12 21:52:59.878358 INFO::Replacing NaNs with NAs.
2026-03-12 21:52:59.879291 INFO::Removing potential empty rows and columns
2026-03-12 21:52:59.880394 INFO::Found  0  missing values.
2026-03-12 21:52:59.883476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:52:59.884054 INFO::Done
2026-03-12 21:52:59.884591 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:52:59.886614 INFO::Starting hierarchical adjustment
2026-03-12 21:52:59.887324 INFO::Found  3  batches.
2026-03-12 21:52:59.887885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:52:59.888538 INFO::Using default BPPARAM
2026-03-12 21:52:59.88906 INFO::Processing subtree level 1
2026-03-12 21:52:59.979538 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:52:59.981522 INFO::Done
2026-03-12 21:52:59.982203 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:52:59.984932 INFO::ASW Batch was -0.0270935154587755 prior to batch effect correction and is now -0.0270935154587755 .
2026-03-12 21:52:59.98594 INFO::Total function execution time is  0.10896897315979  s and adjustment time is  0.0943045616149902 s ( 86.54 )
2026-03-12 21:52:59.999919 INFO::Formatting Data.
2026-03-12 21:53:00.000831 INFO::Typecasting input to dataframe.
2026-03-12 21:53:00.001719 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:00.002686 INFO::Removing potential empty rows and columns
2026-03-12 21:53:00.003813 INFO::Found  0  missing values.
2026-03-12 21:53:00.006846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:00.007374 INFO::Done
2026-03-12 21:53:00.007912 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:53:00.010032 INFO::Starting hierarchical adjustment
2026-03-12 21:53:00.010757 INFO::Found  3  batches.
2026-03-12 21:53:00.011284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:53:00.011922 INFO::Using default BPPARAM
2026-03-12 21:53:00.012455 INFO::Processing subtree level 1
2026-03-12 21:53:00.106001 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:53:00.107852 INFO::Done
2026-03-12 21:53:00.1085 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:53:00.11115 INFO::ASW Batch was -0.0744033171242429 prior to batch effect correction and is now -0.0744033171242429 .
2026-03-12 21:53:00.112119 INFO::Total function execution time is  0.112304210662842  s and adjustment time is  0.0972371101379395 s ( 86.58 )
2026-03-12 21:53:00.248242 INFO::Formatting Data.
2026-03-12 21:53:00.249068 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:00.250171 INFO::Removing potential empty rows and columns
2026-03-12 21:53:00.252927 INFO::Found  1000  missing values.
2026-03-12 21:53:00.271792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:00.272543 INFO::Done
2026-03-12 21:53:00.273096 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:53:00.278594 INFO::Starting hierarchical adjustment
2026-03-12 21:53:00.279377 INFO::Found  10  batches.
2026-03-12 21:53:00.279937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:53:00.28058 INFO::Using default BPPARAM
2026-03-12 21:53:00.281117 INFO::Processing subtree level 1
2026-03-12 21:53:00.416909 INFO::Processing subtree level 2
2026-03-12 21:53:00.561897 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:53:00.563929 INFO::Done
2026-03-12 21:53:00.56467 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:53:00.57043 INFO::ASW Batch was 0.507425002681077 prior to batch effect correction and is now 0.507425002681077 .
2026-03-12 21:53:00.571127 INFO::ASW Label was 0.331431983268174 prior to batch effect correction and is now 0.331431983268173 .
2026-03-12 21:53:00.572074 INFO::Total function execution time is  0.323869705200195  s and adjustment time is  0.284685373306274 s ( 87.9 )
2026-03-12 21:53:00.572963 INFO::Formatting Data.
2026-03-12 21:53:00.573639 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:00.574974 INFO::Removing potential empty rows and columns
2026-03-12 21:53:00.577952 INFO::Found  1000  missing values.
2026-03-12 21:53:00.597174 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:00.597949 INFO::Done
2026-03-12 21:53:00.598521 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:53:00.604094 INFO::Starting hierarchical adjustment
2026-03-12 21:53:00.604881 INFO::Found  10  batches.
2026-03-12 21:53:01.564543 INFO::Set up parallel execution backend with 2 workers
2026-03-12 21:53:01.566307 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-12 21:53:02.827692 INFO::Adjusting the last 2 batches sequentially
2026-03-12 21:53:02.829998 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-12 21:53:02.848599 INFO::Done
2026-03-12 21:53:02.849404 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:53:02.854474 INFO::ASW Batch was 0.507425002681077 prior to batch effect correction and is now 0.507425002681077 .
2026-03-12 21:53:02.85516 INFO::ASW Label was 0.331431983268174 prior to batch effect correction and is now 0.331431983268173 .
2026-03-12 21:53:02.855991 INFO::Total function execution time is  2.28306603431702  s and adjustment time is  2.24379873275757 s ( 98.28 )
2026-03-12 21:53:03.029757 INFO::Formatting Data.
2026-03-12 21:53:03.030748 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.031859 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.033138 INFO::Found  0  missing values.
2026-03-12 21:53:03.051455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.052727 INFO::Done
2026-03-12 21:53:03.053366 INFO::Acquiring quality metrics before batch effect correction.
2026-03-12 21:53:03.057233 INFO::Starting hierarchical adjustment
2026-03-12 21:53:03.0581 INFO::Found  3  batches.
2026-03-12 21:53:03.05867 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-12 21:53:03.059351 INFO::Using default BPPARAM
2026-03-12 21:53:03.059913 INFO::Processing subtree level 1
2026-03-12 21:53:03.213261 INFO::Adjusting the last 1 batches sequentially
2026-03-12 21:53:03.216009 INFO::Done
2026-03-12 21:53:03.216979 INFO::Acquiring quality metrics after batch effect correction.
2026-03-12 21:53:03.221651 INFO::ASW Batch was 0.173056684082472 prior to batch effect correction and is now -0.117192139122517 .
2026-03-12 21:53:03.222424 INFO::ASW Label was -0.208424346834347 prior to batch effect correction and is now -0.0104488049477315 .
2026-03-12 21:53:03.223704 INFO::Total function execution time is  0.193919658660889  s and adjustment time is  0.157999277114868 s ( 81.48 )
2026-03-12 21:53:03.372913 INFO::Formatting Data.
2026-03-12 21:53:03.373964 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.375016 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.376213 INFO::Found  2  missing values.
2026-03-12 21:53:03.379382 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.379988 INFO::Done
2026-03-12 21:53:03.41119 INFO::Found NA in Reference column
2026-03-12 21:53:03.421265 INFO::Require at least two references per batch.
2026-03-12 21:53:03.443602 INFO::Formatting Data.
2026-03-12 21:53:03.444415 INFO::Recognized SummarizedExperiment
2026-03-12 21:53:03.444959 INFO::Typecasting input to dataframe.
2026-03-12 21:53:03.455481 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.456765 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.460205 INFO::Found  0  missing values.
2026-03-12 21:53:03.466874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.467482 INFO::Done
2026-03-12 21:53:03.484363 INFO::Formatting Data.
2026-03-12 21:53:03.485265 INFO::Recognized SummarizedExperiment
2026-03-12 21:53:03.485836 INFO::Typecasting input to dataframe.
2026-03-12 21:53:03.504914 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.506276 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.509836 INFO::Found  0  missing values.
2026-03-12 21:53:03.520822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.521563 INFO::Done
2026-03-12 21:53:03.53788 INFO::Formatting Data.
2026-03-12 21:53:03.538682 INFO::Recognized SummarizedExperiment
2026-03-12 21:53:03.539231 INFO::Typecasting input to dataframe.
2026-03-12 21:53:03.556995 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.55823 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.559373 INFO::Found  0  missing values.
2026-03-12 21:53:03.560364 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.
2026-03-12 21:53:03.565032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.565631 INFO::Done
2026-03-12 21:53:03.576504 INFO::Formatting Data.
2026-03-12 21:53:03.577371 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.578421 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.579461 INFO::Found  0  missing values.
2026-03-12 21:53:03.58243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.582985 INFO::Done
2026-03-12 21:53:03.595436 INFO::Formatting Data.
2026-03-12 21:53:03.5965 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.597708 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.598907 INFO::Found  0  missing values.
2026-03-12 21:53:03.602342 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.602946 INFO::Done
2026-03-12 21:53:03.634242 INFO::Formatting Data.
2026-03-12 21:53:03.635175 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.636269 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.637483 INFO::Found  1  missing values.
2026-03-12 21:53:03.640284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.640859 INFO::Done
2026-03-12 21:53:03.661395 INFO::Formatting Data.
2026-03-12 21:53:03.66234 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.663358 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.664394 INFO::Found  2  missing values.
2026-03-12 21:53:03.665383 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.
2026-03-12 21:53:03.667789 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.668346 INFO::Done
2026-03-12 21:53:03.679064 INFO::Formatting Data.
2026-03-12 21:53:03.679978 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.680919 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.681879 INFO::Found  2  missing values.
2026-03-12 21:53:03.683571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.684122 INFO::Done
2026-03-12 21:53:03.694939 INFO::Formatting Data.
2026-03-12 21:53:03.695779 INFO::Typecasting input to dataframe.
2026-03-12 21:53:03.696578 INFO::Replacing NaNs with NAs.
2026-03-12 21:53:03.697403 INFO::Removing potential empty rows and columns
2026-03-12 21:53:03.698365 INFO::Found  0  missing values.
2026-03-12 21:53:03.701164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-12 21:53:03.701693 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.598   3.434  20.705

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT24.269 1.28717.803
compute_asw0.0240.0000.024
count_existing0.0120.0020.014
generate_data_covariables0.0120.0000.012
generate_dataset0.0110.0000.011