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This page was generated on 2026-03-31 11:57 -0400 (Tue, 31 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4893
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Package 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2026-03-30 13:45 -0400 (Mon, 30 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: 2026-03-30 21:17:07 -0400 (Mon, 30 Mar 2026)
EndedAt: 2026-03-30 21:18:36 -0400 (Mon, 30 Mar 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 24.264  1.225  17.946
* 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")
2026-03-30 21:17:59.038492 INFO::Formatting Data.
2026-03-30 21:17:59.04 INFO::Replacing NaNs with NAs.
2026-03-30 21:17:59.052824 INFO::Removing potential empty rows and columns
2026-03-30 21:17:59.31153 INFO::Found  0  missing values.
2026-03-30 21:17:59.314856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:17:59.315511 INFO::Done
2026-03-30 21:17:59.316057 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:17:59.327254 INFO::Starting hierarchical adjustment
2026-03-30 21:17:59.328133 INFO::Found  3  batches.
2026-03-30 21:17:59.328712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:17:59.329837 INFO::Using default BPPARAM
2026-03-30 21:17:59.330419 INFO::Processing subtree level 1
2026-03-30 21:17:59.427462 INFO::Adjusting the last 1 batches sequentially
2026-03-30 21:17:59.42926 INFO::Done
2026-03-30 21:17:59.429939 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:17:59.432579 INFO::ASW Batch was -3.11897604975786e-05 prior to batch effect correction and is now -3.11897604975786e-05 .
2026-03-30 21:17:59.433641 INFO::Total function execution time is  0.395885229110718  s and adjustment time is  0.101284742355347 s ( 25.58 )
2026-03-30 21:17:59.448015 INFO::Formatting Data.
2026-03-30 21:17:59.448838 INFO::Replacing NaNs with NAs.
2026-03-30 21:17:59.449824 INFO::Removing potential empty rows and columns
2026-03-30 21:17:59.451067 INFO::Found  0  missing values.
2026-03-30 21:17:59.452108 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.
2026-03-30 21:17:59.463433 INFO::Formatting Data.
2026-03-30 21:17:59.46419 INFO::Replacing NaNs with NAs.
2026-03-30 21:17:59.465123 INFO::Removing potential empty rows and columns
2026-03-30 21:17:59.466255 INFO::Found  0  missing values.
2026-03-30 21:17:59.467257 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.
2026-03-30 21:17:59.484213 INFO::Formatting Data.
2026-03-30 21:17:59.485022 INFO::Replacing NaNs with NAs.
2026-03-30 21:17:59.485987 INFO::Removing potential empty rows and columns
2026-03-30 21:17:59.487098 INFO::Found  0  missing values.
2026-03-30 21:17:59.488016 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.
2026-03-30 21:17:59.493491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:17:59.494127 INFO::Done
2026-03-30 21:17:59.494682 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:17:59.496772 INFO::Starting hierarchical adjustment
2026-03-30 21:17:59.497496 INFO::Found  2  batches.
2026-03-30 21:17:59.498037 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:17:59.498702 INFO::Using default BPPARAM
2026-03-30 21:17:59.499235 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:17:59.500183 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-30 21:17:59.521438 INFO::Done
2026-03-30 21:17:59.52213 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:17:59.524282 INFO::ASW Batch was 0.0195532156613349 prior to batch effect correction and is now -0.127884044574035 .
2026-03-30 21:17:59.525209 INFO::Total function execution time is  0.0410704612731934  s and adjustment time is  0.0240840911865234 s ( 58.64 )
2026-03-30 21:17:59.528105 INFO::Formatting Data.
2026-03-30 21:17:59.528747 INFO::Replacing NaNs with NAs.
2026-03-30 21:17:59.537778 INFO::Formatting Data.
2026-03-30 21:17:59.538502 INFO::Replacing NaNs with NAs.
2026-03-30 21:17:59.539425 INFO::Removing potential empty rows and columns
2026-03-30 21:17:59.540518 INFO::Found  0  missing values.
2026-03-30 21:17:59.543573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:17:59.544131 INFO::Done
2026-03-30 21:17:59.544688 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:17:59.572344 INFO::Starting hierarchical adjustment
2026-03-30 21:17:59.573838 INFO::Found  2  batches.
2026-03-30 21:17:59.574424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:17:59.57501 INFO::Using default BPPARAM
2026-03-30 21:17:59.575529 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:17:59.576457 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-30 21:17:59.590868 INFO::Done
2026-03-30 21:17:59.591505 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:17:59.59351 INFO::ASW Batch was -0.0180497054759558 prior to batch effect correction and is now -0.113185124224452 .
2026-03-30 21:17:59.594284 INFO::Total function execution time is  0.0565392971038818  s and adjustment time is  0.0172266960144043 s ( 30.47 )
2026-03-30 21:17:59.595317 INFO::Formatting Data.
2026-03-30 21:17:59.595887 INFO::Replacing NaNs with NAs.
2026-03-30 21:17:59.59673 INFO::Removing potential empty rows and columns
2026-03-30 21:17:59.597683 INFO::Found  0  missing values.
2026-03-30 21:17:59.600324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:17:59.600831 INFO::Done
2026-03-30 21:17:59.601315 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:17:59.603262 INFO::Starting hierarchical adjustment
2026-03-30 21:17:59.603939 INFO::Found  2  batches.
2026-03-30 21:17:59.60444 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:17:59.605006 INFO::Using default BPPARAM
2026-03-30 21:17:59.605492 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:17:59.606345 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-30 21:17:59.620039 INFO::Done
2026-03-30 21:17:59.620635 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:17:59.622472 INFO::ASW Batch was -0.0180497054759558 prior to batch effect correction and is now -0.113185124224452 .
2026-03-30 21:17:59.623185 INFO::Total function execution time is  0.0278751850128174  s and adjustment time is  0.0162334442138672 s ( 58.24 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-30 21:18:02.434833 INFO::Formatting Data.
2026-03-30 21:18:02.43563 INFO::Recognized SummarizedExperiment
2026-03-30 21:18:02.436096 INFO::Typecasting input to dataframe.
2026-03-30 21:18:02.468934 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:02.470221 INFO::Removing potential empty rows and columns
2026-03-30 21:18:02.474165 INFO::Found  0  missing values.
2026-03-30 21:18:02.481474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:02.482149 INFO::Done
2026-03-30 21:18:02.482704 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:02.486471 INFO::Starting hierarchical adjustment
2026-03-30 21:18:02.487202 INFO::Found  2  batches.
2026-03-30 21:18:02.48773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:02.48886 INFO::Using default BPPARAM
2026-03-30 21:18:02.489409 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:02.490489 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-30 21:18:02.549153 INFO::Done
2026-03-30 21:18:02.549894 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:02.553513 INFO::ASW Batch was -0.00744178676560997 prior to batch effect correction and is now -0.0934455810799474 .
2026-03-30 21:18:02.554383 INFO::Total function execution time is  0.119960308074951  s and adjustment time is  0.0620737075805664 s ( 51.75 )
Warning: stack imbalance in '{', 73 then 75
2026-03-30 21:18:02.574534 INFO::Formatting Data.
2026-03-30 21:18:02.575377 INFO::Recognized SummarizedExperiment
2026-03-30 21:18:02.575928 INFO::Typecasting input to dataframe.
2026-03-30 21:18:02.585395 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:02.586699 INFO::Removing potential empty rows and columns
2026-03-30 21:18:02.590449 INFO::Found  0  missing values.
2026-03-30 21:18:02.597813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:02.598495 INFO::Done
2026-03-30 21:18:02.599025 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:02.602618 INFO::Starting hierarchical adjustment
2026-03-30 21:18:02.603369 INFO::Found  2  batches.
2026-03-30 21:18:02.603885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:02.604506 INFO::Using default BPPARAM
2026-03-30 21:18:02.605026 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:02.60601 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-30 21:18:02.631346 INFO::Done
2026-03-30 21:18:02.632058 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:02.635696 INFO::ASW Batch was 0.00935409592211983 prior to batch effect correction and is now 0.00935409592211983 .
2026-03-30 21:18:02.636567 INFO::Total function execution time is  0.0620312690734863  s and adjustment time is  0.0280814170837402 s ( 45.27 )
2026-03-30 21:18:02.655581 INFO::Formatting Data.
2026-03-30 21:18:02.656428 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:02.657365 INFO::Removing potential empty rows and columns
2026-03-30 21:18:02.658419 INFO::Found  0  missing values.
2026-03-30 21:18:02.661422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:02.661992 INFO::Done
2026-03-30 21:18:02.66253 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:02.66457 INFO::Starting hierarchical adjustment
2026-03-30 21:18:02.665267 INFO::Found  3  batches.
2026-03-30 21:18:02.665796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:02.666394 INFO::Using default BPPARAM
2026-03-30 21:18:02.666903 INFO::Processing subtree level 1
2026-03-30 21:18:02.795969 INFO::Adjusting the last 1 batches sequentially
2026-03-30 21:18:02.797723 INFO::Done
2026-03-30 21:18:02.798347 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:02.800763 INFO::ASW Batch was -0.00242867786340325 prior to batch effect correction and is now -0.164385485282875 .
2026-03-30 21:18:02.801692 INFO::Total function execution time is  0.146258115768433  s and adjustment time is  0.132569551467896 s ( 90.64 )
2026-03-30 21:18:02.815998 INFO::Skipping initial DF formatting
2026-03-30 21:18:02.816717 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:02.820965 INFO::Starting hierarchical adjustment
2026-03-30 21:18:02.821806 INFO::Found  5  batches.
2026-03-30 21:18:02.822371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:02.822983 INFO::Using default BPPARAM
2026-03-30 21:18:02.823535 INFO::Processing subtree level 1
2026-03-30 21:18:03.085905 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:03.087712 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-30 21:18:03.108143 INFO::Done
2026-03-30 21:18:03.108982 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:03.113514 INFO::ASW Batch was 0.550852172270859 prior to batch effect correction and is now 0.550852172270859 .
2026-03-30 21:18:03.114154 INFO::ASW Label was 0.310239211930557 prior to batch effect correction and is now 0.310239211930557 .
2026-03-30 21:18:03.115042 INFO::Total function execution time is  0.299099445343018  s and adjustment time is  0.286458492279053 s ( 95.77 )
2026-03-30 21:18:04.143513 INFO::Formatting Data.
2026-03-30 21:18:04.144216 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.144994 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.14582 INFO::Found  0  missing values.
2026-03-30 21:18:04.149053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.149519 INFO::Done
2026-03-30 21:18:04.14994 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.152468 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.153057 INFO::Found  5  batches.
2026-03-30 21:18:04.153508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.153999 INFO::Using default BPPARAM
2026-03-30 21:18:04.154444 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.

2026-03-30 21:18:04.280317 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.2832 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-30 21:18:04.299852 INFO::Done
2026-03-30 21:18:04.300569 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.303828 INFO::ASW Batch was 0.478538051422434 prior to batch effect correction and is now -0.0775146971594154 .
2026-03-30 21:18:04.304457 INFO::ASW Label was 0.225496577453674 prior to batch effect correction and is now 0.843298117880613 .
2026-03-30 21:18:04.305251 INFO::Total function execution time is  0.161853551864624  s and adjustment time is  0.146880149841309 s ( 90.75 )
2026-03-30 21:18:04.306103 INFO::Formatting Data.
2026-03-30 21:18:04.30674 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.307628 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.308675 INFO::Found  0  missing values.
2026-03-30 21:18:04.312662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.313199 INFO::Done
2026-03-30 21:18:04.313717 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.316625 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.317349 INFO::Found  5  batches.
2026-03-30 21:18:04.317875 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.318484 INFO::Using default BPPARAM
2026-03-30 21:18:04.31899 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.

2026-03-30 21:18:04.43636 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.438076 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-30 21:18:04.45472 INFO::Done
2026-03-30 21:18:04.455521 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.459091 INFO::ASW Batch was 0.478538051422434 prior to batch effect correction and is now -0.0775146971594154 .
2026-03-30 21:18:04.459793 INFO::ASW Label was 0.225496577453674 prior to batch effect correction and is now 0.843298117880613 .
2026-03-30 21:18:04.460734 INFO::Total function execution time is  0.154615163803101  s and adjustment time is  0.137508153915405 s ( 88.94 )
2026-03-30 21:18:04.47533 INFO::Formatting Data.
2026-03-30 21:18:04.476178 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.477168 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.478255 INFO::Found  0  missing values.
2026-03-30 21:18:04.482308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.482878 INFO::Done
2026-03-30 21:18:04.483407 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.486413 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.48712 INFO::Found  5  batches.
2026-03-30 21:18:04.487671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.488283 INFO::Using default BPPARAM
2026-03-30 21:18:04.488815 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.

2026-03-30 21:18:04.605475 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.607163 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-30 21:18:04.623417 INFO::Done
2026-03-30 21:18:04.624184 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.627638 INFO::ASW Batch was 0.600483634291055 prior to batch effect correction and is now -0.0198756109494976 .
2026-03-30 21:18:04.628261 INFO::ASW Label was 0.238805579913372 prior to batch effect correction and is now 0.765230171812551 .
2026-03-30 21:18:04.629092 INFO::Total function execution time is  0.15385913848877  s and adjustment time is  0.136377573013306 s ( 88.64 )
2026-03-30 21:18:04.629923 INFO::Formatting Data.
2026-03-30 21:18:04.630552 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.631443 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.632453 INFO::Found  0  missing values.
2026-03-30 21:18:04.636408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.636957 INFO::Done
2026-03-30 21:18:04.637476 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.641226 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.642215 INFO::Found  5  batches.
2026-03-30 21:18:04.642774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.643404 INFO::Using default BPPARAM
2026-03-30 21:18:04.643928 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.

2026-03-30 21:18:04.756358 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.757931 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-30 21:18:04.772358 INFO::Done
2026-03-30 21:18:04.773019 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.776075 INFO::ASW Batch was 0.600483634291055 prior to batch effect correction and is now -0.0198756109494976 .
2026-03-30 21:18:04.776644 INFO::ASW Label was 0.238805579913372 prior to batch effect correction and is now 0.765230171812551 .
2026-03-30 21:18:04.777416 INFO::Total function execution time is  0.147501707077026  s and adjustment time is  0.130307197570801 s ( 88.34 )
2026-03-30 21:18:04.790028 INFO::Formatting Data.
2026-03-30 21:18:04.79076 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.791615 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.792572 INFO::Found  0  missing values.
2026-03-30 21:18:04.795055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.79557 INFO::Done
2026-03-30 21:18:04.796057 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.798778 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.799454 INFO::Found  2  batches.
2026-03-30 21:18:04.799942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.800526 INFO::Using default BPPARAM
2026-03-30 21:18:04.801019 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.801848 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-30 21:18:04.815154 INFO::Done
2026-03-30 21:18:04.81577 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.818516 INFO::ASW Batch was 0.741857544046902 prior to batch effect correction and is now -0.00352161573936967 .
2026-03-30 21:18:04.819058 INFO::ASW Label was 0.318053217228687 prior to batch effect correction and is now 0.905285583005983 .
2026-03-30 21:18:04.819763 INFO::Total function execution time is  0.0298213958740234  s and adjustment time is  0.0158390998840332 s ( 53.11 )
2026-03-30 21:18:04.820481 INFO::Formatting Data.
2026-03-30 21:18:04.821042 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.821838 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.822725 INFO::Found  0  missing values.
2026-03-30 21:18:04.825144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.825662 INFO::Done
2026-03-30 21:18:04.826134 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.828792 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.829446 INFO::Found  2  batches.
2026-03-30 21:18:04.829932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.830539 INFO::Using default BPPARAM
2026-03-30 21:18:04.831015 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.831859 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-30 21:18:04.844989 INFO::Done
2026-03-30 21:18:04.845609 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.848295 INFO::ASW Batch was 0.741857544046902 prior to batch effect correction and is now -0.00352161573936967 .
2026-03-30 21:18:04.848845 INFO::ASW Label was 0.318053217228687 prior to batch effect correction and is now 0.905285583005983 .
2026-03-30 21:18:04.84956 INFO::Total function execution time is  0.0290894508361816  s and adjustment time is  0.0156731605529785 s ( 53.88 )
2026-03-30 21:18:04.859823 INFO::Formatting Data.
2026-03-30 21:18:04.860534 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.861419 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.862286 INFO::Found  0  missing values.
2026-03-30 21:18:04.864218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.864736 INFO::Done
2026-03-30 21:18:04.865205 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.866956 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.867603 INFO::Found  2  batches.
2026-03-30 21:18:04.868085 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.868652 INFO::Using default BPPARAM
2026-03-30 21:18:04.869136 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.86996 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-30 21:18:04.899033 INFO::Done
2026-03-30 21:18:04.899738 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.901602 INFO::ASW Batch was 0.131208575472401 prior to batch effect correction and is now -0.125866597652706 .
2026-03-30 21:18:04.902378 INFO::Total function execution time is  0.0426120758056641  s and adjustment time is  0.0315220355987549 s ( 73.97 )
2026-03-30 21:18:04.913689 INFO::Formatting Data.
2026-03-30 21:18:04.914434 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.915255 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.91621 INFO::Found  0  missing values.
2026-03-30 21:18:04.917289 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.
2026-03-30 21:18:04.921661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.922194 INFO::Done
2026-03-30 21:18:04.922686 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.925582 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.926284 INFO::Found  2  batches.
2026-03-30 21:18:04.926798 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.92739 INFO::Using default BPPARAM
2026-03-30 21:18:04.927907 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.928785 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-30 21:18:04.944469 INFO::Done
2026-03-30 21:18:04.945105 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.947902 INFO::ASW Batch was 0.786378896502288 prior to batch effect correction and is now 0.029525457553356 .
2026-03-30 21:18:04.948483 INFO::ASW Label was 0.234234231766499 prior to batch effect correction and is now 0.783312596972566 .
2026-03-30 21:18:04.949219 INFO::Total function execution time is  0.0356192588806152  s and adjustment time is  0.0183401107788086 s ( 51.49 )
2026-03-30 21:18:04.949979 INFO::Formatting Data.
2026-03-30 21:18:04.950597 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:04.951471 INFO::Removing potential empty rows and columns
2026-03-30 21:18:04.952417 INFO::Found  0  missing values.
2026-03-30 21:18:04.953288 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.
2026-03-30 21:18:04.957609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:04.958141 INFO::Done
2026-03-30 21:18:04.958652 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:04.961546 INFO::Starting hierarchical adjustment
2026-03-30 21:18:04.962242 INFO::Found  2  batches.
2026-03-30 21:18:04.962752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:04.963367 INFO::Using default BPPARAM
2026-03-30 21:18:04.963854 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:04.964757 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-30 21:18:04.980624 INFO::Done
2026-03-30 21:18:04.981311 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:04.984116 INFO::ASW Batch was 0.786378896502288 prior to batch effect correction and is now 0.029525457553356 .
2026-03-30 21:18:04.984694 INFO::ASW Label was 0.234234231766499 prior to batch effect correction and is now 0.783312596972566 .
2026-03-30 21:18:04.985526 INFO::Total function execution time is  0.0355460643768311  s and adjustment time is  0.0185089111328125 s ( 52.07 )
2026-03-30 21:18:05.204475 INFO::Formatting Data.
2026-03-30 21:18:05.205446 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:05.206435 INFO::Removing potential empty rows and columns
2026-03-30 21:18:05.207543 INFO::Found  0  missing values.
2026-03-30 21:18:05.210614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:05.211149 INFO::Done
2026-03-30 21:18:05.211689 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:05.214026 INFO::Starting hierarchical adjustment
2026-03-30 21:18:05.214755 INFO::Found  3  batches.
2026-03-30 21:18:05.215268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:05.215955 INFO::Using default BPPARAM
2026-03-30 21:18:05.216501 INFO::Processing subtree level 1
2026-03-30 21:18:05.308666 INFO::Adjusting the last 1 batches sequentially
2026-03-30 21:18:05.310354 INFO::Done
2026-03-30 21:18:05.310972 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:05.313356 INFO::ASW Batch was -0.0773998736470911 prior to batch effect correction and is now -0.0773998736470911 .
2026-03-30 21:18:05.314311 INFO::Total function execution time is  0.110212564468384  s and adjustment time is  0.0957143306732178 s ( 86.85 )
2026-03-30 21:18:05.315416 INFO::Formatting Data.
2026-03-30 21:18:05.316056 INFO::Typecasting input to dataframe.
2026-03-30 21:18:05.316834 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:05.317738 INFO::Removing potential empty rows and columns
2026-03-30 21:18:05.318885 INFO::Found  0  missing values.
2026-03-30 21:18:05.322083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:05.322663 INFO::Done
2026-03-30 21:18:05.323181 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:05.325232 INFO::Starting hierarchical adjustment
2026-03-30 21:18:05.325947 INFO::Found  3  batches.
2026-03-30 21:18:05.326509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:05.32722 INFO::Using default BPPARAM
2026-03-30 21:18:05.327774 INFO::Processing subtree level 1
2026-03-30 21:18:05.41331 INFO::Adjusting the last 1 batches sequentially
2026-03-30 21:18:05.415116 INFO::Done
2026-03-30 21:18:05.415792 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:05.418311 INFO::ASW Batch was -0.0773998736470911 prior to batch effect correction and is now -0.0773998736470911 .
2026-03-30 21:18:05.419238 INFO::Total function execution time is  0.103819608688354  s and adjustment time is  0.089285135269165 s ( 86 )
2026-03-30 21:18:05.43246 INFO::Formatting Data.
2026-03-30 21:18:05.43324 INFO::Typecasting input to dataframe.
2026-03-30 21:18:05.434219 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:05.435154 INFO::Removing potential empty rows and columns
2026-03-30 21:18:05.436248 INFO::Found  0  missing values.
2026-03-30 21:18:05.439265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:05.439824 INFO::Done
2026-03-30 21:18:05.440361 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:05.442484 INFO::Starting hierarchical adjustment
2026-03-30 21:18:05.443216 INFO::Found  3  batches.
2026-03-30 21:18:05.443753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:05.444395 INFO::Using default BPPARAM
2026-03-30 21:18:05.444931 INFO::Processing subtree level 1
2026-03-30 21:18:05.53247 INFO::Adjusting the last 1 batches sequentially
2026-03-30 21:18:05.534191 INFO::Done
2026-03-30 21:18:05.534848 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:05.537308 INFO::ASW Batch was -0.0335939793581919 prior to batch effect correction and is now -0.0335939793581919 .
2026-03-30 21:18:05.538213 INFO::Total function execution time is  0.105810880661011  s and adjustment time is  0.0911054611206055 s ( 86.1 )
2026-03-30 21:18:05.674905 INFO::Formatting Data.
2026-03-30 21:18:05.675709 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:05.676844 INFO::Removing potential empty rows and columns
2026-03-30 21:18:05.679622 INFO::Found  1000  missing values.
2026-03-30 21:18:05.69935 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:05.700082 INFO::Done
2026-03-30 21:18:05.700646 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:05.706146 INFO::Starting hierarchical adjustment
2026-03-30 21:18:05.706954 INFO::Found  10  batches.
2026-03-30 21:18:05.70752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:05.708165 INFO::Using default BPPARAM
2026-03-30 21:18:05.708721 INFO::Processing subtree level 1
2026-03-30 21:18:05.851632 INFO::Processing subtree level 2
2026-03-30 21:18:06.005493 INFO::Adjusting the last 1 batches sequentially
2026-03-30 21:18:06.007998 INFO::Done
2026-03-30 21:18:06.008899 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:06.01619 INFO::ASW Batch was 0.500517660898498 prior to batch effect correction and is now 0.500517660898498 .
2026-03-30 21:18:06.01715 INFO::ASW Label was 0.337488686693429 prior to batch effect correction and is now 0.337488686693429 .
2026-03-30 21:18:06.018392 INFO::Total function execution time is  0.343461990356445  s and adjustment time is  0.30113673210144 s ( 87.68 )
2026-03-30 21:18:06.019595 INFO::Formatting Data.
2026-03-30 21:18:06.020469 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:06.022102 INFO::Removing potential empty rows and columns
2026-03-30 21:18:06.025762 INFO::Found  1000  missing values.
2026-03-30 21:18:06.059093 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:06.059971 INFO::Done
2026-03-30 21:18:06.06058 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:06.066502 INFO::Starting hierarchical adjustment
2026-03-30 21:18:06.06733 INFO::Found  10  batches.
2026-03-30 21:18:07.113403 INFO::Set up parallel execution backend with 2 workers
2026-03-30 21:18:07.11575 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-30 21:18:08.166839 INFO::Adjusting the last 2 batches sequentially
2026-03-30 21:18:08.168127 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-30 21:18:08.183365 INFO::Done
2026-03-30 21:18:08.18396 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:08.188315 INFO::ASW Batch was 0.500517660898498 prior to batch effect correction and is now 0.500517660898498 .
2026-03-30 21:18:08.188845 INFO::ASW Label was 0.337488686693429 prior to batch effect correction and is now 0.337488686693429 .
2026-03-30 21:18:08.189523 INFO::Total function execution time is  2.17003870010376  s and adjustment time is  2.11621999740601 s ( 97.52 )
2026-03-30 21:18:08.324079 INFO::Formatting Data.
2026-03-30 21:18:08.324836 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.325711 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.326723 INFO::Found  0  missing values.
2026-03-30 21:18:08.330153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.330678 INFO::Done
2026-03-30 21:18:08.331157 INFO::Acquiring quality metrics before batch effect correction.
2026-03-30 21:18:08.333748 INFO::Starting hierarchical adjustment
2026-03-30 21:18:08.334417 INFO::Found  3  batches.
2026-03-30 21:18:08.334908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-30 21:18:08.335496 INFO::Using default BPPARAM
2026-03-30 21:18:08.335979 INFO::Processing subtree level 1
2026-03-30 21:18:08.435077 INFO::Adjusting the last 1 batches sequentially
2026-03-30 21:18:08.436736 INFO::Done
2026-03-30 21:18:08.437353 INFO::Acquiring quality metrics after batch effect correction.
2026-03-30 21:18:08.440327 INFO::ASW Batch was 0.147794946671487 prior to batch effect correction and is now -0.167559104178431 .
2026-03-30 21:18:08.440922 INFO::ASW Label was -0.200992334515577 prior to batch effect correction and is now -0.120053403374764 .
2026-03-30 21:18:08.441782 INFO::Total function execution time is  0.117741346359253  s and adjustment time is  0.102448225021362 s ( 87.01 )
2026-03-30 21:18:08.556039 INFO::Formatting Data.
2026-03-30 21:18:08.564967 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.566043 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.567097 INFO::Found  2  missing values.
2026-03-30 21:18:08.569811 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.570332 INFO::Done
2026-03-30 21:18:08.596719 INFO::Found NA in Reference column
2026-03-30 21:18:08.605866 INFO::Require at least two references per batch.
2026-03-30 21:18:08.62601 INFO::Formatting Data.
2026-03-30 21:18:08.626758 INFO::Recognized SummarizedExperiment
2026-03-30 21:18:08.627283 INFO::Typecasting input to dataframe.
2026-03-30 21:18:08.636566 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.637714 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.64103 INFO::Found  0  missing values.
2026-03-30 21:18:08.647432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.648049 INFO::Done
2026-03-30 21:18:08.663555 INFO::Formatting Data.
2026-03-30 21:18:08.664286 INFO::Recognized SummarizedExperiment
2026-03-30 21:18:08.66481 INFO::Typecasting input to dataframe.
2026-03-30 21:18:08.681264 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.682454 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.685797 INFO::Found  0  missing values.
2026-03-30 21:18:08.6958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.696457 INFO::Done
2026-03-30 21:18:08.711234 INFO::Formatting Data.
2026-03-30 21:18:08.71193 INFO::Recognized SummarizedExperiment
2026-03-30 21:18:08.71245 INFO::Typecasting input to dataframe.
2026-03-30 21:18:08.728379 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.729376 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.730377 INFO::Found  0  missing values.
2026-03-30 21:18:08.731223 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.
2026-03-30 21:18:08.735359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.735861 INFO::Done
2026-03-30 21:18:08.745408 INFO::Formatting Data.
2026-03-30 21:18:08.7461 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.746918 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.747856 INFO::Found  0  missing values.
2026-03-30 21:18:08.750605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.751109 INFO::Done
2026-03-30 21:18:08.761955 INFO::Formatting Data.
2026-03-30 21:18:08.762899 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.763927 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.765049 INFO::Found  0  missing values.
2026-03-30 21:18:08.767937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.768476 INFO::Done
2026-03-30 21:18:08.799409 INFO::Formatting Data.
2026-03-30 21:18:08.800303 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.801435 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.802672 INFO::Found  1  missing values.
2026-03-30 21:18:08.805479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.806009 INFO::Done
2026-03-30 21:18:08.825701 INFO::Formatting Data.
2026-03-30 21:18:08.826622 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.827563 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.828597 INFO::Found  2  missing values.
2026-03-30 21:18:08.829543 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.
2026-03-30 21:18:08.83191 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.832494 INFO::Done
2026-03-30 21:18:08.843163 INFO::Formatting Data.
2026-03-30 21:18:08.844059 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.844974 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.845934 INFO::Found  2  missing values.
2026-03-30 21:18:08.847647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.84821 INFO::Done
2026-03-30 21:18:08.85913 INFO::Formatting Data.
2026-03-30 21:18:08.859982 INFO::Typecasting input to dataframe.
2026-03-30 21:18:08.860808 INFO::Replacing NaNs with NAs.
2026-03-30 21:18:08.861663 INFO::Removing potential empty rows and columns
2026-03-30 21:18:08.86266 INFO::Found  0  missing values.
2026-03-30 21:18:08.865698 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-30 21:18:08.866255 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.170   3.622  20.529

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT24.264 1.22517.946
compute_asw0.0260.0010.026
count_existing0.0120.0010.014
generate_data_covariables0.0110.0020.013
generate_dataset0.0110.0020.013