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This page was generated on 2026-04-04 11:57 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4897
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Package 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-04-03 13:45 -0400 (Fri, 03 Apr 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: 2026-04-03 21:19:45 -0400 (Fri, 03 Apr 2026)
EndedAt: 2026-04-03 21:21:13 -0400 (Fri, 03 Apr 2026)
EllapsedTime: 88.1 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 24.04.4 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 23.661  1.225  16.937
* 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")
2026-04-03 21:20:36.022784 INFO::Formatting Data.
2026-04-03 21:20:36.024251 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:36.035416 INFO::Removing potential empty rows and columns
2026-04-03 21:20:36.275849 INFO::Found  0  missing values.
2026-04-03 21:20:36.27907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:36.27976 INFO::Done
2026-04-03 21:20:36.280307 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:36.291453 INFO::Starting hierarchical adjustment
2026-04-03 21:20:36.292407 INFO::Found  3  batches.
2026-04-03 21:20:36.292973 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:36.294117 INFO::Using default BPPARAM
2026-04-03 21:20:36.294682 INFO::Processing subtree level 1
2026-04-03 21:20:36.385065 INFO::Adjusting the last 1 batches sequentially
2026-04-03 21:20:36.38683 INFO::Done
2026-04-03 21:20:36.387525 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:36.390001 INFO::ASW Batch was -0.109913047716681 prior to batch effect correction and is now -0.109913047716681 .
2026-04-03 21:20:36.391057 INFO::Total function execution time is  0.368987560272217  s and adjustment time is  0.0946266651153564 s ( 25.64 )
2026-04-03 21:20:36.404572 INFO::Formatting Data.
2026-04-03 21:20:36.405358 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:36.406313 INFO::Removing potential empty rows and columns
2026-04-03 21:20:36.407489 INFO::Found  0  missing values.
2026-04-03 21:20:36.408442 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.
2026-04-03 21:20:36.419422 INFO::Formatting Data.
2026-04-03 21:20:36.420219 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:36.421163 INFO::Removing potential empty rows and columns
2026-04-03 21:20:36.422237 INFO::Found  0  missing values.
2026-04-03 21:20:36.423216 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.
2026-04-03 21:20:36.439391 INFO::Formatting Data.
2026-04-03 21:20:36.440173 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:36.441085 INFO::Removing potential empty rows and columns
2026-04-03 21:20:36.442124 INFO::Found  0  missing values.
2026-04-03 21:20:36.443028 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.
2026-04-03 21:20:36.447359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:36.447891 INFO::Done
2026-04-03 21:20:36.448399 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:36.450342 INFO::Starting hierarchical adjustment
2026-04-03 21:20:36.451015 INFO::Found  2  batches.
2026-04-03 21:20:36.451531 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:36.452147 INFO::Using default BPPARAM
2026-04-03 21:20:36.452668 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:36.453573 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 21:20:36.47434 INFO::Done
2026-04-03 21:20:36.475034 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:36.477157 INFO::ASW Batch was 0.0968315588531664 prior to batch effect correction and is now -0.106779898701938 .
2026-04-03 21:20:36.478077 INFO::Total function execution time is  0.0387692451477051  s and adjustment time is  0.0234215259552002 s ( 60.41 )
2026-04-03 21:20:36.480975 INFO::Formatting Data.
2026-04-03 21:20:36.481639 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:36.490468 INFO::Formatting Data.
2026-04-03 21:20:36.491201 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:36.492113 INFO::Removing potential empty rows and columns
2026-04-03 21:20:36.49316 INFO::Found  0  missing values.
2026-04-03 21:20:36.496178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:36.496791 INFO::Done
2026-04-03 21:20:36.49734 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:36.52281 INFO::Starting hierarchical adjustment
2026-04-03 21:20:36.524389 INFO::Found  2  batches.
2026-04-03 21:20:36.525011 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:36.525619 INFO::Using default BPPARAM
2026-04-03 21:20:36.526132 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:36.5271 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 21:20:36.541515 INFO::Done
2026-04-03 21:20:36.542185 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:36.544145 INFO::ASW Batch was -0.0217156658207464 prior to batch effect correction and is now -0.111364742225925 .
2026-04-03 21:20:36.544927 INFO::Total function execution time is  0.054511547088623  s and adjustment time is  0.0173377990722656 s ( 31.81 )
2026-04-03 21:20:36.545966 INFO::Formatting Data.
2026-04-03 21:20:36.546563 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:36.547399 INFO::Removing potential empty rows and columns
2026-04-03 21:20:36.548385 INFO::Found  0  missing values.
2026-04-03 21:20:36.551049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:36.551612 INFO::Done
2026-04-03 21:20:36.552078 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:36.553976 INFO::Starting hierarchical adjustment
2026-04-03 21:20:36.55465 INFO::Found  2  batches.
2026-04-03 21:20:36.55512 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:36.55568 INFO::Using default BPPARAM
2026-04-03 21:20:36.556162 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:36.557029 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 21:20:36.571315 INFO::Done
2026-04-03 21:20:36.571998 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:36.573967 INFO::ASW Batch was -0.0217156658207464 prior to batch effect correction and is now -0.111364742225925 .
2026-04-03 21:20:36.574745 INFO::Total function execution time is  0.0287864208221436  s and adjustment time is  0.0167574882507324 s ( 58.21 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-03 21:20:39.496682 INFO::Formatting Data.
2026-04-03 21:20:39.497317 INFO::Recognized SummarizedExperiment
2026-04-03 21:20:39.497772 INFO::Typecasting input to dataframe.
2026-04-03 21:20:39.527514 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:39.528822 INFO::Removing potential empty rows and columns
2026-04-03 21:20:39.532736 INFO::Found  0  missing values.
2026-04-03 21:20:39.540157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:39.540888 INFO::Done
2026-04-03 21:20:39.541444 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:39.545146 INFO::Starting hierarchical adjustment
2026-04-03 21:20:39.545909 INFO::Found  2  batches.
2026-04-03 21:20:39.54644 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:39.547554 INFO::Using default BPPARAM
2026-04-03 21:20:39.548092 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:39.549099 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 21:20:39.607591 INFO::Done
2026-04-03 21:20:39.608459 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:39.612502 INFO::ASW Batch was 0.0107329490375196 prior to batch effect correction and is now -0.0976009714738404 .
2026-04-03 21:20:39.613533 INFO::Total function execution time is  0.117086172103882  s and adjustment time is  0.0617713928222656 s ( 52.76 )
Warning: stack imbalance in '{', 73 then 75
2026-04-03 21:20:39.634752 INFO::Formatting Data.
2026-04-03 21:20:39.635637 INFO::Recognized SummarizedExperiment
2026-04-03 21:20:39.636204 INFO::Typecasting input to dataframe.
2026-04-03 21:20:39.646499 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:39.647836 INFO::Removing potential empty rows and columns
2026-04-03 21:20:39.651789 INFO::Found  0  missing values.
2026-04-03 21:20:39.659453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:39.660291 INFO::Done
2026-04-03 21:20:39.660866 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:39.665003 INFO::Starting hierarchical adjustment
2026-04-03 21:20:39.665795 INFO::Found  2  batches.
2026-04-03 21:20:39.666339 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:39.666958 INFO::Using default BPPARAM
2026-04-03 21:20:39.667502 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:39.668554 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 21:20:39.694936 INFO::Done
2026-04-03 21:20:39.695772 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:39.699568 INFO::ASW Batch was -0.0103396673343381 prior to batch effect correction and is now -0.0103396673343381 .
2026-04-03 21:20:39.700495 INFO::Total function execution time is  0.0657603740692139  s and adjustment time is  0.0292425155639648 s ( 44.47 )
2026-04-03 21:20:39.719939 INFO::Formatting Data.
2026-04-03 21:20:39.720906 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:39.72191 INFO::Removing potential empty rows and columns
2026-04-03 21:20:39.723084 INFO::Found  0  missing values.
2026-04-03 21:20:39.726162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:39.726794 INFO::Done
2026-04-03 21:20:39.727327 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:39.729548 INFO::Starting hierarchical adjustment
2026-04-03 21:20:39.730294 INFO::Found  3  batches.
2026-04-03 21:20:39.730818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:39.731436 INFO::Using default BPPARAM
2026-04-03 21:20:39.73195 INFO::Processing subtree level 1
2026-04-03 21:20:39.898781 INFO::Adjusting the last 1 batches sequentially
2026-04-03 21:20:39.901619 INFO::Done
2026-04-03 21:20:39.902605 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:39.906599 INFO::ASW Batch was -0.057291424526925 prior to batch effect correction and is now -0.223967682376433 .
2026-04-03 21:20:39.907985 INFO::Total function execution time is  0.188020944595337  s and adjustment time is  0.171392679214478 s ( 91.16 )
2026-04-03 21:20:39.928874 INFO::Skipping initial DF formatting
2026-04-03 21:20:39.930089 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:39.935187 INFO::Starting hierarchical adjustment
2026-04-03 21:20:39.936263 INFO::Found  5  batches.
2026-04-03 21:20:39.936878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:39.93757 INFO::Using default BPPARAM
2026-04-03 21:20:39.938125 INFO::Processing subtree level 1
2026-04-03 21:20:40.210941 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:40.213255 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 21:20:40.235965 INFO::Done
2026-04-03 21:20:40.236987 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:40.241982 INFO::ASW Batch was 0.471278916316273 prior to batch effect correction and is now 0.471278916316273 .
2026-04-03 21:20:40.242751 INFO::ASW Label was 0.414270402932928 prior to batch effect correction and is now 0.414270402932928 .
2026-04-03 21:20:40.243734 INFO::Total function execution time is  0.31530499458313  s and adjustment time is  0.299890756607056 s ( 95.11 )
2026-04-03 21:20:40.328925 INFO::Formatting Data.
2026-04-03 21:20:40.329963 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:40.331098 INFO::Removing potential empty rows and columns
2026-04-03 21:20:40.332238 INFO::Found  0  missing values.
2026-04-03 21:20:40.336673 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:40.337371 INFO::Done
2026-04-03 21:20:40.337926 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:40.341401 INFO::Starting hierarchical adjustment
2026-04-03 21:20:40.342215 INFO::Found  5  batches.
2026-04-03 21:20:40.342791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:40.343441 INFO::Using default BPPARAM
2026-04-03 21:20:40.343993 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.

2026-04-03 21:20:40.489975 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:40.49232 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 21:20:40.513435 INFO::Done
2026-04-03 21:20:40.514392 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:40.518677 INFO::ASW Batch was 0.240384919799839 prior to batch effect correction and is now -0.0352396242250844 .
2026-04-03 21:20:40.519461 INFO::ASW Label was 0.51668189706978 prior to batch effect correction and is now 0.821688612679233 .
2026-04-03 21:20:40.52043 INFO::Total function execution time is  0.191632747650146  s and adjustment time is  0.171308994293213 s ( 89.39 )
2026-04-03 21:20:40.521412 INFO::Formatting Data.
2026-04-03 21:20:40.522109 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:40.523357 INFO::Removing potential empty rows and columns
2026-04-03 21:20:40.52467 INFO::Found  0  missing values.
2026-04-03 21:20:40.529613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:40.530268 INFO::Done
2026-04-03 21:20:40.530851 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:40.534525 INFO::Starting hierarchical adjustment
2026-04-03 21:20:40.535363 INFO::Found  5  batches.
2026-04-03 21:20:40.535954 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:40.536618 INFO::Using default BPPARAM
2026-04-03 21:20:40.537235 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.

2026-04-03 21:20:40.668328 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:40.670186 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 21:20:40.688473 INFO::Done
2026-04-03 21:20:40.689261 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:40.692733 INFO::ASW Batch was 0.240384919799839 prior to batch effect correction and is now -0.0352396242250844 .
2026-04-03 21:20:40.693374 INFO::ASW Label was 0.51668189706978 prior to batch effect correction and is now 0.821688612679233 .
2026-04-03 21:20:40.694219 INFO::Total function execution time is  0.172827959060669  s and adjustment time is  0.153256177902222 s ( 88.68 )
2026-04-03 21:20:40.709566 INFO::Formatting Data.
2026-04-03 21:20:40.710493 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:40.711505 INFO::Removing potential empty rows and columns
2026-04-03 21:20:40.712638 INFO::Found  0  missing values.
2026-04-03 21:20:40.716898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:40.717521 INFO::Done
2026-04-03 21:20:40.718063 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:40.72147 INFO::Starting hierarchical adjustment
2026-04-03 21:20:40.722252 INFO::Found  5  batches.
2026-04-03 21:20:40.722843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:40.723532 INFO::Using default BPPARAM
2026-04-03 21:20:40.724112 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.

2026-04-03 21:20:40.867046 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:40.869521 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 21:20:40.88955 INFO::Done
2026-04-03 21:20:40.890461 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:40.894241 INFO::ASW Batch was 0.554513561573563 prior to batch effect correction and is now -0.0965564214412958 .
2026-04-03 21:20:40.895004 INFO::ASW Label was 0.156156310757487 prior to batch effect correction and is now 0.829723673261842 .
2026-04-03 21:20:40.895915 INFO::Total function execution time is  0.186466455459595  s and adjustment time is  0.167389631271362 s ( 89.77 )
2026-04-03 21:20:40.896889 INFO::Formatting Data.
2026-04-03 21:20:40.897594 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:40.898661 INFO::Removing potential empty rows and columns
2026-04-03 21:20:40.899843 INFO::Found  0  missing values.
2026-04-03 21:20:40.904341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:40.90498 INFO::Done
2026-04-03 21:20:40.905552 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:40.909028 INFO::Starting hierarchical adjustment
2026-04-03 21:20:40.909854 INFO::Found  5  batches.
2026-04-03 21:20:40.910447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:40.91113 INFO::Using default BPPARAM
2026-04-03 21:20:40.911742 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.

2026-04-03 21:20:41.035523 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:41.037756 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 21:20:41.059214 INFO::Done
2026-04-03 21:20:41.060296 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.064502 INFO::ASW Batch was 0.554513561573563 prior to batch effect correction and is now -0.0965564214412958 .
2026-04-03 21:20:41.065223 INFO::ASW Label was 0.156156310757487 prior to batch effect correction and is now 0.829723673261842 .
2026-04-03 21:20:41.066202 INFO::Total function execution time is  0.169314622879028  s and adjustment time is  0.149439811706543 s ( 88.26 )
2026-04-03 21:20:41.082554 INFO::Formatting Data.
2026-04-03 21:20:41.08356 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.084704 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.085925 INFO::Found  0  missing values.
2026-04-03 21:20:41.089067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:41.089694 INFO::Done
2026-04-03 21:20:41.090264 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:41.093626 INFO::Starting hierarchical adjustment
2026-04-03 21:20:41.094392 INFO::Found  2  batches.
2026-04-03 21:20:41.094953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:41.095596 INFO::Using default BPPARAM
2026-04-03 21:20:41.096141 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:41.097135 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 21:20:41.119714 INFO::Done
2026-04-03 21:20:41.120748 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.124687 INFO::ASW Batch was 0.718431155059198 prior to batch effect correction and is now -0.0164119913651459 .
2026-04-03 21:20:41.125465 INFO::ASW Label was 0.3023484994702 prior to batch effect correction and is now 0.852239775296409 .
2026-04-03 21:20:41.126414 INFO::Total function execution time is  0.0440018177032471  s and adjustment time is  0.0253918170928955 s ( 57.71 )
2026-04-03 21:20:41.127366 INFO::Formatting Data.
2026-04-03 21:20:41.128073 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.129137 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.130325 INFO::Found  0  missing values.
2026-04-03 21:20:41.133451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:41.134066 INFO::Done
2026-04-03 21:20:41.134668 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:41.138268 INFO::Starting hierarchical adjustment
2026-04-03 21:20:41.139102 INFO::Found  2  batches.
2026-04-03 21:20:41.139687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:41.140371 INFO::Using default BPPARAM
2026-04-03 21:20:41.140924 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:41.141972 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-03 21:20:41.159059 INFO::Done
2026-04-03 21:20:41.159928 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.163513 INFO::ASW Batch was 0.718431155059198 prior to batch effect correction and is now -0.0164119913651459 .
2026-04-03 21:20:41.164311 INFO::ASW Label was 0.3023484994702 prior to batch effect correction and is now 0.852239775296409 .
2026-04-03 21:20:41.16515 INFO::Total function execution time is  0.0378408432006836  s and adjustment time is  0.0200788974761963 s ( 53.06 )
2026-04-03 21:20:41.177959 INFO::Formatting Data.
2026-04-03 21:20:41.178826 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.179776 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.180727 INFO::Found  0  missing values.
2026-04-03 21:20:41.182957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:41.183513 INFO::Done
2026-04-03 21:20:41.184031 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:41.186146 INFO::Starting hierarchical adjustment
2026-04-03 21:20:41.186898 INFO::Found  2  batches.
2026-04-03 21:20:41.187476 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:41.18813 INFO::Using default BPPARAM
2026-04-03 21:20:41.188703 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:41.18968 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 21:20:41.223804 INFO::Done
2026-04-03 21:20:41.224565 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.226526 INFO::ASW Batch was -0.102385731817881 prior to batch effect correction and is now -0.134990742991249 .
2026-04-03 21:20:41.227338 INFO::Total function execution time is  0.0494976043701172  s and adjustment time is  0.0370399951934814 s ( 74.83 )
2026-04-03 21:20:41.239156 INFO::Formatting Data.
2026-04-03 21:20:41.239968 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.240845 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.241822 INFO::Found  0  missing values.
2026-04-03 21:20:41.242959 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.
2026-04-03 21:20:41.247417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:41.247975 INFO::Done
2026-04-03 21:20:41.248486 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:41.251366 INFO::Starting hierarchical adjustment
2026-04-03 21:20:41.252078 INFO::Found  2  batches.
2026-04-03 21:20:41.252602 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:41.253177 INFO::Using default BPPARAM
2026-04-03 21:20:41.253682 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:41.254582 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 21:20:41.270793 INFO::Done
2026-04-03 21:20:41.271526 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.274451 INFO::ASW Batch was 0.396775941755481 prior to batch effect correction and is now 0.0742006221169551 .
2026-04-03 21:20:41.275035 INFO::ASW Label was 0.625726478185146 prior to batch effect correction and is now 0.873986994042154 .
2026-04-03 21:20:41.2758 INFO::Total function execution time is  0.036747932434082  s and adjustment time is  0.0188214778900146 s ( 51.22 )
2026-04-03 21:20:41.276607 INFO::Formatting Data.
2026-04-03 21:20:41.277203 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.278078 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.279009 INFO::Found  0  missing values.
2026-04-03 21:20:41.279873 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.
2026-04-03 21:20:41.284261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:41.284828 INFO::Done
2026-04-03 21:20:41.285367 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:41.288448 INFO::Starting hierarchical adjustment
2026-04-03 21:20:41.289177 INFO::Found  2  batches.
2026-04-03 21:20:41.289722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:41.290335 INFO::Using default BPPARAM
2026-04-03 21:20:41.290851 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:41.291786 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 21:20:41.308472 INFO::Done
2026-04-03 21:20:41.309207 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.312336 INFO::ASW Batch was 0.396775941755481 prior to batch effect correction and is now 0.0742006221169551 .
2026-04-03 21:20:41.312964 INFO::ASW Label was 0.625726478185146 prior to batch effect correction and is now 0.873986994042154 .
2026-04-03 21:20:41.313776 INFO::Total function execution time is  0.0371942520141602  s and adjustment time is  0.0194005966186523 s ( 52.16 )
2026-04-03 21:20:41.526557 INFO::Formatting Data.
2026-04-03 21:20:41.527558 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.528536 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.529645 INFO::Found  0  missing values.
2026-04-03 21:20:41.532776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:41.533386 INFO::Done
2026-04-03 21:20:41.533899 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:41.535956 INFO::Starting hierarchical adjustment
2026-04-03 21:20:41.536665 INFO::Found  3  batches.
2026-04-03 21:20:41.537185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:41.537808 INFO::Using default BPPARAM
2026-04-03 21:20:41.538333 INFO::Processing subtree level 1
2026-04-03 21:20:41.619735 INFO::Adjusting the last 1 batches sequentially
2026-04-03 21:20:41.621873 INFO::Done
2026-04-03 21:20:41.622671 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.625413 INFO::ASW Batch was -0.0409575005316768 prior to batch effect correction and is now -0.0409575005316768 .
2026-04-03 21:20:41.626469 INFO::Total function execution time is  0.0999696254730225  s and adjustment time is  0.08530592918396 s ( 85.33 )
2026-04-03 21:20:41.627578 INFO::Formatting Data.
2026-04-03 21:20:41.628226 INFO::Typecasting input to dataframe.
2026-04-03 21:20:41.633162 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.634281 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.635459 INFO::Found  0  missing values.
2026-04-03 21:20:41.638765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:41.639358 INFO::Done
2026-04-03 21:20:41.639914 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:41.64219 INFO::Starting hierarchical adjustment
2026-04-03 21:20:41.642936 INFO::Found  3  batches.
2026-04-03 21:20:41.643496 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:41.644141 INFO::Using default BPPARAM
2026-04-03 21:20:41.644701 INFO::Processing subtree level 1
2026-04-03 21:20:41.731465 INFO::Adjusting the last 1 batches sequentially
2026-04-03 21:20:41.733443 INFO::Done
2026-04-03 21:20:41.734147 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.736773 INFO::ASW Batch was -0.0409575005316768 prior to batch effect correction and is now -0.0409575005316768 .
2026-04-03 21:20:41.737873 INFO::Total function execution time is  0.110244750976562  s and adjustment time is  0.0906233787536621 s ( 82.2 )
2026-04-03 21:20:41.754194 INFO::Formatting Data.
2026-04-03 21:20:41.755481 INFO::Typecasting input to dataframe.
2026-04-03 21:20:41.756592 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.757706 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.758935 INFO::Found  0  missing values.
2026-04-03 21:20:41.762241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:41.762895 INFO::Done
2026-04-03 21:20:41.763473 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:41.765842 INFO::Starting hierarchical adjustment
2026-04-03 21:20:41.766647 INFO::Found  3  batches.
2026-04-03 21:20:41.767183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:41.767826 INFO::Using default BPPARAM
2026-04-03 21:20:41.768383 INFO::Processing subtree level 1
2026-04-03 21:20:41.849841 INFO::Adjusting the last 1 batches sequentially
2026-04-03 21:20:41.851829 INFO::Done
2026-04-03 21:20:41.852598 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:41.855392 INFO::ASW Batch was -0.0308334569478727 prior to batch effect correction and is now -0.0308334569478727 .
2026-04-03 21:20:41.856459 INFO::Total function execution time is  0.102396011352539  s and adjustment time is  0.0853078365325928 s ( 83.31 )
2026-04-03 21:20:41.992528 INFO::Formatting Data.
2026-04-03 21:20:41.99338 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:41.994513 INFO::Removing potential empty rows and columns
2026-04-03 21:20:41.997335 INFO::Found  1000  missing values.
2026-04-03 21:20:42.016586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:42.017366 INFO::Done
2026-04-03 21:20:42.017927 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:42.023505 INFO::Starting hierarchical adjustment
2026-04-03 21:20:42.024313 INFO::Found  10  batches.
2026-04-03 21:20:42.024864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:42.025496 INFO::Using default BPPARAM
2026-04-03 21:20:42.026024 INFO::Processing subtree level 1
2026-04-03 21:20:42.144926 INFO::Processing subtree level 2
2026-04-03 21:20:42.283573 INFO::Adjusting the last 1 batches sequentially
2026-04-03 21:20:42.28589 INFO::Done
2026-04-03 21:20:42.287173 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:42.293305 INFO::ASW Batch was 0.531423338027406 prior to batch effect correction and is now 0.531423338027406 .
2026-04-03 21:20:42.294111 INFO::ASW Label was 0.32482044114449 prior to batch effect correction and is now 0.32482044114449 .
2026-04-03 21:20:42.295113 INFO::Total function execution time is  0.302643775939941  s and adjustment time is  0.261709690093994 s ( 86.47 )
2026-04-03 21:20:42.295987 INFO::Formatting Data.
2026-04-03 21:20:42.296669 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:42.297904 INFO::Removing potential empty rows and columns
2026-04-03 21:20:42.300798 INFO::Found  1000  missing values.
2026-04-03 21:20:42.320834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:42.321594 INFO::Done
2026-04-03 21:20:42.322166 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:42.327973 INFO::Starting hierarchical adjustment
2026-04-03 21:20:42.328824 INFO::Found  10  batches.
2026-04-03 21:20:43.451131 INFO::Set up parallel execution backend with 2 workers
2026-04-03 21:20:43.453677 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-03 21:20:44.568035 INFO::Adjusting the last 2 batches sequentially
2026-04-03 21:20:44.569978 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-03 21:20:44.586945 INFO::Done
2026-04-03 21:20:44.587624 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:44.592215 INFO::ASW Batch was 0.531423338027406 prior to batch effect correction and is now 0.531423338027406 .
2026-04-03 21:20:44.592806 INFO::ASW Label was 0.32482044114449 prior to batch effect correction and is now 0.32482044114449 .
2026-04-03 21:20:44.593532 INFO::Total function execution time is  2.29758024215698  s and adjustment time is  2.25827050209045 s ( 98.29 )
2026-04-03 21:20:44.725466 INFO::Formatting Data.
2026-04-03 21:20:44.726206 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:44.727085 INFO::Removing potential empty rows and columns
2026-04-03 21:20:44.728089 INFO::Found  0  missing values.
2026-04-03 21:20:44.731543 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:44.732043 INFO::Done
2026-04-03 21:20:44.732542 INFO::Acquiring quality metrics before batch effect correction.
2026-04-03 21:20:44.735127 INFO::Starting hierarchical adjustment
2026-04-03 21:20:44.735803 INFO::Found  3  batches.
2026-04-03 21:20:44.736311 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-03 21:20:44.736884 INFO::Using default BPPARAM
2026-04-03 21:20:44.737392 INFO::Processing subtree level 1
2026-04-03 21:20:44.832758 INFO::Adjusting the last 1 batches sequentially
2026-04-03 21:20:44.834506 INFO::Done
2026-04-03 21:20:44.835153 INFO::Acquiring quality metrics after batch effect correction.
2026-04-03 21:20:44.838309 INFO::ASW Batch was 0.163742479840348 prior to batch effect correction and is now -0.162821536226309 .
2026-04-03 21:20:44.838906 INFO::ASW Label was -0.191812729439101 prior to batch effect correction and is now -0.0720360834118248 .
2026-04-03 21:20:44.839794 INFO::Total function execution time is  0.114394187927246  s and adjustment time is  0.0988051891326904 s ( 86.37 )
2026-04-03 21:20:44.955015 INFO::Formatting Data.
2026-04-03 21:20:44.955982 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:44.956921 INFO::Removing potential empty rows and columns
2026-04-03 21:20:44.95796 INFO::Found  2  missing values.
2026-04-03 21:20:44.960698 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:44.961222 INFO::Done
2026-04-03 21:20:44.988669 INFO::Found NA in Reference column
2026-04-03 21:20:44.99798 INFO::Require at least two references per batch.
2026-04-03 21:20:45.017731 INFO::Formatting Data.
2026-04-03 21:20:45.01848 INFO::Recognized SummarizedExperiment
2026-04-03 21:20:45.018997 INFO::Typecasting input to dataframe.
2026-04-03 21:20:45.028361 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.029504 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.032821 INFO::Found  0  missing values.
2026-04-03 21:20:45.039157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.039715 INFO::Done
2026-04-03 21:20:45.054724 INFO::Formatting Data.
2026-04-03 21:20:45.055409 INFO::Recognized SummarizedExperiment
2026-04-03 21:20:45.055916 INFO::Typecasting input to dataframe.
2026-04-03 21:20:45.072373 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.073532 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.076798 INFO::Found  0  missing values.
2026-04-03 21:20:45.086706 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.087328 INFO::Done
2026-04-03 21:20:45.102537 INFO::Formatting Data.
2026-04-03 21:20:45.103218 INFO::Recognized SummarizedExperiment
2026-04-03 21:20:45.103735 INFO::Typecasting input to dataframe.
2026-04-03 21:20:45.119703 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.120715 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.121745 INFO::Found  0  missing values.
2026-04-03 21:20:45.122631 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.
2026-04-03 21:20:45.126718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.127237 INFO::Done
2026-04-03 21:20:45.136714 INFO::Formatting Data.
2026-04-03 21:20:45.137401 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.1382 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.139123 INFO::Found  0  missing values.
2026-04-03 21:20:45.141761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.142253 INFO::Done
2026-04-03 21:20:45.153028 INFO::Formatting Data.
2026-04-03 21:20:45.153862 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.15481 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.155777 INFO::Found  0  missing values.
2026-04-03 21:20:45.15853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.159067 INFO::Done
2026-04-03 21:20:45.188956 INFO::Formatting Data.
2026-04-03 21:20:45.189836 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.190939 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.192125 INFO::Found  1  missing values.
2026-04-03 21:20:45.194799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.19534 INFO::Done
2026-04-03 21:20:45.21484 INFO::Formatting Data.
2026-04-03 21:20:45.215796 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.21674 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.217759 INFO::Found  2  missing values.
2026-04-03 21:20:45.218712 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.
2026-04-03 21:20:45.220944 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.221479 INFO::Done
2026-04-03 21:20:45.231376 INFO::Formatting Data.
2026-04-03 21:20:45.232132 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.233122 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.234073 INFO::Found  2  missing values.
2026-04-03 21:20:45.235739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.236258 INFO::Done
2026-04-03 21:20:45.24668 INFO::Formatting Data.
2026-04-03 21:20:45.247425 INFO::Typecasting input to dataframe.
2026-04-03 21:20:45.248212 INFO::Replacing NaNs with NAs.
2026-04-03 21:20:45.24905 INFO::Removing potential empty rows and columns
2026-04-03 21:20:45.250037 INFO::Found  0  missing values.
2026-04-03 21:20:45.252913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-03 21:20:45.253457 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.494   3.102  20.418

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT23.661 1.22516.937
compute_asw0.0240.0010.025
count_existing0.0130.0010.013
generate_data_covariables0.0120.0000.012
generate_dataset0.0100.0000.012