Yannis Schumann
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:33 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 167/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.9.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz |
| StartedAt: 2026-05-05 21:32:35 -0400 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 21:34:08 -0400 (Tue, 05 May 2026) |
| EllapsedTime: 93.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-06 01:32:35 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 24.103 1.08 17.067
* 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
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.9.0’ ** 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 version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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")
2026-05-05 21:33:27.416193 INFO::Formatting Data.
2026-05-05 21:33:27.41765 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:27.42901 INFO::Removing potential empty rows and columns
2026-05-05 21:33:27.674384 INFO::Found 0 missing values.
2026-05-05 21:33:27.677933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:27.678744 INFO::Done
2026-05-05 21:33:27.679327 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:27.692771 INFO::Starting hierarchical adjustment
2026-05-05 21:33:27.693725 INFO::Found 3 batches.
2026-05-05 21:33:27.694343 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:27.695511 INFO::Using default BPPARAM
2026-05-05 21:33:27.696088 INFO::Processing subtree level 1
2026-05-05 21:33:27.795692 INFO::Adjusting the last 1 batches sequentially
2026-05-05 21:33:27.797596 INFO::Done
2026-05-05 21:33:27.798318 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:27.801016 INFO::ASW Batch was -0.0346581628930444 prior to batch effect correction and is now -0.0346581628930444 .
2026-05-05 21:33:27.802109 INFO::Total function execution time is 0.386587381362915 s and adjustment time is 0.104043960571289 s ( 26.91 )
2026-05-05 21:33:27.816574 INFO::Formatting Data.
2026-05-05 21:33:27.817538 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:27.818539 INFO::Removing potential empty rows and columns
2026-05-05 21:33:27.819682 INFO::Found 0 missing values.
2026-05-05 21:33:27.820646 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.
2026-05-05 21:33:27.83227 INFO::Formatting Data.
2026-05-05 21:33:27.833404 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:27.834615 INFO::Removing potential empty rows and columns
2026-05-05 21:33:27.835964 INFO::Found 0 missing values.
2026-05-05 21:33:27.83711 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.
2026-05-05 21:33:27.854368 INFO::Formatting Data.
2026-05-05 21:33:27.855347 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:27.856409 INFO::Removing potential empty rows and columns
2026-05-05 21:33:27.857565 INFO::Found 0 missing values.
2026-05-05 21:33:27.858549 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.
2026-05-05 21:33:27.863106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:27.863782 INFO::Done
2026-05-05 21:33:27.864343 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:27.866452 INFO::Starting hierarchical adjustment
2026-05-05 21:33:27.867197 INFO::Found 2 batches.
2026-05-05 21:33:27.867786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:27.868471 INFO::Using default BPPARAM
2026-05-05 21:33:27.86905 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:27.870079 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 21:33:27.891042 INFO::Done
2026-05-05 21:33:27.891807 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:27.893849 INFO::ASW Batch was -0.0477183282858372 prior to batch effect correction and is now -0.119725915643738 .
2026-05-05 21:33:27.894656 INFO::Total function execution time is 0.0403685569763184 s and adjustment time is 0.0239615440368652 s ( 59.36 )
2026-05-05 21:33:27.897584 INFO::Formatting Data.
2026-05-05 21:33:27.89827 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:27.907188 INFO::Formatting Data.
2026-05-05 21:33:27.907992 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:27.908957 INFO::Removing potential empty rows and columns
2026-05-05 21:33:27.910061 INFO::Found 0 missing values.
2026-05-05 21:33:27.913104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:27.913695 INFO::Done
2026-05-05 21:33:27.914252 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:27.916455 INFO::Starting hierarchical adjustment
2026-05-05 21:33:27.917241 INFO::Found 2 batches.
2026-05-05 21:33:27.917835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:27.918519 INFO::Using default BPPARAM
2026-05-05 21:33:27.919111 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:27.920115 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 21:33:27.93665 INFO::Done
2026-05-05 21:33:27.937528 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:27.940031 INFO::ASW Batch was 0.0569151904420403 prior to batch effect correction and is now -0.118864957343619 .
2026-05-05 21:33:27.941052 INFO::Total function execution time is 0.0338966846466064 s and adjustment time is 0.0195324420928955 s ( 57.62 )
2026-05-05 21:33:27.942328 INFO::Formatting Data.
2026-05-05 21:33:27.943051 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:27.94401 INFO::Removing potential empty rows and columns
2026-05-05 21:33:27.945176 INFO::Found 0 missing values.
2026-05-05 21:33:27.948313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:27.948908 INFO::Done
2026-05-05 21:33:27.949492 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:27.95177 INFO::Starting hierarchical adjustment
2026-05-05 21:33:27.952656 INFO::Found 2 batches.
2026-05-05 21:33:27.95326 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:27.953952 INFO::Using default BPPARAM
2026-05-05 21:33:27.954572 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:27.955683 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 21:33:27.971644 INFO::Done
2026-05-05 21:33:27.972459 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:27.974735 INFO::ASW Batch was 0.0569151904420403 prior to batch effect correction and is now -0.118864957343619 .
2026-05-05 21:33:27.975612 INFO::Total function execution time is 0.0333013534545898 s and adjustment time is 0.0191159248352051 s ( 57.4 )
2026-05-05 21:33:31.222277 INFO::Formatting Data.
2026-05-05 21:33:31.223102 INFO::Recognized SummarizedExperiment
2026-05-05 21:33:31.223649 INFO::Typecasting input to dataframe.
2026-05-05 21:33:31.253702 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:31.254921 INFO::Removing potential empty rows and columns
2026-05-05 21:33:31.258219 INFO::Found 0 missing values.
2026-05-05 21:33:31.264391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:31.265018 INFO::Done
2026-05-05 21:33:31.265545 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:31.268707 INFO::Starting hierarchical adjustment
2026-05-05 21:33:31.269391 INFO::Found 2 batches.
2026-05-05 21:33:31.269912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:31.270989 INFO::Using default BPPARAM
2026-05-05 21:33:31.271542 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:31.272527 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 21:33:31.322278 INFO::Done
2026-05-05 21:33:31.323023 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:31.326298 INFO::ASW Batch was -0.00839216668906871 prior to batch effect correction and is now -0.111079405637313 .
2026-05-05 21:33:31.327164 INFO::Total function execution time is 0.105158567428589 s and adjustment time is 0.0529868602752686 s ( 50.39 )
2026-05-05 21:33:31.344835 INFO::Formatting Data.
2026-05-05 21:33:31.345722 INFO::Recognized SummarizedExperiment
2026-05-05 21:33:31.346291 INFO::Typecasting input to dataframe.
2026-05-05 21:33:31.355286 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:31.35659 INFO::Removing potential empty rows and columns
2026-05-05 21:33:31.359988 INFO::Found 0 missing values.
2026-05-05 21:33:31.366585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:31.367234 INFO::Done
2026-05-05 21:33:31.367775 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:31.371085 INFO::Starting hierarchical adjustment
2026-05-05 21:33:31.371795 INFO::Found 2 batches.
2026-05-05 21:33:31.372309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:31.37291 INFO::Using default BPPARAM
2026-05-05 21:33:31.373435 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:31.374363 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 21:33:31.398965 INFO::Done
2026-05-05 21:33:31.399838 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:31.403676 INFO::ASW Batch was 0.0119951278616837 prior to batch effect correction and is now 0.0119951278616837 .
2026-05-05 21:33:31.404653 INFO::Total function execution time is 0.0597786903381348 s and adjustment time is 0.0272419452667236 s ( 45.57 )
2026-05-05 21:33:31.424242 INFO::Formatting Data.
2026-05-05 21:33:31.425161 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:31.426271 INFO::Removing potential empty rows and columns
2026-05-05 21:33:31.427399 INFO::Found 0 missing values.
2026-05-05 21:33:31.430569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:31.431153 INFO::Done
2026-05-05 21:33:31.431724 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:31.433889 INFO::Starting hierarchical adjustment
2026-05-05 21:33:31.434664 INFO::Found 3 batches.
2026-05-05 21:33:31.435219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:31.435874 INFO::Using default BPPARAM
2026-05-05 21:33:31.436449 INFO::Processing subtree level 1
2026-05-05 21:33:31.581824 INFO::Adjusting the last 1 batches sequentially
2026-05-05 21:33:31.584013 INFO::Done
2026-05-05 21:33:31.584754 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:31.58754 INFO::ASW Batch was -0.0920026539639117 prior to batch effect correction and is now -0.158742778204603 .
2026-05-05 21:33:31.588662 INFO::Total function execution time is 0.164441585540771 s and adjustment time is 0.149469137191772 s ( 90.89 )
2026-05-05 21:33:31.605644 INFO::Skipping initial DF formatting
2026-05-05 21:33:31.606549 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:31.610956 INFO::Starting hierarchical adjustment
2026-05-05 21:33:31.611907 INFO::Found 5 batches.
2026-05-05 21:33:31.612581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:31.613266 INFO::Using default BPPARAM
2026-05-05 21:33:31.613892 INFO::Processing subtree level 1
2026-05-05 21:33:31.742645 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:31.744712 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 21:33:31.76614 INFO::Done
2026-05-05 21:33:31.76711 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:31.771758 INFO::ASW Batch was 0.4780425392161 prior to batch effect correction and is now 0.4780425392161 .
2026-05-05 21:33:31.77249 INFO::ASW Label was 0.430049807966643 prior to batch effect correction and is now 0.430049807966643 .
2026-05-05 21:33:31.773464 INFO::Total function execution time is 0.167913198471069 s and adjustment time is 0.154365062713623 s ( 91.93 )
2026-05-05 21:33:31.793288 INFO::Formatting Data.
2026-05-05 21:33:31.79437 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:31.795556 INFO::Removing potential empty rows and columns
2026-05-05 21:33:31.796727 INFO::Found 0 missing values.
2026-05-05 21:33:31.801297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:31.801985 INFO::Done
2026-05-05 21:33:31.802608 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:31.806035 INFO::Starting hierarchical adjustment
2026-05-05 21:33:31.80693 INFO::Found 5 batches.
2026-05-05 21:33:31.807545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:31.808234 INFO::Using default BPPARAM
2026-05-05 21:33:31.808864 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.
2026-05-05 21:33:31.939304 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:31.94131 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 21:33:31.960966 INFO::Done
2026-05-05 21:33:31.962078 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:31.966363 INFO::ASW Batch was 0.350215091057497 prior to batch effect correction and is now -0.090497894295871 .
2026-05-05 21:33:31.967269 INFO::ASW Label was 0.380488471263649 prior to batch effect correction and is now 0.823856041977159 .
2026-05-05 21:33:31.968327 INFO::Total function execution time is 0.17511248588562 s and adjustment time is 0.154094934463501 s ( 88 )
2026-05-05 21:33:31.969433 INFO::Formatting Data.
2026-05-05 21:33:31.970164 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:31.971265 INFO::Removing potential empty rows and columns
2026-05-05 21:33:31.972466 INFO::Found 0 missing values.
2026-05-05 21:33:31.976986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:31.977674 INFO::Done
2026-05-05 21:33:31.978268 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:31.981977 INFO::Starting hierarchical adjustment
2026-05-05 21:33:31.983056 INFO::Found 5 batches.
2026-05-05 21:33:31.983765 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:31.98453 INFO::Using default BPPARAM
2026-05-05 21:33:31.985135 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.
2026-05-05 21:33:32.114117 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:32.116368 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 21:33:32.134197 INFO::Done
2026-05-05 21:33:32.135114 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:32.138796 INFO::ASW Batch was 0.350215091057497 prior to batch effect correction and is now -0.090497894295871 .
2026-05-05 21:33:32.139502 INFO::ASW Label was 0.380488471263649 prior to batch effect correction and is now 0.823856041977159 .
2026-05-05 21:33:32.140438 INFO::Total function execution time is 0.171032905578613 s and adjustment time is 0.15131950378418 s ( 88.47 )
2026-05-05 21:33:32.155274 INFO::Formatting Data.
2026-05-05 21:33:32.156268 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:32.157349 INFO::Removing potential empty rows and columns
2026-05-05 21:33:32.158489 INFO::Found 0 missing values.
2026-05-05 21:33:32.162828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:32.163473 INFO::Done
2026-05-05 21:33:32.164062 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:32.167332 INFO::Starting hierarchical adjustment
2026-05-05 21:33:32.168125 INFO::Found 5 batches.
2026-05-05 21:33:32.168708 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:32.169406 INFO::Using default BPPARAM
2026-05-05 21:33:32.169997 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.
2026-05-05 21:33:32.279745 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:32.281545 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 21:33:32.29895 INFO::Done
2026-05-05 21:33:32.299863 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:32.303364 INFO::ASW Batch was 0.441637293819643 prior to batch effect correction and is now -0.011006594699325 .
2026-05-05 21:33:32.304066 INFO::ASW Label was 0.176729866779759 prior to batch effect correction and is now 0.671239598144076 .
2026-05-05 21:33:32.304973 INFO::Total function execution time is 0.149797916412354 s and adjustment time is 0.130933284759521 s ( 87.41 )
2026-05-05 21:33:32.305901 INFO::Formatting Data.
2026-05-05 21:33:32.306604 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:32.307578 INFO::Removing potential empty rows and columns
2026-05-05 21:33:32.308677 INFO::Found 0 missing values.
2026-05-05 21:33:32.313152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:32.313967 INFO::Done
2026-05-05 21:33:32.314595 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:32.318043 INFO::Starting hierarchical adjustment
2026-05-05 21:33:32.318954 INFO::Found 5 batches.
2026-05-05 21:33:32.319583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:32.320274 INFO::Using default BPPARAM
2026-05-05 21:33:32.320894 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.
2026-05-05 21:33:32.431169 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:32.432981 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 21:33:32.450065 INFO::Done
2026-05-05 21:33:32.450965 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:32.454537 INFO::ASW Batch was 0.441637293819643 prior to batch effect correction and is now -0.011006594699325 .
2026-05-05 21:33:32.455231 INFO::ASW Label was 0.176729866779759 prior to batch effect correction and is now 0.671239598144076 .
2026-05-05 21:33:32.456151 INFO::Total function execution time is 0.15025520324707 s and adjustment time is 0.131249666213989 s ( 87.35 )
2026-05-05 21:33:32.470994 INFO::Formatting Data.
2026-05-05 21:33:32.471934 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:32.472964 INFO::Removing potential empty rows and columns
2026-05-05 21:33:32.474062 INFO::Found 0 missing values.
2026-05-05 21:33:32.477079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:32.47771 INFO::Done
2026-05-05 21:33:32.478293 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:32.481831 INFO::Starting hierarchical adjustment
2026-05-05 21:33:32.482701 INFO::Found 2 batches.
2026-05-05 21:33:32.483293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:32.484013 INFO::Using default BPPARAM
2026-05-05 21:33:32.484612 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:32.48571 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 21:33:32.502466 INFO::Done
2026-05-05 21:33:32.503356 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:32.506815 INFO::ASW Batch was 0.585487903911498 prior to batch effect correction and is now -0.0369806061603438 .
2026-05-05 21:33:32.507536 INFO::ASW Label was 0.442087587188785 prior to batch effect correction and is now 0.931052174564483 .
2026-05-05 21:33:32.508428 INFO::Total function execution time is 0.0374908447265625 s and adjustment time is 0.0198664665222168 s ( 52.99 )
2026-05-05 21:33:32.509295 INFO::Formatting Data.
2026-05-05 21:33:32.510005 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:32.511019 INFO::Removing potential empty rows and columns
2026-05-05 21:33:32.512132 INFO::Found 0 missing values.
2026-05-05 21:33:32.515314 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:32.516009 INFO::Done
2026-05-05 21:33:32.516629 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:32.519947 INFO::Starting hierarchical adjustment
2026-05-05 21:33:32.520762 INFO::Found 2 batches.
2026-05-05 21:33:32.52135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:32.522031 INFO::Using default BPPARAM
2026-05-05 21:33:32.522633 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:32.523696 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-05 21:33:32.539491 INFO::Done
2026-05-05 21:33:32.540266 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:32.543476 INFO::ASW Batch was 0.585487903911498 prior to batch effect correction and is now -0.0369806061603438 .
2026-05-05 21:33:32.544163 INFO::ASW Label was 0.442087587188785 prior to batch effect correction and is now 0.931052174564483 .
2026-05-05 21:33:32.545052 INFO::Total function execution time is 0.0357601642608643 s and adjustment time is 0.0188460350036621 s ( 52.7 )
2026-05-05 21:33:32.557544 INFO::Formatting Data.
2026-05-05 21:33:32.558557 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:32.559594 INFO::Removing potential empty rows and columns
2026-05-05 21:33:32.560618 INFO::Found 0 missing values.
2026-05-05 21:33:32.562912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:32.563514 INFO::Done
2026-05-05 21:33:32.564079 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:32.566264 INFO::Starting hierarchical adjustment
2026-05-05 21:33:32.56706 INFO::Found 2 batches.
2026-05-05 21:33:32.56766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:32.568309 INFO::Using default BPPARAM
2026-05-05 21:33:32.568897 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:32.569902 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 21:33:32.612433 INFO::Done
2026-05-05 21:33:32.613231 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:32.615462 INFO::ASW Batch was 0.176954188736323 prior to batch effect correction and is now -0.118768390489373 .
2026-05-05 21:33:32.6164 INFO::Total function execution time is 0.0589394569396973 s and adjustment time is 0.045485258102417 s ( 77.17 )
2026-05-05 21:33:32.629277 INFO::Formatting Data.
2026-05-05 21:33:32.630193 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:32.631166 INFO::Removing potential empty rows and columns
2026-05-05 21:33:32.632228 INFO::Found 0 missing values.
2026-05-05 21:33:32.633436 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.
2026-05-05 21:33:32.638226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:32.638858 INFO::Done
2026-05-05 21:33:32.639435 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:32.642557 INFO::Starting hierarchical adjustment
2026-05-05 21:33:32.643309 INFO::Found 2 batches.
2026-05-05 21:33:32.64389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:32.644556 INFO::Using default BPPARAM
2026-05-05 21:33:32.645115 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:32.646096 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 21:33:32.663295 INFO::Done
2026-05-05 21:33:32.664096 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:32.66725 INFO::ASW Batch was 0.466698079205857 prior to batch effect correction and is now 0.0324843195289375 .
2026-05-05 21:33:32.667919 INFO::ASW Label was 0.61804810248012 prior to batch effect correction and is now 0.909217341966893 .
2026-05-05 21:33:32.668778 INFO::Total function execution time is 0.0395989418029785 s and adjustment time is 0.020078182220459 s ( 50.7 )
2026-05-05 21:33:32.66965 INFO::Formatting Data.
2026-05-05 21:33:32.670311 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:32.671292 INFO::Removing potential empty rows and columns
2026-05-05 21:33:32.672353 INFO::Found 0 missing values.
2026-05-05 21:33:32.673324 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.
2026-05-05 21:33:32.678095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:32.678751 INFO::Done
2026-05-05 21:33:32.679317 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:32.682447 INFO::Starting hierarchical adjustment
2026-05-05 21:33:32.683235 INFO::Found 2 batches.
2026-05-05 21:33:32.683825 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:32.68449 INFO::Using default BPPARAM
2026-05-05 21:33:32.685068 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:32.686146 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 21:33:32.703326 INFO::Done
2026-05-05 21:33:32.70415 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:32.707273 INFO::ASW Batch was 0.466698079205857 prior to batch effect correction and is now 0.0324843195289375 .
2026-05-05 21:33:32.707965 INFO::ASW Label was 0.61804810248012 prior to batch effect correction and is now 0.909217341966893 .
2026-05-05 21:33:32.708836 INFO::Total function execution time is 0.0391983985900879 s and adjustment time is 0.0202131271362305 s ( 51.57 )
2026-05-05 21:33:32.929076 INFO::Formatting Data.
2026-05-05 21:33:32.930108 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:32.931188 INFO::Removing potential empty rows and columns
2026-05-05 21:33:32.932364 INFO::Found 0 missing values.
2026-05-05 21:33:32.935764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:32.936452 INFO::Done
2026-05-05 21:33:32.937045 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:32.939446 INFO::Starting hierarchical adjustment
2026-05-05 21:33:32.940258 INFO::Found 3 batches.
2026-05-05 21:33:32.940862 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:32.941564 INFO::Using default BPPARAM
2026-05-05 21:33:32.942136 INFO::Processing subtree level 1
2026-05-05 21:33:33.036186 INFO::Adjusting the last 1 batches sequentially
2026-05-05 21:33:33.03855 INFO::Done
2026-05-05 21:33:33.039385 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:33.042465 INFO::ASW Batch was -0.116785215233861 prior to batch effect correction and is now -0.116785215233861 .
2026-05-05 21:33:33.0437 INFO::Total function execution time is 0.114682197570801 s and adjustment time is 0.0984106063842773 s ( 85.81 )
2026-05-05 21:33:33.04498 INFO::Formatting Data.
2026-05-05 21:33:33.045768 INFO::Typecasting input to dataframe.
2026-05-05 21:33:33.046656 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:33.047772 INFO::Removing potential empty rows and columns
2026-05-05 21:33:33.049034 INFO::Found 0 missing values.
2026-05-05 21:33:33.052612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:33.053273 INFO::Done
2026-05-05 21:33:33.053894 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:33.056453 INFO::Starting hierarchical adjustment
2026-05-05 21:33:33.057289 INFO::Found 3 batches.
2026-05-05 21:33:33.057914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:33.058634 INFO::Using default BPPARAM
2026-05-05 21:33:33.059222 INFO::Processing subtree level 1
2026-05-05 21:33:33.156337 INFO::Adjusting the last 1 batches sequentially
2026-05-05 21:33:33.158686 INFO::Done
2026-05-05 21:33:33.159582 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:33.162551 INFO::ASW Batch was -0.116785215233861 prior to batch effect correction and is now -0.116785215233861 .
2026-05-05 21:33:33.163707 INFO::Total function execution time is 0.118681907653809 s and adjustment time is 0.101523399353027 s ( 85.54 )
2026-05-05 21:33:33.17963 INFO::Formatting Data.
2026-05-05 21:33:33.180758 INFO::Typecasting input to dataframe.
2026-05-05 21:33:33.181811 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:33.182909 INFO::Removing potential empty rows and columns
2026-05-05 21:33:33.184097 INFO::Found 0 missing values.
2026-05-05 21:33:33.187395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:33.188024 INFO::Done
2026-05-05 21:33:33.188609 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:33.190988 INFO::Starting hierarchical adjustment
2026-05-05 21:33:33.191791 INFO::Found 3 batches.
2026-05-05 21:33:33.192384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:33.193072 INFO::Using default BPPARAM
2026-05-05 21:33:33.193663 INFO::Processing subtree level 1
2026-05-05 21:33:33.292001 INFO::Adjusting the last 1 batches sequentially
2026-05-05 21:33:33.294274 INFO::Done
2026-05-05 21:33:33.295134 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:33.298074 INFO::ASW Batch was -0.0989388267598789 prior to batch effect correction and is now -0.0989388267598789 .
2026-05-05 21:33:33.29923 INFO::Total function execution time is 0.119745492935181 s and adjustment time is 0.102589130401611 s ( 85.67 )
2026-05-05 21:33:33.460479 INFO::Formatting Data.
2026-05-05 21:33:33.461622 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:33.463002 INFO::Removing potential empty rows and columns
2026-05-05 21:33:33.4661 INFO::Found 1000 missing values.
2026-05-05 21:33:33.486901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:33.487924 INFO::Done
2026-05-05 21:33:33.488563 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:33.494837 INFO::Starting hierarchical adjustment
2026-05-05 21:33:33.495941 INFO::Found 10 batches.
2026-05-05 21:33:33.496598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:33.497297 INFO::Using default BPPARAM
2026-05-05 21:33:33.497893 INFO::Processing subtree level 1
2026-05-05 21:33:33.656165 INFO::Processing subtree level 2
2026-05-05 21:33:33.81004 INFO::Adjusting the last 1 batches sequentially
2026-05-05 21:33:33.812682 INFO::Done
2026-05-05 21:33:33.813635 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:33.820448 INFO::ASW Batch was 0.489536882988584 prior to batch effect correction and is now 0.489536882988584 .
2026-05-05 21:33:33.821395 INFO::ASW Label was 0.310745435314565 prior to batch effect correction and is now 0.310745435314565 .
2026-05-05 21:33:33.822632 INFO::Total function execution time is 0.3622887134552 s and adjustment time is 0.316910266876221 s ( 87.47 )
2026-05-05 21:33:33.823743 INFO::Formatting Data.
2026-05-05 21:33:33.824897 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:33.82688 INFO::Removing potential empty rows and columns
2026-05-05 21:33:33.830404 INFO::Found 1000 missing values.
2026-05-05 21:33:33.854757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:33.855855 INFO::Done
2026-05-05 21:33:33.85657 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:33.863036 INFO::Starting hierarchical adjustment
2026-05-05 21:33:33.864138 INFO::Found 10 batches.
2026-05-05 21:33:35.397811 INFO::Set up parallel execution backend with 2 workers
2026-05-05 21:33:35.402507 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-05 21:33:37.51042 INFO::Adjusting the last 2 batches sequentially
2026-05-05 21:33:37.514473 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-05 21:33:37.532469 INFO::Done
2026-05-05 21:33:37.5333 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:37.538393 INFO::ASW Batch was 0.489536882988584 prior to batch effect correction and is now 0.489536882988584 .
2026-05-05 21:33:37.539068 INFO::ASW Label was 0.310745435314565 prior to batch effect correction and is now 0.310745435314565 .
2026-05-05 21:33:37.539869 INFO::Total function execution time is 3.71623635292053 s and adjustment time is 3.66850876808167 s ( 98.72 )
2026-05-05 21:33:37.704557 INFO::Formatting Data.
2026-05-05 21:33:37.705543 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:37.706589 INFO::Removing potential empty rows and columns
2026-05-05 21:33:37.707801 INFO::Found 0 missing values.
2026-05-05 21:33:37.711706 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:37.712293 INFO::Done
2026-05-05 21:33:37.712855 INFO::Acquiring quality metrics before batch effect correction.
2026-05-05 21:33:37.715754 INFO::Starting hierarchical adjustment
2026-05-05 21:33:37.716512 INFO::Found 3 batches.
2026-05-05 21:33:37.717071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-05 21:33:37.717738 INFO::Using default BPPARAM
2026-05-05 21:33:37.718294 INFO::Processing subtree level 1
2026-05-05 21:33:37.831203 INFO::Adjusting the last 1 batches sequentially
2026-05-05 21:33:37.833695 INFO::Done
2026-05-05 21:33:37.834782 INFO::Acquiring quality metrics after batch effect correction.
2026-05-05 21:33:37.838391 INFO::ASW Batch was 0.212057526164237 prior to batch effect correction and is now -0.160836930267292 .
2026-05-05 21:33:37.839124 INFO::ASW Label was -0.207252454207145 prior to batch effect correction and is now -0.0931666398104607 .
2026-05-05 21:33:37.84012 INFO::Total function execution time is 0.135662317276001 s and adjustment time is 0.117234230041504 s ( 86.42 )
2026-05-05 21:33:37.969526 INFO::Formatting Data.
2026-05-05 21:33:37.970532 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:37.971592 INFO::Removing potential empty rows and columns
2026-05-05 21:33:37.972804 INFO::Found 2 missing values.
2026-05-05 21:33:37.976151 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:37.976807 INFO::Done
2026-05-05 21:33:38.009771 INFO::Found NA in Reference column
2026-05-05 21:33:38.020696 INFO::Require at least two references per batch.
2026-05-05 21:33:38.044271 INFO::Formatting Data.
2026-05-05 21:33:38.045252 INFO::Recognized SummarizedExperiment
2026-05-05 21:33:38.045919 INFO::Typecasting input to dataframe.
2026-05-05 21:33:38.056717 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.058186 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.062335 INFO::Found 0 missing values.
2026-05-05 21:33:38.070735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.0716 INFO::Done
2026-05-05 21:33:38.088978 INFO::Formatting Data.
2026-05-05 21:33:38.089892 INFO::Recognized SummarizedExperiment
2026-05-05 21:33:38.090572 INFO::Typecasting input to dataframe.
2026-05-05 21:33:38.110494 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.112098 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.116402 INFO::Found 0 missing values.
2026-05-05 21:33:38.129317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.130239 INFO::Done
2026-05-05 21:33:38.147667 INFO::Formatting Data.
2026-05-05 21:33:38.148596 INFO::Recognized SummarizedExperiment
2026-05-05 21:33:38.149235 INFO::Typecasting input to dataframe.
2026-05-05 21:33:38.167342 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.168628 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.169862 INFO::Found 0 missing values.
2026-05-05 21:33:38.170883 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.
2026-05-05 21:33:38.17531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.175909 INFO::Done
2026-05-05 21:33:38.186098 INFO::Formatting Data.
2026-05-05 21:33:38.18698 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.187917 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.188973 INFO::Found 0 missing values.
2026-05-05 21:33:38.191949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.192544 INFO::Done
2026-05-05 21:33:38.203944 INFO::Formatting Data.
2026-05-05 21:33:38.204833 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.205789 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.206815 INFO::Found 0 missing values.
2026-05-05 21:33:38.20972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.210273 INFO::Done
2026-05-05 21:33:38.240858 INFO::Formatting Data.
2026-05-05 21:33:38.241789 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.242909 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.244128 INFO::Found 1 missing values.
2026-05-05 21:33:38.246784 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.247365 INFO::Done
2026-05-05 21:33:38.267242 INFO::Formatting Data.
2026-05-05 21:33:38.268279 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.269279 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.270517 INFO::Found 2 missing values.
2026-05-05 21:33:38.271589 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.
2026-05-05 21:33:38.273937 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.274524 INFO::Done
2026-05-05 21:33:38.298188 INFO::Formatting Data.
2026-05-05 21:33:38.299586 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.300789 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.301939 INFO::Found 2 missing values.
2026-05-05 21:33:38.30389 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.304483 INFO::Done
2026-05-05 21:33:38.317151 INFO::Formatting Data.
2026-05-05 21:33:38.318191 INFO::Typecasting input to dataframe.
2026-05-05 21:33:38.319165 INFO::Replacing NaNs with NAs.
2026-05-05 21:33:38.320176 INFO::Removing potential empty rows and columns
2026-05-05 21:33:38.32134 INFO::Found 0 missing values.
2026-05-05 21:33:38.324436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-05 21:33:38.325021 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.129 4.277 23.141
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.103 | 1.080 | 17.067 | |
| compute_asw | 0.023 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.013 | |
| generate_data_covariables | 0.011 | 0.002 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.011 | |