Yannis Schumann
| Snapshot Date: 2026-03-26 13:40 -0400 (Thu, 26 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-27 11:33 -0400 (Fri, 27 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4880 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4577 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 170/2372 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-03-26 18:23:12 -0400 (Thu, 26 Mar 2026) |
| EndedAt: 2026-03-26 18:23:44 -0400 (Thu, 26 Mar 2026) |
| EllapsedTime: 32.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-03-20 r89666)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-26 22:23:12 UTC
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 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 9.806 0.413 7.008
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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")
2026-03-26 18:23:36.687061 INFO::Formatting Data.
2026-03-26 18:23:36.68846 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:36.69239 INFO::Removing potential empty rows and columns
2026-03-26 18:23:36.790421 INFO::Found 0 missing values.
2026-03-26 18:23:36.791674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:36.791989 INFO::Done
2026-03-26 18:23:36.792275 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:36.797933 INFO::Starting hierarchical adjustment
2026-03-26 18:23:36.798354 INFO::Found 3 batches.
2026-03-26 18:23:36.798668 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:36.799143 INFO::Using default BPPARAM
2026-03-26 18:23:36.799424 INFO::Processing subtree level 1
2026-03-26 18:23:36.871839 INFO::Adjusting the last 1 batches sequentially
2026-03-26 18:23:36.873113 INFO::Done
2026-03-26 18:23:36.873528 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:36.874707 INFO::ASW Batch was -0.0570673042783333 prior to batch effect correction and is now -0.0570673042783333 .
2026-03-26 18:23:36.875265 INFO::Total function execution time is 0.188541889190674 s and adjustment time is 0.074815034866333 s ( 39.68 )
2026-03-26 18:23:36.884885 INFO::Formatting Data.
2026-03-26 18:23:36.88534 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:36.88578 INFO::Removing potential empty rows and columns
2026-03-26 18:23:36.886365 INFO::Found 0 missing values.
2026-03-26 18:23:36.886919 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.
2026-03-26 18:23:36.891946 INFO::Formatting Data.
2026-03-26 18:23:36.892349 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:36.892847 INFO::Removing potential empty rows and columns
2026-03-26 18:23:36.893379 INFO::Found 0 missing values.
2026-03-26 18:23:36.893814 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.
2026-03-26 18:23:36.901842 INFO::Formatting Data.
2026-03-26 18:23:36.902269 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:36.902767 INFO::Removing potential empty rows and columns
2026-03-26 18:23:36.903291 INFO::Found 0 missing values.
2026-03-26 18:23:36.903769 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.
2026-03-26 18:23:36.905932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:36.906284 INFO::Done
2026-03-26 18:23:36.906665 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:36.908292 INFO::Starting hierarchical adjustment
2026-03-26 18:23:36.908723 INFO::Found 2 batches.
2026-03-26 18:23:36.909492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:36.909902 INFO::Using default BPPARAM
2026-03-26 18:23:36.910343 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:36.910825 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 18:23:36.922824 INFO::Done
2026-03-26 18:23:36.92332 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:36.924621 INFO::ASW Batch was -0.0738859396551682 prior to batch effect correction and is now -0.117705937233645 .
2026-03-26 18:23:36.925221 INFO::Total function execution time is 0.0233948230743408 s and adjustment time is 0.0141220092773438 s ( 60.36 )
2026-03-26 18:23:36.927342 INFO::Formatting Data.
2026-03-26 18:23:36.927898 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:36.931766 INFO::Formatting Data.
2026-03-26 18:23:36.932204 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:36.932633 INFO::Removing potential empty rows and columns
2026-03-26 18:23:36.93311 INFO::Found 0 missing values.
2026-03-26 18:23:36.934225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:36.934554 INFO::Done
2026-03-26 18:23:36.934853 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:36.935694 INFO::Starting hierarchical adjustment
2026-03-26 18:23:36.936059 INFO::Found 2 batches.
2026-03-26 18:23:36.936333 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:36.936629 INFO::Using default BPPARAM
2026-03-26 18:23:36.936917 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:36.937343 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 18:23:36.943176 INFO::Done
2026-03-26 18:23:36.943581 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:36.944374 INFO::ASW Batch was -0.00308814540245421 prior to batch effect correction and is now -0.119950880916823 .
2026-03-26 18:23:36.944823 INFO::Total function execution time is 0.0130798816680908 s and adjustment time is 0.00715804100036621 s ( 54.73 )
2026-03-26 18:23:36.945305 INFO::Formatting Data.
2026-03-26 18:23:36.945644 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:36.946097 INFO::Removing potential empty rows and columns
2026-03-26 18:23:36.94657 INFO::Found 0 missing values.
2026-03-26 18:23:36.947789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:36.948144 INFO::Done
2026-03-26 18:23:36.948461 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:36.949359 INFO::Starting hierarchical adjustment
2026-03-26 18:23:36.949841 INFO::Found 2 batches.
2026-03-26 18:23:36.950173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:36.950514 INFO::Using default BPPARAM
2026-03-26 18:23:36.950809 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:36.951234 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 18:23:36.956946 INFO::Done
2026-03-26 18:23:36.957434 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:36.958289 INFO::ASW Batch was -0.00308814540245421 prior to batch effect correction and is now -0.119950880916823 .
2026-03-26 18:23:36.958672 INFO::Total function execution time is 0.0133709907531738 s and adjustment time is 0.0071418285369873 s ( 53.41 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-26 18:23:38.212654 INFO::Formatting Data.
2026-03-26 18:23:38.213124 INFO::Recognized SummarizedExperiment
2026-03-26 18:23:38.213414 INFO::Typecasting input to dataframe.
2026-03-26 18:23:38.223299 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.223847 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.225055 INFO::Found 0 missing values.
2026-03-26 18:23:38.227168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.227463 INFO::Done
2026-03-26 18:23:38.227719 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.228952 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.229248 INFO::Found 2 batches.
2026-03-26 18:23:38.229485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.229876 INFO::Using default BPPARAM
2026-03-26 18:23:38.23011 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.230475 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 18:23:38.246495 INFO::Done
2026-03-26 18:23:38.246911 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.2482 INFO::ASW Batch was -0.00137607353499863 prior to batch effect correction and is now -0.0926834626377784 .
2026-03-26 18:23:38.248591 INFO::Total function execution time is 0.036038875579834 s and adjustment time is 0.0172741413116455 s ( 47.93 )
Warning: stack imbalance in '{', 73 then 75
2026-03-26 18:23:38.254988 INFO::Formatting Data.
2026-03-26 18:23:38.255383 INFO::Recognized SummarizedExperiment
2026-03-26 18:23:38.255657 INFO::Typecasting input to dataframe.
2026-03-26 18:23:38.258818 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.259332 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.260601 INFO::Found 0 missing values.
2026-03-26 18:23:38.262856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.263159 INFO::Done
2026-03-26 18:23:38.26342 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.264765 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.265102 INFO::Found 2 batches.
2026-03-26 18:23:38.265356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.265636 INFO::Using default BPPARAM
2026-03-26 18:23:38.265898 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.266308 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 18:23:38.274619 INFO::Done
2026-03-26 18:23:38.275032 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.276335 INFO::ASW Batch was -0.0128464125897647 prior to batch effect correction and is now -0.0128464125897647 .
2026-03-26 18:23:38.276728 INFO::Total function execution time is 0.0217368602752686 s and adjustment time is 0.00954914093017578 s ( 43.93 )
2026-03-26 18:23:38.283232 INFO::Formatting Data.
2026-03-26 18:23:38.283574 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.283932 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.284345 INFO::Found 0 missing values.
2026-03-26 18:23:38.285295 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.285578 INFO::Done
2026-03-26 18:23:38.285827 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.286504 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.286808 INFO::Found 3 batches.
2026-03-26 18:23:38.287062 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.287349 INFO::Using default BPPARAM
2026-03-26 18:23:38.287585 INFO::Processing subtree level 1
2026-03-26 18:23:38.388372 INFO::Adjusting the last 1 batches sequentially
2026-03-26 18:23:38.389493 INFO::Done
2026-03-26 18:23:38.389869 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.391213 INFO::ASW Batch was -0.0886605958049301 prior to batch effect correction and is now -0.166305032861885 .
2026-03-26 18:23:38.391708 INFO::Total function execution time is 0.108469009399414 s and adjustment time is 0.102715969085693 s ( 94.7 )
2026-03-26 18:23:38.399983 INFO::Skipping initial DF formatting
2026-03-26 18:23:38.400383 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.403289 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.403739 INFO::Found 5 batches.
2026-03-26 18:23:38.40405 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.404395 INFO::Using default BPPARAM
2026-03-26 18:23:38.404665 INFO::Processing subtree level 1
2026-03-26 18:23:38.470138 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.471135 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 18:23:38.479153 INFO::Done
2026-03-26 18:23:38.479705 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.48174 INFO::ASW Batch was 0.442354871307869 prior to batch effect correction and is now 0.442354871307869 .
2026-03-26 18:23:38.482126 INFO::ASW Label was 0.401708186475128 prior to batch effect correction and is now 0.401708186475128 .
2026-03-26 18:23:38.482706 INFO::Total function execution time is 0.0826971530914307 s and adjustment time is 0.0754599571228027 s ( 91.25 )
2026-03-26 18:23:38.491032 INFO::Formatting Data.
2026-03-26 18:23:38.491479 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.491985 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.492576 INFO::Found 0 missing values.
2026-03-26 18:23:38.494119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.49444 INFO::Done
2026-03-26 18:23:38.494829 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.496121 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.496576 INFO::Found 5 batches.
2026-03-26 18:23:38.496903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.497312 INFO::Using default BPPARAM
2026-03-26 18:23:38.497591 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.
2026-03-26 18:23:38.564168 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.565127 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 18:23:38.574689 INFO::Done
2026-03-26 18:23:38.575077 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.576274 INFO::ASW Batch was 0.607758706502597 prior to batch effect correction and is now -0.0584856508991851 .
2026-03-26 18:23:38.576571 INFO::ASW Label was 0.180690427327824 prior to batch effect correction and is now 0.69233611996746 .
2026-03-26 18:23:38.576956 INFO::Total function execution time is 0.0859630107879639 s and adjustment time is 0.0782091617584229 s ( 90.98 )
2026-03-26 18:23:38.577312 INFO::Formatting Data.
2026-03-26 18:23:38.577919 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.57871 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.579418 INFO::Found 0 missing values.
2026-03-26 18:23:38.581962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.582372 INFO::Done
2026-03-26 18:23:38.582718 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.585033 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.585823 INFO::Found 5 batches.
2026-03-26 18:23:38.586249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.586909 INFO::Using default BPPARAM
2026-03-26 18:23:38.58723 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.
2026-03-26 18:23:38.662419 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.663643 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 18:23:38.671712 INFO::Done
2026-03-26 18:23:38.672194 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.674663 INFO::ASW Batch was 0.607758706502597 prior to batch effect correction and is now -0.0584856508991851 .
2026-03-26 18:23:38.67528 INFO::ASW Label was 0.180690427327824 prior to batch effect correction and is now 0.69233611996746 .
2026-03-26 18:23:38.676444 INFO::Total function execution time is 0.099064826965332 s and adjustment time is 0.0860588550567627 s ( 86.87 )
2026-03-26 18:23:38.684316 INFO::Formatting Data.
2026-03-26 18:23:38.684856 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.685477 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.686194 INFO::Found 0 missing values.
2026-03-26 18:23:38.687737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.688127 INFO::Done
2026-03-26 18:23:38.688929 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.691699 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.692346 INFO::Found 5 batches.
2026-03-26 18:23:38.692838 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.693524 INFO::Using default BPPARAM
2026-03-26 18:23:38.693878 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.
2026-03-26 18:23:38.754885 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.756447 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 18:23:38.764575 INFO::Done
2026-03-26 18:23:38.765027 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.766612 INFO::ASW Batch was 0.349851488554327 prior to batch effect correction and is now -0.0289748044252199 .
2026-03-26 18:23:38.766963 INFO::ASW Label was 0.258518887135697 prior to batch effect correction and is now 0.781538683874806 .
2026-03-26 18:23:38.76751 INFO::Total function execution time is 0.0831830501556396 s and adjustment time is 0.0723669528961182 s ( 87 )
2026-03-26 18:23:38.767995 INFO::Formatting Data.
2026-03-26 18:23:38.768316 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.768771 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.769286 INFO::Found 0 missing values.
2026-03-26 18:23:38.77067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.770999 INFO::Done
2026-03-26 18:23:38.771303 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.772363 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.772729 INFO::Found 5 batches.
2026-03-26 18:23:38.773011 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.773371 INFO::Using default BPPARAM
2026-03-26 18:23:38.773674 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.
2026-03-26 18:23:38.833186 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.835061 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 18:23:38.847219 INFO::Done
2026-03-26 18:23:38.848135 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.849957 INFO::ASW Batch was 0.349851488554327 prior to batch effect correction and is now -0.0289748044252199 .
2026-03-26 18:23:38.85072 INFO::ASW Label was 0.258518887135697 prior to batch effect correction and is now 0.781538683874806 .
2026-03-26 18:23:38.851252 INFO::Total function execution time is 0.0832180976867676 s and adjustment time is 0.074470043182373 s ( 89.49 )
2026-03-26 18:23:38.863388 INFO::Formatting Data.
2026-03-26 18:23:38.863875 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.864666 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.865542 INFO::Found 0 missing values.
2026-03-26 18:23:38.867055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.867688 INFO::Done
2026-03-26 18:23:38.868099 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.870045 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.870776 INFO::Found 2 batches.
2026-03-26 18:23:38.871234 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.871935 INFO::Using default BPPARAM
2026-03-26 18:23:38.872385 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.873361 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 18:23:38.882478 INFO::Done
2026-03-26 18:23:38.882974 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.884865 INFO::ASW Batch was 0.586098823783273 prior to batch effect correction and is now 0.0633541202491744 .
2026-03-26 18:23:38.885628 INFO::ASW Label was 0.518702000238673 prior to batch effect correction and is now 0.882199154085588 .
2026-03-26 18:23:38.886159 INFO::Total function execution time is 0.022791862487793 s and adjustment time is 0.0116980075836182 s ( 51.33 )
2026-03-26 18:23:38.886682 INFO::Formatting Data.
2026-03-26 18:23:38.887232 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.887948 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.889189 INFO::Found 0 missing values.
2026-03-26 18:23:38.891027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.891385 INFO::Done
2026-03-26 18:23:38.891681 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.893236 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.893722 INFO::Found 2 batches.
2026-03-26 18:23:38.894319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.894786 INFO::Using default BPPARAM
2026-03-26 18:23:38.895136 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.896005 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 18:23:38.904815 INFO::Done
2026-03-26 18:23:38.905426 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.906924 INFO::ASW Batch was 0.586098823783273 prior to batch effect correction and is now 0.0633541202491744 .
2026-03-26 18:23:38.907439 INFO::ASW Label was 0.518702000238673 prior to batch effect correction and is now 0.882199154085588 .
2026-03-26 18:23:38.908157 INFO::Total function execution time is 0.0214431285858154 s and adjustment time is 0.0111417770385742 s ( 51.96 )
2026-03-26 18:23:38.916397 INFO::Formatting Data.
2026-03-26 18:23:38.917123 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.917633 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.918188 INFO::Found 0 missing values.
2026-03-26 18:23:38.919584 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.920149 INFO::Done
2026-03-26 18:23:38.9206 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.921783 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.922286 INFO::Found 2 batches.
2026-03-26 18:23:38.923001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.924193 INFO::Using default BPPARAM
2026-03-26 18:23:38.925118 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.926304 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 18:23:38.945975 INFO::Done
2026-03-26 18:23:38.946828 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.94863 INFO::ASW Batch was -0.0576099859260617 prior to batch effect correction and is now -0.118900369406228 .
2026-03-26 18:23:38.949576 INFO::Total function execution time is 0.033221960067749 s and adjustment time is 0.0237569808959961 s ( 71.51 )
2026-03-26 18:23:38.955546 INFO::Formatting Data.
2026-03-26 18:23:38.956021 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.956479 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.956947 INFO::Found 0 missing values.
2026-03-26 18:23:38.957578 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.
2026-03-26 18:23:38.959147 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.959485 INFO::Done
2026-03-26 18:23:38.959781 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.960901 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.961263 INFO::Found 2 batches.
2026-03-26 18:23:38.961533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.961834 INFO::Using default BPPARAM
2026-03-26 18:23:38.962086 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.962472 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 18:23:38.968003 INFO::Done
2026-03-26 18:23:38.968388 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.969444 INFO::ASW Batch was 0.384968334691215 prior to batch effect correction and is now -0.00026281227743862 .
2026-03-26 18:23:38.969782 INFO::ASW Label was 0.667889256021587 prior to batch effect correction and is now 0.907840350659066 .
2026-03-26 18:23:38.970177 INFO::Total function execution time is 0.0146758556365967 s and adjustment time is 0.0067908763885498 s ( 46.27 )
2026-03-26 18:23:38.970558 INFO::Formatting Data.
2026-03-26 18:23:38.970848 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:38.971223 INFO::Removing potential empty rows and columns
2026-03-26 18:23:38.971671 INFO::Found 0 missing values.
2026-03-26 18:23:38.972055 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.
2026-03-26 18:23:38.973479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:38.973786 INFO::Done
2026-03-26 18:23:38.974051 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:38.975059 INFO::Starting hierarchical adjustment
2026-03-26 18:23:38.97539 INFO::Found 2 batches.
2026-03-26 18:23:38.975655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:38.97595 INFO::Using default BPPARAM
2026-03-26 18:23:38.976199 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:38.97657 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 18:23:38.982086 INFO::Done
2026-03-26 18:23:38.982483 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:38.983535 INFO::ASW Batch was 0.384968334691215 prior to batch effect correction and is now -0.00026281227743862 .
2026-03-26 18:23:38.983843 INFO::ASW Label was 0.667889256021587 prior to batch effect correction and is now 0.907840350659066 .
2026-03-26 18:23:38.984247 INFO::Total function execution time is 0.0136711597442627 s and adjustment time is 0.00673007965087891 s ( 49.23 )
2026-03-26 18:23:39.09334 INFO::Formatting Data.
2026-03-26 18:23:39.093835 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:39.094307 INFO::Removing potential empty rows and columns
2026-03-26 18:23:39.094814 INFO::Found 0 missing values.
2026-03-26 18:23:39.095905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:39.096212 INFO::Done
2026-03-26 18:23:39.096499 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:39.097353 INFO::Starting hierarchical adjustment
2026-03-26 18:23:39.097736 INFO::Found 3 batches.
2026-03-26 18:23:39.098016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:39.098397 INFO::Using default BPPARAM
2026-03-26 18:23:39.098683 INFO::Processing subtree level 1
2026-03-26 18:23:39.163901 INFO::Adjusting the last 1 batches sequentially
2026-03-26 18:23:39.16659 INFO::Done
2026-03-26 18:23:39.167098 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:39.169442 INFO::ASW Batch was -0.050793763417393 prior to batch effect correction and is now -0.050793763417393 .
2026-03-26 18:23:39.170454 INFO::Total function execution time is 0.0770721435546875 s and adjustment time is 0.0688800811767578 s ( 89.37 )
2026-03-26 18:23:39.171311 INFO::Formatting Data.
2026-03-26 18:23:39.171928 INFO::Typecasting input to dataframe.
2026-03-26 18:23:39.172539 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:39.173301 INFO::Removing potential empty rows and columns
2026-03-26 18:23:39.174425 INFO::Found 0 missing values.
2026-03-26 18:23:39.177139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:39.177582 INFO::Done
2026-03-26 18:23:39.178164 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:39.179309 INFO::Starting hierarchical adjustment
2026-03-26 18:23:39.179841 INFO::Found 3 batches.
2026-03-26 18:23:39.18033 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:39.180779 INFO::Using default BPPARAM
2026-03-26 18:23:39.181321 INFO::Processing subtree level 1
2026-03-26 18:23:39.237822 INFO::Adjusting the last 1 batches sequentially
2026-03-26 18:23:39.239478 INFO::Done
2026-03-26 18:23:39.23999 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:39.241732 INFO::ASW Batch was -0.050793763417393 prior to batch effect correction and is now -0.050793763417393 .
2026-03-26 18:23:39.24243 INFO::Total function execution time is 0.071112871170044 s and adjustment time is 0.059704065322876 s ( 83.96 )
2026-03-26 18:23:39.250335 INFO::Formatting Data.
2026-03-26 18:23:39.250834 INFO::Typecasting input to dataframe.
2026-03-26 18:23:39.251419 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:39.251989 INFO::Removing potential empty rows and columns
2026-03-26 18:23:39.252606 INFO::Found 0 missing values.
2026-03-26 18:23:39.253943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:39.254293 INFO::Done
2026-03-26 18:23:39.254622 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:39.255526 INFO::Starting hierarchical adjustment
2026-03-26 18:23:39.25594 INFO::Found 3 batches.
2026-03-26 18:23:39.25625 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:39.256636 INFO::Using default BPPARAM
2026-03-26 18:23:39.256958 INFO::Processing subtree level 1
2026-03-26 18:23:39.30831 INFO::Adjusting the last 1 batches sequentially
2026-03-26 18:23:39.310055 INFO::Done
2026-03-26 18:23:39.310515 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:39.312427 INFO::ASW Batch was -0.0767417634793092 prior to batch effect correction and is now -0.0767417634793092 .
2026-03-26 18:23:39.313307 INFO::Total function execution time is 0.0629560947418213 s and adjustment time is 0.0541059970855713 s ( 85.94 )
2026-03-26 18:23:39.413364 INFO::Formatting Data.
2026-03-26 18:23:39.41388 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:39.414519 INFO::Removing potential empty rows and columns
2026-03-26 18:23:39.416076 INFO::Found 1000 missing values.
2026-03-26 18:23:39.426811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:39.427285 INFO::Done
2026-03-26 18:23:39.427724 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:39.430841 INFO::Starting hierarchical adjustment
2026-03-26 18:23:39.43131 INFO::Found 10 batches.
2026-03-26 18:23:39.431638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:39.43208 INFO::Using default BPPARAM
2026-03-26 18:23:39.432421 INFO::Processing subtree level 1
2026-03-26 18:23:39.539984 INFO::Processing subtree level 2
2026-03-26 18:23:39.628664 INFO::Adjusting the last 1 batches sequentially
2026-03-26 18:23:39.630928 INFO::Done
2026-03-26 18:23:39.631361 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:39.634776 INFO::ASW Batch was 0.472333318205108 prior to batch effect correction and is now 0.472333318205108 .
2026-03-26 18:23:39.635232 INFO::ASW Label was 0.337177629332068 prior to batch effect correction and is now 0.337177629332068 .
2026-03-26 18:23:39.635929 INFO::Total function execution time is 0.222582101821899 s and adjustment time is 0.199664831161499 s ( 89.7 )
2026-03-26 18:23:39.636434 INFO::Formatting Data.
2026-03-26 18:23:39.636808 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:39.637518 INFO::Removing potential empty rows and columns
2026-03-26 18:23:39.639124 INFO::Found 1000 missing values.
2026-03-26 18:23:39.650984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:39.651597 INFO::Done
2026-03-26 18:23:39.652191 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:39.655061 INFO::Starting hierarchical adjustment
2026-03-26 18:23:39.655579 INFO::Found 10 batches.
2026-03-26 18:23:40.0506 INFO::Set up parallel execution backend with 2 workers
2026-03-26 18:23:40.05114 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-26 18:23:40.631717 INFO::Adjusting the last 2 batches sequentially
2026-03-26 18:23:40.632667 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 18:23:40.638926 INFO::Done
2026-03-26 18:23:40.639375 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:40.64132 INFO::ASW Batch was 0.472333318205108 prior to batch effect correction and is now 0.472333318205108 .
2026-03-26 18:23:40.641667 INFO::ASW Label was 0.337177629332068 prior to batch effect correction and is now 0.337177629332068 .
2026-03-26 18:23:40.64204 INFO::Total function execution time is 1.00562691688538 s and adjustment time is 0.983415126800537 s ( 97.79 )
2026-03-26 18:23:40.762112 INFO::Formatting Data.
2026-03-26 18:23:40.76254 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:40.762978 INFO::Removing potential empty rows and columns
2026-03-26 18:23:40.763568 INFO::Found 0 missing values.
2026-03-26 18:23:40.765089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:40.765456 INFO::Done
2026-03-26 18:23:40.765759 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 18:23:40.766879 INFO::Starting hierarchical adjustment
2026-03-26 18:23:40.767243 INFO::Found 3 batches.
2026-03-26 18:23:40.767515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 18:23:40.767827 INFO::Using default BPPARAM
2026-03-26 18:23:40.768246 INFO::Processing subtree level 1
2026-03-26 18:23:40.831318 INFO::Adjusting the last 1 batches sequentially
2026-03-26 18:23:40.832742 INFO::Done
2026-03-26 18:23:40.833334 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 18:23:40.835275 INFO::ASW Batch was 0.280070361791955 prior to batch effect correction and is now -0.186485167347695 .
2026-03-26 18:23:40.835861 INFO::ASW Label was -0.187293695355682 prior to batch effect correction and is now 0.0645734122714351 .
2026-03-26 18:23:40.836476 INFO::Total function execution time is 0.0743460655212402 s and adjustment time is 0.065546989440918 s ( 88.16 )
2026-03-26 18:23:40.894514 INFO::Formatting Data.
2026-03-26 18:23:40.895077 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:40.89558 INFO::Removing potential empty rows and columns
2026-03-26 18:23:40.896151 INFO::Found 2 missing values.
2026-03-26 18:23:40.897286 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:40.897611 INFO::Done
2026-03-26 18:23:40.911694 INFO::Found NA in Reference column
2026-03-26 18:23:40.916637 INFO::Require at least two references per batch.
2026-03-26 18:23:40.925757 INFO::Formatting Data.
2026-03-26 18:23:40.926235 INFO::Recognized SummarizedExperiment
2026-03-26 18:23:40.926572 INFO::Typecasting input to dataframe.
2026-03-26 18:23:40.930397 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:40.93099 INFO::Removing potential empty rows and columns
2026-03-26 18:23:40.93237 INFO::Found 0 missing values.
2026-03-26 18:23:40.934863 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:40.935213 INFO::Done
2026-03-26 18:23:40.941692 INFO::Formatting Data.
2026-03-26 18:23:40.942218 INFO::Recognized SummarizedExperiment
2026-03-26 18:23:40.942563 INFO::Typecasting input to dataframe.
2026-03-26 18:23:40.949881 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:40.950585 INFO::Removing potential empty rows and columns
2026-03-26 18:23:40.952011 INFO::Found 0 missing values.
2026-03-26 18:23:40.956114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:40.956507 INFO::Done
2026-03-26 18:23:40.962421 INFO::Formatting Data.
2026-03-26 18:23:40.962858 INFO::Recognized SummarizedExperiment
2026-03-26 18:23:40.963212 INFO::Typecasting input to dataframe.
2026-03-26 18:23:40.96881 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:40.969338 INFO::Removing potential empty rows and columns
2026-03-26 18:23:40.969859 INFO::Found 0 missing values.
2026-03-26 18:23:40.970351 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.
2026-03-26 18:23:40.971989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:40.972333 INFO::Done
2026-03-26 18:23:40.976994 INFO::Formatting Data.
2026-03-26 18:23:40.977393 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:40.977858 INFO::Removing potential empty rows and columns
2026-03-26 18:23:40.978363 INFO::Found 0 missing values.
2026-03-26 18:23:40.979495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:40.979833 INFO::Done
2026-03-26 18:23:40.985374 INFO::Formatting Data.
2026-03-26 18:23:40.985805 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:40.986262 INFO::Removing potential empty rows and columns
2026-03-26 18:23:40.986843 INFO::Found 0 missing values.
2026-03-26 18:23:40.9879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:40.988242 INFO::Done
2026-03-26 18:23:41.002363 INFO::Formatting Data.
2026-03-26 18:23:41.002908 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:41.003511 INFO::Removing potential empty rows and columns
2026-03-26 18:23:41.004062 INFO::Found 1 missing values.
2026-03-26 18:23:41.005274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:41.005587 INFO::Done
2026-03-26 18:23:41.013928 INFO::Formatting Data.
2026-03-26 18:23:41.014426 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:41.014836 INFO::Removing potential empty rows and columns
2026-03-26 18:23:41.015286 INFO::Found 2 missing values.
2026-03-26 18:23:41.015704 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.
2026-03-26 18:23:41.016634 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:41.016936 INFO::Done
2026-03-26 18:23:41.021322 INFO::Formatting Data.
2026-03-26 18:23:41.021752 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:41.022186 INFO::Removing potential empty rows and columns
2026-03-26 18:23:41.022668 INFO::Found 2 missing values.
2026-03-26 18:23:41.023336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:41.023624 INFO::Done
2026-03-26 18:23:41.028001 INFO::Formatting Data.
2026-03-26 18:23:41.028408 INFO::Typecasting input to dataframe.
2026-03-26 18:23:41.028829 INFO::Replacing NaNs with NAs.
2026-03-26 18:23:41.029288 INFO::Removing potential empty rows and columns
2026-03-26 18:23:41.029841 INFO::Found 0 missing values.
2026-03-26 18:23:41.030875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 18:23:41.031198 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.122 1.922 9.317
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.806 | 0.413 | 7.008 | |
| compute_asw | 0.009 | 0.000 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.004 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |