Yannis Schumann
| Snapshot Date: 2026-01-23 13:40 -0500 (Fri, 23 Jan 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 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-24 11:34 -0500 (Sat, 24 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4811 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4545 |
| 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 168/2345 | 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 | | ||||||||
|
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: 2026-01-23 18:44:33 -0500 (Fri, 23 Jan 2026) |
| EndedAt: 2026-01-23 18:45:13 -0500 (Fri, 23 Jan 2026) |
| EllapsedTime: 39.9 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) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* 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 10.76 0.489 8.253
* 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-arm64/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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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")
2026-01-23 18:45:02.138635 INFO::Formatting Data.
2026-01-23 18:45:02.140607 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:02.145758 INFO::Removing potential empty rows and columns
2026-01-23 18:45:02.274007 INFO::Found 0 missing values.
2026-01-23 18:45:02.275413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:02.275692 INFO::Done
2026-01-23 18:45:02.275936 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:02.283533 INFO::Starting hierarchical adjustment
2026-01-23 18:45:02.283845 INFO::Found 3 batches.
2026-01-23 18:45:02.284045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:02.284514 INFO::Using default BPPARAM
2026-01-23 18:45:02.284705 INFO::Processing subtree level 1
2026-01-23 18:45:02.348497 INFO::Adjusting the last 1 batches sequentially
2026-01-23 18:45:02.358297 INFO::Done
2026-01-23 18:45:02.35896 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:02.361411 INFO::ASW Batch was -0.0257345801153088 prior to batch effect correction and is now -0.0257345801153088 .
2026-01-23 18:45:02.362265 INFO::Total function execution time is 0.223866939544678 s and adjustment time is 0.0744621753692627 s ( 33.26 )
2026-01-23 18:45:02.377528 INFO::Formatting Data.
2026-01-23 18:45:02.377901 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:02.378327 INFO::Removing potential empty rows and columns
2026-01-23 18:45:02.378908 INFO::Found 0 missing values.
2026-01-23 18:45:02.379332 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.
2026-01-23 18:45:02.385823 INFO::Formatting Data.
2026-01-23 18:45:02.386121 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:02.386487 INFO::Removing potential empty rows and columns
2026-01-23 18:45:02.386955 INFO::Found 0 missing values.
2026-01-23 18:45:02.38737 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.
2026-01-23 18:45:02.394793 INFO::Formatting Data.
2026-01-23 18:45:02.395071 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:02.395411 INFO::Removing potential empty rows and columns
2026-01-23 18:45:02.395815 INFO::Found 0 missing values.
2026-01-23 18:45:02.396157 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.
2026-01-23 18:45:02.398035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:02.398231 INFO::Done
2026-01-23 18:45:02.39843 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:02.399269 INFO::Starting hierarchical adjustment
2026-01-23 18:45:02.399502 INFO::Found 2 batches.
2026-01-23 18:45:02.399677 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:02.39999 INFO::Using default BPPARAM
2026-01-23 18:45:02.400163 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:02.400464 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-23 18:45:02.410305 INFO::Done
2026-01-23 18:45:02.410731 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:02.411468 INFO::ASW Batch was 0.0177222851232399 prior to batch effect correction and is now -0.110027237244343 .
2026-01-23 18:45:02.411735 INFO::Total function execution time is 0.0169601440429688 s and adjustment time is 0.0108041763305664 s ( 63.7 )
2026-01-23 18:45:02.412869 INFO::Formatting Data.
2026-01-23 18:45:02.413096 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:02.416364 INFO::Formatting Data.
2026-01-23 18:45:02.416607 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:02.416914 INFO::Removing potential empty rows and columns
2026-01-23 18:45:02.417295 INFO::Found 0 missing values.
2026-01-23 18:45:02.418345 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:02.41854 INFO::Done
2026-01-23 18:45:02.41874 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:02.419438 INFO::Starting hierarchical adjustment
2026-01-23 18:45:02.419675 INFO::Found 2 batches.
2026-01-23 18:45:02.419903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:02.420109 INFO::Using default BPPARAM
2026-01-23 18:45:02.420294 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:02.420594 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-23 18:45:02.456984 INFO::Done
2026-01-23 18:45:02.45722 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:02.457915 INFO::ASW Batch was 0.0243792023868014 prior to batch effect correction and is now -0.118376311884686 .
2026-01-23 18:45:02.458167 INFO::Total function execution time is 0.0418047904968262 s and adjustment time is 0.0373489856719971 s ( 89.34 )
2026-01-23 18:45:02.458484 INFO::Formatting Data.
2026-01-23 18:45:02.458671 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:02.458938 INFO::Removing potential empty rows and columns
2026-01-23 18:45:02.459266 INFO::Found 0 missing values.
2026-01-23 18:45:02.460179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:02.460356 INFO::Done
2026-01-23 18:45:02.460522 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:02.46112 INFO::Starting hierarchical adjustment
2026-01-23 18:45:02.461338 INFO::Found 2 batches.
2026-01-23 18:45:02.461521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:02.461718 INFO::Using default BPPARAM
2026-01-23 18:45:02.461886 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:02.462147 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-23 18:45:02.47528 INFO::Done
2026-01-23 18:45:02.475828 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:02.476905 INFO::ASW Batch was 0.0243792023868014 prior to batch effect correction and is now -0.118376311884686 .
2026-01-23 18:45:02.477286 INFO::Total function execution time is 0.0187749862670898 s and adjustment time is 0.0139269828796387 s ( 74.18 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-23 18:45:03.747555 INFO::Formatting Data.
2026-01-23 18:45:03.747895 INFO::Recognized SummarizedExperiment
2026-01-23 18:45:03.74811 INFO::Typecasting input to dataframe.
2026-01-23 18:45:03.75967 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:03.760094 INFO::Removing potential empty rows and columns
2026-01-23 18:45:03.761277 INFO::Found 0 missing values.
2026-01-23 18:45:03.763665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:03.763832 INFO::Done
2026-01-23 18:45:03.763988 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:03.765186 INFO::Starting hierarchical adjustment
2026-01-23 18:45:03.765394 INFO::Found 2 batches.
2026-01-23 18:45:03.765546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:03.765864 INFO::Using default BPPARAM
2026-01-23 18:45:03.766013 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:03.766311 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-23 18:45:03.785098 INFO::Done
2026-01-23 18:45:03.785449 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:03.786742 INFO::ASW Batch was 0.00590763705059858 prior to batch effect correction and is now -0.0946413155150088 .
2026-01-23 18:45:03.787016 INFO::Total function execution time is 0.0396039485931396 s and adjustment time is 0.0197291374206543 s ( 49.82 )
Warning: stack imbalance in '{', 73 then 75
2026-01-23 18:45:03.793979 INFO::Formatting Data.
2026-01-23 18:45:03.794213 INFO::Recognized SummarizedExperiment
2026-01-23 18:45:03.794376 INFO::Typecasting input to dataframe.
2026-01-23 18:45:03.797449 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:03.797817 INFO::Removing potential empty rows and columns
2026-01-23 18:45:03.799021 INFO::Found 0 missing values.
2026-01-23 18:45:03.801288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:03.801454 INFO::Done
2026-01-23 18:45:03.801611 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:03.802855 INFO::Starting hierarchical adjustment
2026-01-23 18:45:03.803073 INFO::Found 2 batches.
2026-01-23 18:45:03.803228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:03.80341 INFO::Using default BPPARAM
2026-01-23 18:45:03.803566 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:03.803853 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-23 18:45:03.812337 INFO::Done
2026-01-23 18:45:03.812589 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:03.813854 INFO::ASW Batch was 0.00694223267982694 prior to batch effect correction and is now 0.00694223267982694 .
2026-01-23 18:45:03.814164 INFO::Total function execution time is 0.0201790332794189 s and adjustment time is 0.00928688049316406 s ( 46.02 )
2026-01-23 18:45:03.823806 INFO::Formatting Data.
2026-01-23 18:45:03.824346 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:03.825057 INFO::Removing potential empty rows and columns
2026-01-23 18:45:03.82562 INFO::Found 0 missing values.
2026-01-23 18:45:03.827307 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:03.827673 INFO::Done
2026-01-23 18:45:03.827943 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:03.828782 INFO::Starting hierarchical adjustment
2026-01-23 18:45:03.829027 INFO::Found 3 batches.
2026-01-23 18:45:03.829208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:03.829418 INFO::Using default BPPARAM
2026-01-23 18:45:03.82958 INFO::Processing subtree level 1
2026-01-23 18:45:03.917335 INFO::Adjusting the last 1 batches sequentially
2026-01-23 18:45:03.919582 INFO::Done
2026-01-23 18:45:03.920042 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:03.922427 INFO::ASW Batch was -0.0806457591395667 prior to batch effect correction and is now -0.166284875869793 .
2026-01-23 18:45:03.934964 INFO::Total function execution time is 0.110725164413452 s and adjustment time is 0.0905978679656982 s ( 81.82 )
2026-01-23 18:45:03.945319 INFO::Skipping initial DF formatting
2026-01-23 18:45:03.945577 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:03.947065 INFO::Starting hierarchical adjustment
2026-01-23 18:45:03.947337 INFO::Found 5 batches.
2026-01-23 18:45:03.947511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:03.947726 INFO::Using default BPPARAM
2026-01-23 18:45:03.947898 INFO::Processing subtree level 1
2026-01-23 18:45:04.668557 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:04.670654 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-23 18:45:04.688258 INFO::Done
2026-01-23 18:45:04.694738 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:04.75417 INFO::ASW Batch was 0.53129911281641 prior to batch effect correction and is now 0.53129911281641 .
2026-01-23 18:45:04.754562 INFO::ASW Label was 0.33538249917651 prior to batch effect correction and is now 0.33538249917651 .
2026-01-23 18:45:04.755074 INFO::Total function execution time is 0.809749841690063 s and adjustment time is 0.740960121154785 s ( 91.5 )
2026-01-23 18:45:04.766047 INFO::Formatting Data.
2026-01-23 18:45:04.766388 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:04.766894 INFO::Removing potential empty rows and columns
2026-01-23 18:45:04.767311 INFO::Found 0 missing values.
2026-01-23 18:45:04.769504 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:04.769756 INFO::Done
2026-01-23 18:45:04.770006 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:04.771321 INFO::Starting hierarchical adjustment
2026-01-23 18:45:04.771732 INFO::Found 5 batches.
2026-01-23 18:45:04.771965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:04.77222 INFO::Using default BPPARAM
2026-01-23 18:45:04.78307 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.
2026-01-23 18:45:04.865787 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:04.875108 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-23 18:45:04.887404 INFO::Done
2026-01-23 18:45:04.88812 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:04.891175 INFO::ASW Batch was 0.884074628460316 prior to batch effect correction and is now -0.0935144671053971 .
2026-01-23 18:45:04.891601 INFO::ASW Label was 0.0444876494599198 prior to batch effect correction and is now 0.562722372223429 .
2026-01-23 18:45:04.892119 INFO::Total function execution time is 0.126054048538208 s and adjustment time is 0.115801811218262 s ( 91.87 )
2026-01-23 18:45:04.892792 INFO::Formatting Data.
2026-01-23 18:45:04.893151 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:04.893731 INFO::Removing potential empty rows and columns
2026-01-23 18:45:04.894333 INFO::Found 0 missing values.
2026-01-23 18:45:04.896553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:04.896842 INFO::Done
2026-01-23 18:45:04.897196 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:04.898949 INFO::Starting hierarchical adjustment
2026-01-23 18:45:04.899319 INFO::Found 5 batches.
2026-01-23 18:45:04.899557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:04.899915 INFO::Using default BPPARAM
2026-01-23 18:45:04.900187 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.
2026-01-23 18:45:04.979912 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:04.985632 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-23 18:45:04.997777 INFO::Done
2026-01-23 18:45:04.99818 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:04.999631 INFO::ASW Batch was 0.884074628460316 prior to batch effect correction and is now -0.0935144671053971 .
2026-01-23 18:45:04.999875 INFO::ASW Label was 0.0444876494599198 prior to batch effect correction and is now 0.562722372223429 .
2026-01-23 18:45:05.000242 INFO::Total function execution time is 0.107434988021851 s and adjustment time is 0.0985240936279297 s ( 91.71 )
2026-01-23 18:45:05.00814 INFO::Formatting Data.
2026-01-23 18:45:05.008452 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.008858 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.009285 INFO::Found 0 missing values.
2026-01-23 18:45:05.010821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.011015 INFO::Done
2026-01-23 18:45:05.011216 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.012534 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.01283 INFO::Found 5 batches.
2026-01-23 18:45:05.013032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.013306 INFO::Using default BPPARAM
2026-01-23 18:45:05.013537 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.
2026-01-23 18:45:05.101509 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:05.104749 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-23 18:45:05.117048 INFO::Done
2026-01-23 18:45:05.117574 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.119409 INFO::ASW Batch was 0.335831278046909 prior to batch effect correction and is now -0.105024941468594 .
2026-01-23 18:45:05.119816 INFO::ASW Label was 0.38310343074867 prior to batch effect correction and is now 0.888621706705759 .
2026-01-23 18:45:05.120234 INFO::Total function execution time is 0.112088203430176 s and adjustment time is 0.104238986968994 s ( 93 )
2026-01-23 18:45:05.120684 INFO::Formatting Data.
2026-01-23 18:45:05.120964 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.121363 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.122069 INFO::Found 0 missing values.
2026-01-23 18:45:05.12421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.124557 INFO::Done
2026-01-23 18:45:05.124843 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.126258 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.127278 INFO::Found 5 batches.
2026-01-23 18:45:05.127802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.128151 INFO::Using default BPPARAM
2026-01-23 18:45:05.128436 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.
2026-01-23 18:45:05.207872 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:05.209917 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-23 18:45:05.22286 INFO::Done
2026-01-23 18:45:05.223507 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.225347 INFO::ASW Batch was 0.335831278046909 prior to batch effect correction and is now -0.105024941468594 .
2026-01-23 18:45:05.225628 INFO::ASW Label was 0.38310343074867 prior to batch effect correction and is now 0.888621706705759 .
2026-01-23 18:45:05.226022 INFO::Total function execution time is 0.105307102203369 s and adjustment time is 0.0957591533660889 s ( 90.93 )
2026-01-23 18:45:05.233904 INFO::Formatting Data.
2026-01-23 18:45:05.234301 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.234674 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.235124 INFO::Found 0 missing values.
2026-01-23 18:45:05.236846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.237162 INFO::Done
2026-01-23 18:45:05.23737 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.238735 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.239028 INFO::Found 2 batches.
2026-01-23 18:45:05.239224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.239451 INFO::Using default BPPARAM
2026-01-23 18:45:05.239633 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:05.239953 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-23 18:45:05.246467 INFO::Done
2026-01-23 18:45:05.246751 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.247983 INFO::ASW Batch was 0.521466438926028 prior to batch effect correction and is now -0.0246183592344469 .
2026-01-23 18:45:05.248246 INFO::ASW Label was 0.564139515891513 prior to batch effect correction and is now 0.932002538785266 .
2026-01-23 18:45:05.24854 INFO::Total function execution time is 0.0146770477294922 s and adjustment time is 0.00749611854553223 s ( 51.07 )
2026-01-23 18:45:05.248808 INFO::Formatting Data.
2026-01-23 18:45:05.249041 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.249352 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.24971 INFO::Found 0 missing values.
2026-01-23 18:45:05.250713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.250918 INFO::Done
2026-01-23 18:45:05.251104 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.25215 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.252414 INFO::Found 2 batches.
2026-01-23 18:45:05.252608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.252821 INFO::Using default BPPARAM
2026-01-23 18:45:05.253014 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:05.253335 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-23 18:45:05.268721 INFO::Done
2026-01-23 18:45:05.269246 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.270882 INFO::ASW Batch was 0.521466438926028 prior to batch effect correction and is now -0.0246183592344469 .
2026-01-23 18:45:05.27112 INFO::ASW Label was 0.564139515891513 prior to batch effect correction and is now 0.932002538785266 .
2026-01-23 18:45:05.271389 INFO::Total function execution time is 0.0225729942321777 s and adjustment time is 0.0163190364837646 s ( 72.29 )
2026-01-23 18:45:05.279717 INFO::Formatting Data.
2026-01-23 18:45:05.280017 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.28032 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.280643 INFO::Found 0 missing values.
2026-01-23 18:45:05.281338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.281513 INFO::Done
2026-01-23 18:45:05.281681 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.282336 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.282559 INFO::Found 2 batches.
2026-01-23 18:45:05.282721 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.282942 INFO::Using default BPPARAM
2026-01-23 18:45:05.283104 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:05.283377 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-23 18:45:05.295975 INFO::Done
2026-01-23 18:45:05.296253 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.296963 INFO::ASW Batch was 0.0386282847023277 prior to batch effect correction and is now -0.062883329406137 .
2026-01-23 18:45:05.297532 INFO::Total function execution time is 0.017786979675293 s and adjustment time is 0.0134389400482178 s ( 75.55 )
2026-01-23 18:45:05.304568 INFO::Formatting Data.
2026-01-23 18:45:05.304881 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.305229 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.305649 INFO::Found 0 missing values.
2026-01-23 18:45:05.306143 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.
2026-01-23 18:45:05.307867 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.308071 INFO::Done
2026-01-23 18:45:05.308259 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.309392 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.310182 INFO::Found 2 batches.
2026-01-23 18:45:05.310438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.310666 INFO::Using default BPPARAM
2026-01-23 18:45:05.31086 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:05.311223 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-23 18:45:05.317481 INFO::Done
2026-01-23 18:45:05.317747 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.319141 INFO::ASW Batch was 0.510739788733862 prior to batch effect correction and is now -0.0226576847675899 .
2026-01-23 18:45:05.319351 INFO::ASW Label was 0.562762486859157 prior to batch effect correction and is now 0.8792371848887 .
2026-01-23 18:45:05.319615 INFO::Total function execution time is 0.015099048614502 s and adjustment time is 0.00736403465270996 s ( 48.77 )
2026-01-23 18:45:05.319882 INFO::Formatting Data.
2026-01-23 18:45:05.320072 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.320451 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.320774 INFO::Found 0 missing values.
2026-01-23 18:45:05.321048 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.
2026-01-23 18:45:05.322602 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.322791 INFO::Done
2026-01-23 18:45:05.322955 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.323955 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.324192 INFO::Found 2 batches.
2026-01-23 18:45:05.324389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.324595 INFO::Using default BPPARAM
2026-01-23 18:45:05.324758 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:05.325087 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-23 18:45:05.331085 INFO::Done
2026-01-23 18:45:05.331311 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.332315 INFO::ASW Batch was 0.510739788733862 prior to batch effect correction and is now -0.0226576847675899 .
2026-01-23 18:45:05.332507 INFO::ASW Label was 0.562762486859157 prior to batch effect correction and is now 0.8792371848887 .
2026-01-23 18:45:05.332783 INFO::Total function execution time is 0.0128941535949707 s and adjustment time is 0.00692391395568848 s ( 53.7 )
2026-01-23 18:45:05.412084 INFO::Formatting Data.
2026-01-23 18:45:05.412427 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.412741 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.413112 INFO::Found 0 missing values.
2026-01-23 18:45:05.414061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.414235 INFO::Done
2026-01-23 18:45:05.414404 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.415148 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.415369 INFO::Found 3 batches.
2026-01-23 18:45:05.415539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.415723 INFO::Using default BPPARAM
2026-01-23 18:45:05.415874 INFO::Processing subtree level 1
2026-01-23 18:45:05.487533 INFO::Adjusting the last 1 batches sequentially
2026-01-23 18:45:05.491019 INFO::Done
2026-01-23 18:45:05.491603 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.493605 INFO::ASW Batch was -0.0694179076902656 prior to batch effect correction and is now -0.0694179076902656 .
2026-01-23 18:45:05.494219 INFO::Total function execution time is 0.0821659564971924 s and adjustment time is 0.0756618976593018 s ( 92.08 )
2026-01-23 18:45:05.494728 INFO::Formatting Data.
2026-01-23 18:45:05.495056 INFO::Typecasting input to dataframe.
2026-01-23 18:45:05.495334 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.495918 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.496462 INFO::Found 0 missing values.
2026-01-23 18:45:05.497641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.497828 INFO::Done
2026-01-23 18:45:05.497997 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.498622 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.499011 INFO::Found 3 batches.
2026-01-23 18:45:05.499173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.499524 INFO::Using default BPPARAM
2026-01-23 18:45:05.499696 INFO::Processing subtree level 1
2026-01-23 18:45:05.562021 INFO::Adjusting the last 1 batches sequentially
2026-01-23 18:45:05.563013 INFO::Done
2026-01-23 18:45:05.563204 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.564513 INFO::ASW Batch was -0.0694179076902656 prior to batch effect correction and is now -0.0694179076902656 .
2026-01-23 18:45:05.5649 INFO::Total function execution time is 0.070159912109375 s and adjustment time is 0.0641717910766602 s ( 91.47 )
2026-01-23 18:45:05.57403 INFO::Formatting Data.
2026-01-23 18:45:05.574345 INFO::Typecasting input to dataframe.
2026-01-23 18:45:05.574666 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.575009 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.575416 INFO::Found 0 missing values.
2026-01-23 18:45:05.57637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.576559 INFO::Done
2026-01-23 18:45:05.576733 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.577487 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.577721 INFO::Found 3 batches.
2026-01-23 18:45:05.578042 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.578269 INFO::Using default BPPARAM
2026-01-23 18:45:05.578434 INFO::Processing subtree level 1
2026-01-23 18:45:05.632022 INFO::Adjusting the last 1 batches sequentially
2026-01-23 18:45:05.634547 INFO::Done
2026-01-23 18:45:05.63484 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.636968 INFO::ASW Batch was -0.0476221049097503 prior to batch effect correction and is now -0.0476221049097503 .
2026-01-23 18:45:05.637457 INFO::Total function execution time is 0.0634491443634033 s and adjustment time is 0.0568549633026123 s ( 89.61 )
2026-01-23 18:45:05.732868 INFO::Formatting Data.
2026-01-23 18:45:05.733152 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.733558 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.734519 INFO::Found 1000 missing values.
2026-01-23 18:45:05.740446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.740681 INFO::Done
2026-01-23 18:45:05.749024 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.751787 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.752105 INFO::Found 10 batches.
2026-01-23 18:45:05.752297 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:05.752536 INFO::Using default BPPARAM
2026-01-23 18:45:05.752892 INFO::Processing subtree level 1
2026-01-23 18:45:05.829164 INFO::Processing subtree level 2
2026-01-23 18:45:05.92851 INFO::Adjusting the last 1 batches sequentially
2026-01-23 18:45:05.940805 INFO::Done
2026-01-23 18:45:05.941415 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:05.944665 INFO::ASW Batch was 0.499744627532473 prior to batch effect correction and is now 0.499744627532473 .
2026-01-23 18:45:05.945627 INFO::ASW Label was 0.318487168766093 prior to batch effect correction and is now 0.318487168766093 .
2026-01-23 18:45:05.946668 INFO::Total function execution time is 0.213780879974365 s and adjustment time is 0.188732862472534 s ( 88.28 )
2026-01-23 18:45:05.947192 INFO::Formatting Data.
2026-01-23 18:45:05.947457 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:05.948207 INFO::Removing potential empty rows and columns
2026-01-23 18:45:05.949453 INFO::Found 1000 missing values.
2026-01-23 18:45:05.956119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:05.956905 INFO::Done
2026-01-23 18:45:05.957246 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:05.963452 INFO::Starting hierarchical adjustment
2026-01-23 18:45:05.963824 INFO::Found 10 batches.
2026-01-23 18:45:06.514684 INFO::Set up parallel execution backend with 2 workers
2026-01-23 18:45:06.515099 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-23 18:45:07.115267 INFO::Adjusting the last 2 batches sequentially
2026-01-23 18:45:07.116037 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-23 18:45:07.124162 INFO::Done
2026-01-23 18:45:07.124471 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:07.126577 INFO::ASW Batch was 0.499744627532473 prior to batch effect correction and is now 0.499744627532473 .
2026-01-23 18:45:07.126784 INFO::ASW Label was 0.318487168766093 prior to batch effect correction and is now 0.318487168766093 .
2026-01-23 18:45:07.127033 INFO::Total function execution time is 1.17985606193542 s and adjustment time is 1.16038513183594 s ( 98.35 )
2026-01-23 18:45:07.214885 INFO::Formatting Data.
2026-01-23 18:45:07.215429 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.215915 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.216459 INFO::Found 0 missing values.
2026-01-23 18:45:07.218164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.218545 INFO::Done
2026-01-23 18:45:07.218755 INFO::Acquiring quality metrics before batch effect correction.
2026-01-23 18:45:07.220398 INFO::Starting hierarchical adjustment
2026-01-23 18:45:07.221016 INFO::Found 3 batches.
2026-01-23 18:45:07.221296 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-23 18:45:07.221737 INFO::Using default BPPARAM
2026-01-23 18:45:07.222043 INFO::Processing subtree level 1
2026-01-23 18:45:07.296477 INFO::Adjusting the last 1 batches sequentially
2026-01-23 18:45:07.299161 INFO::Done
2026-01-23 18:45:07.299579 INFO::Acquiring quality metrics after batch effect correction.
2026-01-23 18:45:07.302079 INFO::ASW Batch was 0.214375195688265 prior to batch effect correction and is now -0.140149081647636 .
2026-01-23 18:45:07.302474 INFO::ASW Label was -0.196728257178098 prior to batch effect correction and is now 0.109926177255943 .
2026-01-23 18:45:07.303393 INFO::Total function execution time is 0.0883300304412842 s and adjustment time is 0.078261137008667 s ( 88.6 )
2026-01-23 18:45:07.38566 INFO::Formatting Data.
2026-01-23 18:45:07.386082 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.386563 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.387039 INFO::Found 2 missing values.
2026-01-23 18:45:07.388272 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.3885 INFO::Done
2026-01-23 18:45:07.405944 INFO::Found NA in Reference column
2026-01-23 18:45:07.412373 INFO::Require at least two references per batch.
2026-01-23 18:45:07.423304 INFO::Formatting Data.
2026-01-23 18:45:07.423646 INFO::Recognized SummarizedExperiment
2026-01-23 18:45:07.423854 INFO::Typecasting input to dataframe.
2026-01-23 18:45:07.428302 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.429219 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.431172 INFO::Found 0 missing values.
2026-01-23 18:45:07.434573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.434933 INFO::Done
2026-01-23 18:45:07.443805 INFO::Formatting Data.
2026-01-23 18:45:07.444196 INFO::Recognized SummarizedExperiment
2026-01-23 18:45:07.444413 INFO::Typecasting input to dataframe.
2026-01-23 18:45:07.451331 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.451946 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.454005 INFO::Found 0 missing values.
2026-01-23 18:45:07.458674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.45898 INFO::Done
2026-01-23 18:45:07.466592 INFO::Formatting Data.
2026-01-23 18:45:07.47348 INFO::Recognized SummarizedExperiment
2026-01-23 18:45:07.473822 INFO::Typecasting input to dataframe.
2026-01-23 18:45:07.480444 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.480923 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.48142 INFO::Found 0 missing values.
2026-01-23 18:45:07.481765 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.
2026-01-23 18:45:07.483524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.4848 INFO::Done
2026-01-23 18:45:07.50005 INFO::Formatting Data.
2026-01-23 18:45:07.50047 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.500831 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.501243 INFO::Found 0 missing values.
2026-01-23 18:45:07.502268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.502477 INFO::Done
2026-01-23 18:45:07.508002 INFO::Formatting Data.
2026-01-23 18:45:07.508274 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.508572 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.508939 INFO::Found 0 missing values.
2026-01-23 18:45:07.509866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.510044 INFO::Done
2026-01-23 18:45:07.530579 INFO::Formatting Data.
2026-01-23 18:45:07.530964 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.531506 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.531958 INFO::Found 1 missing values.
2026-01-23 18:45:07.532875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.533062 INFO::Done
2026-01-23 18:45:07.543211 INFO::Formatting Data.
2026-01-23 18:45:07.54352 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.543906 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.544351 INFO::Found 2 missing values.
2026-01-23 18:45:07.544718 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.
2026-01-23 18:45:07.54568 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.545941 INFO::Done
2026-01-23 18:45:07.551464 INFO::Formatting Data.
2026-01-23 18:45:07.551781 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.552137 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.552473 INFO::Found 2 missing values.
2026-01-23 18:45:07.553021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.553204 INFO::Done
2026-01-23 18:45:07.558534 INFO::Formatting Data.
2026-01-23 18:45:07.558866 INFO::Typecasting input to dataframe.
2026-01-23 18:45:07.559141 INFO::Replacing NaNs with NAs.
2026-01-23 18:45:07.55944 INFO::Removing potential empty rows and columns
2026-01-23 18:45:07.55978 INFO::Found 0 missing values.
2026-01-23 18:45:07.560996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-23 18:45:07.561263 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.862 2.183 11.121
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.760 | 0.489 | 8.253 | |
| compute_asw | 0.010 | 0.000 | 0.012 | |
| count_existing | 0.004 | 0.000 | 0.005 | |
| generate_data_covariables | 0.005 | 0.001 | 0.007 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |