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This page was generated on 2026-03-10 11:57 -0400 (Tue, 10 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: 2026-03-09 13:45 -0400 (Mon, 09 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: 2026-03-09 21:22:56 -0400 (Mon, 09 Mar 2026)
EndedAt: 2026-03-09 21:24:24 -0400 (Mon, 09 Mar 2026)
EllapsedTime: 88.0 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 24.332  1.303  17.662
* 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")
2026-03-09 21:23:48.577825 INFO::Formatting Data.
2026-03-09 21:23:48.579101 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:48.589595 INFO::Removing potential empty rows and columns
2026-03-09 21:23:48.825569 INFO::Found  0  missing values.
2026-03-09 21:23:48.829036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:48.829711 INFO::Done
2026-03-09 21:23:48.830264 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:48.841758 INFO::Starting hierarchical adjustment
2026-03-09 21:23:48.842661 INFO::Found  3  batches.
2026-03-09 21:23:48.84322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:48.844405 INFO::Using default BPPARAM
2026-03-09 21:23:48.844956 INFO::Processing subtree level 1
2026-03-09 21:23:48.949162 INFO::Adjusting the last 1 batches sequentially
2026-03-09 21:23:48.950971 INFO::Done
2026-03-09 21:23:48.951652 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:48.954283 INFO::ASW Batch was -0.0911534238925516 prior to batch effect correction and is now -0.0911534238925516 .
2026-03-09 21:23:48.95541 INFO::Total function execution time is  0.378186464309692  s and adjustment time is  0.108491897583008 s ( 28.69 )
2026-03-09 21:23:48.969098 INFO::Formatting Data.
2026-03-09 21:23:48.969909 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:48.970843 INFO::Removing potential empty rows and columns
2026-03-09 21:23:48.971998 INFO::Found  0  missing values.
2026-03-09 21:23:48.97295 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.
2026-03-09 21:23:48.98368 INFO::Formatting Data.
2026-03-09 21:23:48.98441 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:48.98529 INFO::Removing potential empty rows and columns
2026-03-09 21:23:48.986387 INFO::Found  0  missing values.
2026-03-09 21:23:48.987342 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.
2026-03-09 21:23:49.003231 INFO::Formatting Data.
2026-03-09 21:23:49.004011 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:49.004916 INFO::Removing potential empty rows and columns
2026-03-09 21:23:49.005938 INFO::Found  0  missing values.
2026-03-09 21:23:49.006935 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.
2026-03-09 21:23:49.01125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:49.011792 INFO::Done
2026-03-09 21:23:49.012306 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:49.014218 INFO::Starting hierarchical adjustment
2026-03-09 21:23:49.014927 INFO::Found  2  batches.
2026-03-09 21:23:49.015448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:49.016074 INFO::Using default BPPARAM
2026-03-09 21:23:49.016602 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:49.01749 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-09 21:23:49.038152 INFO::Done
2026-03-09 21:23:49.038865 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:49.041072 INFO::ASW Batch was 0.0810832824757822 prior to batch effect correction and is now -0.118531719713719 .
2026-03-09 21:23:49.041892 INFO::Total function execution time is  0.0387322902679443  s and adjustment time is  0.0233554840087891 s ( 60.3 )
2026-03-09 21:23:49.044703 INFO::Formatting Data.
2026-03-09 21:23:49.045321 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:49.054098 INFO::Formatting Data.
2026-03-09 21:23:49.054799 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:49.055674 INFO::Removing potential empty rows and columns
2026-03-09 21:23:49.056766 INFO::Found  0  missing values.
2026-03-09 21:23:49.059671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:49.060207 INFO::Done
2026-03-09 21:23:49.060738 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:49.084763 INFO::Starting hierarchical adjustment
2026-03-09 21:23:49.086079 INFO::Found  2  batches.
2026-03-09 21:23:49.095585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:49.096832 INFO::Using default BPPARAM
2026-03-09 21:23:49.097375 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:49.09868 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-09 21:23:49.115476 INFO::Done
2026-03-09 21:23:49.116128 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:49.118316 INFO::ASW Batch was -0.0363080835327373 prior to batch effect correction and is now -0.100238582228426 .
2026-03-09 21:23:49.119164 INFO::Total function execution time is  0.0650742053985596  s and adjustment time is  0.0295426845550537 s ( 45.4 )
2026-03-09 21:23:49.120164 INFO::Formatting Data.
2026-03-09 21:23:49.120728 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:49.12156 INFO::Removing potential empty rows and columns
2026-03-09 21:23:49.122541 INFO::Found  0  missing values.
2026-03-09 21:23:49.125193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:49.125708 INFO::Done
2026-03-09 21:23:49.126185 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:49.128103 INFO::Starting hierarchical adjustment
2026-03-09 21:23:49.128778 INFO::Found  2  batches.
2026-03-09 21:23:49.129256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:49.129833 INFO::Using default BPPARAM
2026-03-09 21:23:49.130324 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:49.131191 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-09 21:23:49.144801 INFO::Done
2026-03-09 21:23:49.145413 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:49.147248 INFO::ASW Batch was -0.0363080835327373 prior to batch effect correction and is now -0.100238582228426 .
2026-03-09 21:23:49.14797 INFO::Total function execution time is  0.0278077125549316  s and adjustment time is  0.0161449909210205 s ( 58.06 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-09 21:23:51.965907 INFO::Formatting Data.
2026-03-09 21:23:51.966659 INFO::Recognized SummarizedExperiment
2026-03-09 21:23:51.967147 INFO::Typecasting input to dataframe.
2026-03-09 21:23:51.998811 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:52.000049 INFO::Removing potential empty rows and columns
2026-03-09 21:23:52.003825 INFO::Found  0  missing values.
2026-03-09 21:23:52.010841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:52.011443 INFO::Done
2026-03-09 21:23:52.011974 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:52.015795 INFO::Starting hierarchical adjustment
2026-03-09 21:23:52.016501 INFO::Found  2  batches.
2026-03-09 21:23:52.017026 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:52.01812 INFO::Using default BPPARAM
2026-03-09 21:23:52.018668 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:52.01962 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-09 21:23:52.076205 INFO::Done
2026-03-09 21:23:52.076897 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:52.08043 INFO::ASW Batch was -0.0105162674233129 prior to batch effect correction and is now -0.0951453703571529 .
2026-03-09 21:23:52.081281 INFO::Total function execution time is  0.115720272064209  s and adjustment time is  0.0598161220550537 s ( 51.69 )
Warning: stack imbalance in '{', 73 then 75
2026-03-09 21:23:52.100048 INFO::Formatting Data.
2026-03-09 21:23:52.100778 INFO::Recognized SummarizedExperiment
2026-03-09 21:23:52.101303 INFO::Typecasting input to dataframe.
2026-03-09 21:23:52.11045 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:52.111614 INFO::Removing potential empty rows and columns
2026-03-09 21:23:52.11527 INFO::Found  0  missing values.
2026-03-09 21:23:52.122391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:52.123058 INFO::Done
2026-03-09 21:23:52.123576 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:52.127091 INFO::Starting hierarchical adjustment
2026-03-09 21:23:52.127816 INFO::Found  2  batches.
2026-03-09 21:23:52.128328 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:52.12893 INFO::Using default BPPARAM
2026-03-09 21:23:52.129429 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:52.130393 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-09 21:23:52.155155 INFO::Done
2026-03-09 21:23:52.155894 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:52.159529 INFO::ASW Batch was -0.0124438606246844 prior to batch effect correction and is now -0.0124438606246844 .
2026-03-09 21:23:52.160402 INFO::Total function execution time is  0.0603461265563965  s and adjustment time is  0.0274360179901123 s ( 45.46 )
2026-03-09 21:23:52.178344 INFO::Formatting Data.
2026-03-09 21:23:52.179133 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:52.180025 INFO::Removing potential empty rows and columns
2026-03-09 21:23:52.181026 INFO::Found  0  missing values.
2026-03-09 21:23:52.183935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:52.184457 INFO::Done
2026-03-09 21:23:52.184984 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:52.186936 INFO::Starting hierarchical adjustment
2026-03-09 21:23:52.187625 INFO::Found  3  batches.
2026-03-09 21:23:52.188134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:52.188725 INFO::Using default BPPARAM
2026-03-09 21:23:52.189229 INFO::Processing subtree level 1
2026-03-09 21:23:52.320613 INFO::Adjusting the last 1 batches sequentially
2026-03-09 21:23:52.322403 INFO::Done
2026-03-09 21:23:52.323049 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:52.325523 INFO::ASW Batch was -0.0523148585496104 prior to batch effect correction and is now -0.156219711683308 .
2026-03-09 21:23:52.326422 INFO::Total function execution time is  0.148111820220947  s and adjustment time is  0.134917736053467 s ( 91.09 )
2026-03-09 21:23:52.34068 INFO::Skipping initial DF formatting
2026-03-09 21:23:52.341359 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:52.34531 INFO::Starting hierarchical adjustment
2026-03-09 21:23:52.346177 INFO::Found  5  batches.
2026-03-09 21:23:52.346729 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:52.347334 INFO::Using default BPPARAM
2026-03-09 21:23:52.347879 INFO::Processing subtree level 1
2026-03-09 21:23:52.564716 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:52.566301 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-09 21:23:52.585729 INFO::Done
2026-03-09 21:23:52.586436 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:52.59073 INFO::ASW Batch was 0.548853675042398 prior to batch effect correction and is now 0.548853675042398 .
2026-03-09 21:23:52.591339 INFO::ASW Label was 0.394524905600139 prior to batch effect correction and is now 0.394524905600139 .
2026-03-09 21:23:52.592205 INFO::Total function execution time is  0.251590967178345  s and adjustment time is  0.239689111709595 s ( 95.27 )
2026-03-09 21:23:52.65321 INFO::Formatting Data.
2026-03-09 21:23:52.653966 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:52.654862 INFO::Removing potential empty rows and columns
2026-03-09 21:23:52.655831 INFO::Found  0  missing values.
2026-03-09 21:23:52.659588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:52.660105 INFO::Done
2026-03-09 21:23:52.66063 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:52.66341 INFO::Starting hierarchical adjustment
2026-03-09 21:23:52.664115 INFO::Found  5  batches.
2026-03-09 21:23:52.664616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:52.665205 INFO::Using default BPPARAM
2026-03-09 21:23:52.665712 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.

2026-03-09 21:23:52.796942 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:52.798761 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-09 21:23:52.817812 INFO::Done
2026-03-09 21:23:52.818617 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:52.822399 INFO::ASW Batch was 0.425163196673476 prior to batch effect correction and is now 0.0270565679619803 .
2026-03-09 21:23:52.823089 INFO::ASW Label was 0.530850740239451 prior to batch effect correction and is now 0.541210197765456 .
2026-03-09 21:23:52.82397 INFO::Total function execution time is  0.170807123184204  s and adjustment time is  0.153798341751099 s ( 90.04 )
2026-03-09 21:23:52.824906 INFO::Formatting Data.
2026-03-09 21:23:52.82561 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:52.82655 INFO::Removing potential empty rows and columns
2026-03-09 21:23:52.827701 INFO::Found  0  missing values.
2026-03-09 21:23:52.832716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:52.833377 INFO::Done
2026-03-09 21:23:52.833938 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:52.837173 INFO::Starting hierarchical adjustment
2026-03-09 21:23:52.837926 INFO::Found  5  batches.
2026-03-09 21:23:52.838502 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:52.839178 INFO::Using default BPPARAM
2026-03-09 21:23:52.839762 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.

2026-03-09 21:23:52.970936 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:52.97296 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-09 21:23:52.99232 INFO::Done
2026-03-09 21:23:52.993215 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:52.997237 INFO::ASW Batch was 0.425163196673476 prior to batch effect correction and is now 0.0270565679619803 .
2026-03-09 21:23:52.997973 INFO::ASW Label was 0.530850740239451 prior to batch effect correction and is now 0.541210197765456 .
2026-03-09 21:23:52.99891 INFO::Total function execution time is  0.174003839492798  s and adjustment time is  0.154483556747437 s ( 88.78 )
2026-03-09 21:23:53.015035 INFO::Formatting Data.
2026-03-09 21:23:53.016019 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.017148 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.018307 INFO::Found  0  missing values.
2026-03-09 21:23:53.022751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.023345 INFO::Done
2026-03-09 21:23:53.023919 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.027384 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.028181 INFO::Found  5  batches.
2026-03-09 21:23:53.028761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.02941 INFO::Using default BPPARAM
2026-03-09 21:23:53.029986 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.

2026-03-09 21:23:53.160385 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:53.162058 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-09 21:23:53.178104 INFO::Done
2026-03-09 21:23:53.178972 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.182352 INFO::ASW Batch was 0.406614605948409 prior to batch effect correction and is now -0.0817572089722282 .
2026-03-09 21:23:53.182984 INFO::ASW Label was 0.224376269079324 prior to batch effect correction and is now 0.767414453157962 .
2026-03-09 21:23:53.183813 INFO::Total function execution time is  0.168930292129517  s and adjustment time is  0.150064468383789 s ( 88.83 )
2026-03-09 21:23:53.184666 INFO::Formatting Data.
2026-03-09 21:23:53.185306 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.186215 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.187244 INFO::Found  0  missing values.
2026-03-09 21:23:53.191334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.191894 INFO::Done
2026-03-09 21:23:53.192424 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.195481 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.196214 INFO::Found  5  batches.
2026-03-09 21:23:53.196762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.197384 INFO::Using default BPPARAM
2026-03-09 21:23:53.197935 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.

2026-03-09 21:23:53.329203 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:53.331196 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-09 21:23:53.351028 INFO::Done
2026-03-09 21:23:53.352009 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.356619 INFO::ASW Batch was 0.406614605948409 prior to batch effect correction and is now -0.0817572089722282 .
2026-03-09 21:23:53.357437 INFO::ASW Label was 0.224376269079324 prior to batch effect correction and is now 0.767414453157962 .
2026-03-09 21:23:53.358399 INFO::Total function execution time is  0.173714876174927  s and adjustment time is  0.154877185821533 s ( 89.16 )
2026-03-09 21:23:53.374127 INFO::Formatting Data.
2026-03-09 21:23:53.375028 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.376047 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.377183 INFO::Found  0  missing values.
2026-03-09 21:23:53.380867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.381738 INFO::Done
2026-03-09 21:23:53.382331 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.385876 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.386742 INFO::Found  2  batches.
2026-03-09 21:23:53.387347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.388031 INFO::Using default BPPARAM
2026-03-09 21:23:53.388639 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:53.389772 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-09 21:23:53.407265 INFO::Done
2026-03-09 21:23:53.408043 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.411215 INFO::ASW Batch was 0.439967083731055 prior to batch effect correction and is now -0.0355370752173546 .
2026-03-09 21:23:53.411868 INFO::ASW Label was 0.624887234917951 prior to batch effect correction and is now 0.938939730686748 .
2026-03-09 21:23:53.412701 INFO::Total function execution time is  0.03871750831604  s and adjustment time is  0.0206899642944336 s ( 53.44 )
2026-03-09 21:23:53.41356 INFO::Formatting Data.
2026-03-09 21:23:53.414201 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.415129 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.416165 INFO::Found  0  missing values.
2026-03-09 21:23:53.418947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.419519 INFO::Done
2026-03-09 21:23:53.420067 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.423146 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.423895 INFO::Found  2  batches.
2026-03-09 21:23:53.424422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.425037 INFO::Using default BPPARAM
2026-03-09 21:23:53.42558 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:53.426493 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-09 21:23:53.441185 INFO::Done
2026-03-09 21:23:53.44184 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.444959 INFO::ASW Batch was 0.439967083731055 prior to batch effect correction and is now -0.0355370752173546 .
2026-03-09 21:23:53.445598 INFO::ASW Label was 0.624887234917951 prior to batch effect correction and is now 0.938939730686748 .
2026-03-09 21:23:53.446408 INFO::Total function execution time is  0.0328793525695801  s and adjustment time is  0.0174384117126465 s ( 53.04 )
2026-03-09 21:23:53.458588 INFO::Formatting Data.
2026-03-09 21:23:53.459328 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.46021 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.461098 INFO::Found  0  missing values.
2026-03-09 21:23:53.463168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.463729 INFO::Done
2026-03-09 21:23:53.464249 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.466223 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.466954 INFO::Found  2  batches.
2026-03-09 21:23:53.467486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.468111 INFO::Using default BPPARAM
2026-03-09 21:23:53.468661 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:53.469568 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-09 21:23:53.500215 INFO::Done
2026-03-09 21:23:53.500916 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.502846 INFO::ASW Batch was -0.0842512925224095 prior to batch effect correction and is now -0.105695539123031 .
2026-03-09 21:23:53.503638 INFO::Total function execution time is  0.0451583862304688  s and adjustment time is  0.0333824157714844 s ( 73.92 )
2026-03-09 21:23:53.515386 INFO::Formatting Data.
2026-03-09 21:23:53.516138 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.516996 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.517958 INFO::Found  0  missing values.
2026-03-09 21:23:53.519078 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.
2026-03-09 21:23:53.523491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.524037 INFO::Done
2026-03-09 21:23:53.524541 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.527397 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.528104 INFO::Found  2  batches.
2026-03-09 21:23:53.528628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.529203 INFO::Using default BPPARAM
2026-03-09 21:23:53.529718 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:53.530616 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-09 21:23:53.546301 INFO::Done
2026-03-09 21:23:53.546954 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.549779 INFO::ASW Batch was 0.483066955970334 prior to batch effect correction and is now -0.0258436062785487 .
2026-03-09 21:23:53.550344 INFO::ASW Label was 0.546918772923884 prior to batch effect correction and is now 0.904915743200318 .
2026-03-09 21:23:53.551083 INFO::Total function execution time is  0.035780668258667  s and adjustment time is  0.0183200836181641 s ( 51.2 )
2026-03-09 21:23:53.551851 INFO::Formatting Data.
2026-03-09 21:23:53.552444 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.553328 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.554275 INFO::Found  0  missing values.
2026-03-09 21:23:53.555141 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.
2026-03-09 21:23:53.559392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.559917 INFO::Done
2026-03-09 21:23:53.56041 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.563216 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.563909 INFO::Found  2  batches.
2026-03-09 21:23:53.564426 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.565013 INFO::Using default BPPARAM
2026-03-09 21:23:53.565516 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:53.566399 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-09 21:23:53.58196 INFO::Done
2026-03-09 21:23:53.582614 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.585447 INFO::ASW Batch was 0.483066955970334 prior to batch effect correction and is now -0.0258436062785487 .
2026-03-09 21:23:53.586039 INFO::ASW Label was 0.546918772923884 prior to batch effect correction and is now 0.904915743200318 .
2026-03-09 21:23:53.586846 INFO::Total function execution time is  0.0350000858306885  s and adjustment time is  0.0181758403778076 s ( 51.93 )
2026-03-09 21:23:53.789087 INFO::Formatting Data.
2026-03-09 21:23:53.789933 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.790851 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.791912 INFO::Found  0  missing values.
2026-03-09 21:23:53.799684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.80039 INFO::Done
2026-03-09 21:23:53.800952 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.80316 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.803911 INFO::Found  3  batches.
2026-03-09 21:23:53.804448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.805102 INFO::Using default BPPARAM
2026-03-09 21:23:53.805666 INFO::Processing subtree level 1
2026-03-09 21:23:53.890029 INFO::Adjusting the last 1 batches sequentially
2026-03-09 21:23:53.891791 INFO::Done
2026-03-09 21:23:53.892419 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.894874 INFO::ASW Batch was -0.1168547052807 prior to batch effect correction and is now -0.1168547052807 .
2026-03-09 21:23:53.895821 INFO::Total function execution time is  0.10676121711731  s and adjustment time is  0.0880129337310791 s ( 82.44 )
2026-03-09 21:23:53.896903 INFO::Formatting Data.
2026-03-09 21:23:53.897568 INFO::Typecasting input to dataframe.
2026-03-09 21:23:53.898333 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:53.899287 INFO::Removing potential empty rows and columns
2026-03-09 21:23:53.900399 INFO::Found  0  missing values.
2026-03-09 21:23:53.90355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:53.904099 INFO::Done
2026-03-09 21:23:53.904665 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:53.906717 INFO::Starting hierarchical adjustment
2026-03-09 21:23:53.907438 INFO::Found  3  batches.
2026-03-09 21:23:53.90801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:53.908655 INFO::Using default BPPARAM
2026-03-09 21:23:53.909195 INFO::Processing subtree level 1
2026-03-09 21:23:53.991898 INFO::Adjusting the last 1 batches sequentially
2026-03-09 21:23:53.993677 INFO::Done
2026-03-09 21:23:53.994299 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:53.996769 INFO::ASW Batch was -0.1168547052807 prior to batch effect correction and is now -0.1168547052807 .
2026-03-09 21:23:53.997722 INFO::Total function execution time is  0.100788354873657  s and adjustment time is  0.0863690376281738 s ( 85.69 )
2026-03-09 21:23:54.010854 INFO::Formatting Data.
2026-03-09 21:23:54.011664 INFO::Typecasting input to dataframe.
2026-03-09 21:23:54.012536 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:54.01345 INFO::Removing potential empty rows and columns
2026-03-09 21:23:54.014652 INFO::Found  0  missing values.
2026-03-09 21:23:54.017711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:54.018263 INFO::Done
2026-03-09 21:23:54.018813 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:54.02092 INFO::Starting hierarchical adjustment
2026-03-09 21:23:54.021651 INFO::Found  3  batches.
2026-03-09 21:23:54.022192 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:54.022828 INFO::Using default BPPARAM
2026-03-09 21:23:54.023365 INFO::Processing subtree level 1
2026-03-09 21:23:54.1069 INFO::Adjusting the last 1 batches sequentially
2026-03-09 21:23:54.108804 INFO::Done
2026-03-09 21:23:54.109514 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:54.112144 INFO::ASW Batch was -0.110099937853623 prior to batch effect correction and is now -0.110099937853623 .
2026-03-09 21:23:54.113153 INFO::Total function execution time is  0.102333068847656  s and adjustment time is  0.0872862339019775 s ( 85.3 )
2026-03-09 21:23:54.247173 INFO::Formatting Data.
2026-03-09 21:23:54.247973 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:54.24909 INFO::Removing potential empty rows and columns
2026-03-09 21:23:54.251902 INFO::Found  1000  missing values.
2026-03-09 21:23:54.270985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:54.271726 INFO::Done
2026-03-09 21:23:54.272278 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:54.277763 INFO::Starting hierarchical adjustment
2026-03-09 21:23:54.278545 INFO::Found  10  batches.
2026-03-09 21:23:54.279098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:54.279748 INFO::Using default BPPARAM
2026-03-09 21:23:54.280389 INFO::Processing subtree level 1
2026-03-09 21:23:54.40556 INFO::Processing subtree level 2
2026-03-09 21:23:54.540686 INFO::Adjusting the last 1 batches sequentially
2026-03-09 21:23:54.542865 INFO::Done
2026-03-09 21:23:54.5436 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:54.54928 INFO::ASW Batch was 0.52888610848776 prior to batch effect correction and is now 0.52888610848776 .
2026-03-09 21:23:54.550048 INFO::ASW Label was 0.3338366672137 prior to batch effect correction and is now 0.3338366672137 .
2026-03-09 21:23:54.550948 INFO::Total function execution time is  0.303826332092285  s and adjustment time is  0.264456748962402 s ( 87.04 )
2026-03-09 21:23:54.551785 INFO::Formatting Data.
2026-03-09 21:23:54.552426 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:54.553663 INFO::Removing potential empty rows and columns
2026-03-09 21:23:54.556477 INFO::Found  1000  missing values.
2026-03-09 21:23:54.576242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:54.577014 INFO::Done
2026-03-09 21:23:54.577615 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:54.583469 INFO::Starting hierarchical adjustment
2026-03-09 21:23:54.58446 INFO::Found  10  batches.
2026-03-09 21:23:55.622729 INFO::Set up parallel execution backend with 2 workers
2026-03-09 21:23:55.624839 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-09 21:23:56.751552 INFO::Adjusting the last 2 batches sequentially
2026-03-09 21:23:56.753369 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-09 21:23:56.769755 INFO::Done
2026-03-09 21:23:56.770424 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:56.775027 INFO::ASW Batch was 0.52888610848776 prior to batch effect correction and is now 0.52888610848776 .
2026-03-09 21:23:56.77562 INFO::ASW Label was 0.3338366672137 prior to batch effect correction and is now 0.3338366672137 .
2026-03-09 21:23:56.776349 INFO::Total function execution time is  2.22459244728088  s and adjustment time is  2.18542647361755 s ( 98.24 )
2026-03-09 21:23:56.920768 INFO::Formatting Data.
2026-03-09 21:23:56.921574 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:56.922474 INFO::Removing potential empty rows and columns
2026-03-09 21:23:56.923539 INFO::Found  0  missing values.
2026-03-09 21:23:56.927079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:56.927618 INFO::Done
2026-03-09 21:23:56.928115 INFO::Acquiring quality metrics before batch effect correction.
2026-03-09 21:23:56.930837 INFO::Starting hierarchical adjustment
2026-03-09 21:23:56.931529 INFO::Found  3  batches.
2026-03-09 21:23:56.932039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-09 21:23:56.932651 INFO::Using default BPPARAM
2026-03-09 21:23:56.933163 INFO::Processing subtree level 1
2026-03-09 21:23:57.049239 INFO::Adjusting the last 1 batches sequentially
2026-03-09 21:23:57.051228 INFO::Done
2026-03-09 21:23:57.051972 INFO::Acquiring quality metrics after batch effect correction.
2026-03-09 21:23:57.055484 INFO::ASW Batch was 0.184047683709354 prior to batch effect correction and is now -0.161876222320722 .
2026-03-09 21:23:57.05617 INFO::ASW Label was -0.180392031413193 prior to batch effect correction and is now 0.0613441795221511 .
2026-03-09 21:23:57.057126 INFO::Total function execution time is  0.13642406463623  s and adjustment time is  0.119812488555908 s ( 87.82 )
2026-03-09 21:23:57.186928 INFO::Formatting Data.
2026-03-09 21:23:57.18778 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.188729 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.189855 INFO::Found  2  missing values.
2026-03-09 21:23:57.19299 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.193583 INFO::Done
2026-03-09 21:23:57.224011 INFO::Found NA in Reference column
2026-03-09 21:23:57.234623 INFO::Require at least two references per batch.
2026-03-09 21:23:57.256612 INFO::Formatting Data.
2026-03-09 21:23:57.257374 INFO::Recognized SummarizedExperiment
2026-03-09 21:23:57.257942 INFO::Typecasting input to dataframe.
2026-03-09 21:23:57.267945 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.269195 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.272917 INFO::Found  0  missing values.
2026-03-09 21:23:57.280046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.280688 INFO::Done
2026-03-09 21:23:57.297127 INFO::Formatting Data.
2026-03-09 21:23:57.297917 INFO::Recognized SummarizedExperiment
2026-03-09 21:23:57.298464 INFO::Typecasting input to dataframe.
2026-03-09 21:23:57.316967 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.318302 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.322055 INFO::Found  0  missing values.
2026-03-09 21:23:57.333597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.334321 INFO::Done
2026-03-09 21:23:57.351043 INFO::Formatting Data.
2026-03-09 21:23:57.351901 INFO::Recognized SummarizedExperiment
2026-03-09 21:23:57.352471 INFO::Typecasting input to dataframe.
2026-03-09 21:23:57.370913 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.372126 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.373322 INFO::Found  0  missing values.
2026-03-09 21:23:57.374348 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.
2026-03-09 21:23:57.379332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.380024 INFO::Done
2026-03-09 21:23:57.391913 INFO::Formatting Data.
2026-03-09 21:23:57.392769 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.393771 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.394847 INFO::Found  0  missing values.
2026-03-09 21:23:57.397847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.398401 INFO::Done
2026-03-09 21:23:57.410703 INFO::Formatting Data.
2026-03-09 21:23:57.411591 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.412631 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.413717 INFO::Found  0  missing values.
2026-03-09 21:23:57.416687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.417245 INFO::Done
2026-03-09 21:23:57.448461 INFO::Formatting Data.
2026-03-09 21:23:57.449333 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.4504 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.451599 INFO::Found  1  missing values.
2026-03-09 21:23:57.454233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.454812 INFO::Done
2026-03-09 21:23:57.474704 INFO::Formatting Data.
2026-03-09 21:23:57.47548 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.476455 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.477425 INFO::Found  2  missing values.
2026-03-09 21:23:57.478328 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.
2026-03-09 21:23:57.480577 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.481124 INFO::Done
2026-03-09 21:23:57.491692 INFO::Formatting Data.
2026-03-09 21:23:57.492515 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.493426 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.494358 INFO::Found  2  missing values.
2026-03-09 21:23:57.496021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.496597 INFO::Done
2026-03-09 21:23:57.507972 INFO::Formatting Data.
2026-03-09 21:23:57.508799 INFO::Typecasting input to dataframe.
2026-03-09 21:23:57.509633 INFO::Replacing NaNs with NAs.
2026-03-09 21:23:57.510494 INFO::Removing potential empty rows and columns
2026-03-09 21:23:57.51152 INFO::Found  0  missing values.
2026-03-09 21:23:57.514519 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-09 21:23:57.515145 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.163   3.318  20.295

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT24.332 1.30317.662
compute_asw0.0240.0000.025
count_existing0.0130.0010.014
generate_data_covariables0.0120.0010.012
generate_dataset0.0110.0000.011