Yannis Schumann
| Snapshot Date: 2026-01-04 13:40 -0500 (Sun, 04 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 2026-01-05 11:35 -0500 (Mon, 05 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 168/2332 | 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: 2026-01-04 18:37:09 -0500 (Sun, 04 Jan 2026) |
| EndedAt: 2026-01-04 18:37:44 -0500 (Sun, 04 Jan 2026) |
| EllapsedTime: 35.5 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) (2025-11-04 r88984)
* 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 10.236 0.423 7.562
* 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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
2026-01-04 18:37:36.106016 INFO::Formatting Data.
2026-01-04 18:37:36.108662 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:36.113626 INFO::Removing potential empty rows and columns
2026-01-04 18:37:36.221374 INFO::Found 0 missing values.
2026-01-04 18:37:36.222503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:36.222757 INFO::Done
2026-01-04 18:37:36.222947 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:36.228501 INFO::Starting hierarchical adjustment
2026-01-04 18:37:36.228813 INFO::Found 3 batches.
2026-01-04 18:37:36.229002 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:36.229415 INFO::Using default BPPARAM
2026-01-04 18:37:36.229593 INFO::Processing subtree level 1
2026-01-04 18:37:36.281981 INFO::Adjusting the last 1 batches sequentially
2026-01-04 18:37:36.283188 INFO::Done
2026-01-04 18:37:36.283496 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:36.285089 INFO::ASW Batch was 0.0201136747912341 prior to batch effect correction and is now 0.0201136747912341 .
2026-01-04 18:37:36.285563 INFO::Total function execution time is 0.179964065551758 s and adjustment time is 0.0544300079345703 s ( 30.24 )
2026-01-04 18:37:36.294207 INFO::Formatting Data.
2026-01-04 18:37:36.294557 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:36.29495 INFO::Removing potential empty rows and columns
2026-01-04 18:37:36.295485 INFO::Found 0 missing values.
2026-01-04 18:37:36.295883 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.
2026-01-04 18:37:36.30134 INFO::Formatting Data.
2026-01-04 18:37:36.301686 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:36.302042 INFO::Removing potential empty rows and columns
2026-01-04 18:37:36.302956 INFO::Found 0 missing values.
2026-01-04 18:37:36.303333 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.
2026-01-04 18:37:36.310444 INFO::Formatting Data.
2026-01-04 18:37:36.310731 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:36.311081 INFO::Removing potential empty rows and columns
2026-01-04 18:37:36.311485 INFO::Found 0 missing values.
2026-01-04 18:37:36.31181 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.
2026-01-04 18:37:36.313571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:36.313801 INFO::Done
2026-01-04 18:37:36.314038 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:36.315538 INFO::Starting hierarchical adjustment
2026-01-04 18:37:36.315853 INFO::Found 2 batches.
2026-01-04 18:37:36.316085 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:36.316387 INFO::Using default BPPARAM
2026-01-04 18:37:36.316646 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:36.31712 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-04 18:37:36.327864 INFO::Done
2026-01-04 18:37:36.32814 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:36.328918 INFO::ASW Batch was 0.0551914679418217 prior to batch effect correction and is now -0.114813689574291 .
2026-01-04 18:37:36.32923 INFO::Total function execution time is 0.0188109874725342 s and adjustment time is 0.0120689868927002 s ( 64.16 )
2026-01-04 18:37:36.330463 INFO::Formatting Data.
2026-01-04 18:37:36.330835 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:36.334335 INFO::Formatting Data.
2026-01-04 18:37:36.334564 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:36.334879 INFO::Removing potential empty rows and columns
2026-01-04 18:37:36.336732 INFO::Found 0 missing values.
2026-01-04 18:37:36.338322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:36.338566 INFO::Done
2026-01-04 18:37:36.338816 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:36.339659 INFO::Starting hierarchical adjustment
2026-01-04 18:37:36.339959 INFO::Found 2 batches.
2026-01-04 18:37:36.34014 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:36.340354 INFO::Using default BPPARAM
2026-01-04 18:37:36.340532 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:36.34084 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-04 18:37:36.368449 INFO::Done
2026-01-04 18:37:36.368714 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:36.369359 INFO::ASW Batch was -0.0491444819375745 prior to batch effect correction and is now -0.120859490195251 .
2026-01-04 18:37:36.369607 INFO::Total function execution time is 0.0352718830108643 s and adjustment time is 0.0285329818725586 s ( 80.89 )
2026-01-04 18:37:36.369944 INFO::Formatting Data.
2026-01-04 18:37:36.37014 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:36.370414 INFO::Removing potential empty rows and columns
2026-01-04 18:37:36.370732 INFO::Found 0 missing values.
2026-01-04 18:37:36.371607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:36.371783 INFO::Done
2026-01-04 18:37:36.371938 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:36.372511 INFO::Starting hierarchical adjustment
2026-01-04 18:37:36.372751 INFO::Found 2 batches.
2026-01-04 18:37:36.372945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:36.373173 INFO::Using default BPPARAM
2026-01-04 18:37:36.373354 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:36.373656 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-04 18:37:36.379565 INFO::Done
2026-01-04 18:37:36.379842 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:36.38064 INFO::ASW Batch was -0.0491444819375745 prior to batch effect correction and is now -0.120859490195251 .
2026-01-04 18:37:36.380931 INFO::Total function execution time is 0.0109658241271973 s and adjustment time is 0.0068519115447998 s ( 62.48 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-04 18:37:37.673385 INFO::Formatting Data.
2026-01-04 18:37:37.673674 INFO::Recognized SummarizedExperiment
2026-01-04 18:37:37.673873 INFO::Typecasting input to dataframe.
2026-01-04 18:37:37.685016 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:37.685456 INFO::Removing potential empty rows and columns
2026-01-04 18:37:37.686624 INFO::Found 0 missing values.
2026-01-04 18:37:37.688615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:37.688785 INFO::Done
2026-01-04 18:37:37.688928 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:37.690158 INFO::Starting hierarchical adjustment
2026-01-04 18:37:37.690398 INFO::Found 2 batches.
2026-01-04 18:37:37.690548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:37.690889 INFO::Using default BPPARAM
2026-01-04 18:37:37.691035 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:37.691307 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-04 18:37:37.70818 INFO::Done
2026-01-04 18:37:37.708406 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:37.709602 INFO::ASW Batch was -0.00521436914528872 prior to batch effect correction and is now -0.094635922133254 .
2026-01-04 18:37:37.709873 INFO::Total function execution time is 0.0366160869598389 s and adjustment time is 0.0178239345550537 s ( 48.68 )
Warning: stack imbalance in '{', 73 then 75
2026-01-04 18:37:37.716519 INFO::Formatting Data.
2026-01-04 18:37:37.716746 INFO::Recognized SummarizedExperiment
2026-01-04 18:37:37.71691 INFO::Typecasting input to dataframe.
2026-01-04 18:37:37.71987 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:37.720228 INFO::Removing potential empty rows and columns
2026-01-04 18:37:37.721365 INFO::Found 0 missing values.
2026-01-04 18:37:37.723514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:37.723682 INFO::Done
2026-01-04 18:37:37.723838 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:37.725031 INFO::Starting hierarchical adjustment
2026-01-04 18:37:37.725245 INFO::Found 2 batches.
2026-01-04 18:37:37.725399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:37.72558 INFO::Using default BPPARAM
2026-01-04 18:37:37.725727 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:37.726011 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-04 18:37:37.734073 INFO::Done
2026-01-04 18:37:37.734323 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:37.735778 INFO::ASW Batch was -0.00771101334005464 prior to batch effect correction and is now -0.00771101334005464 .
2026-01-04 18:37:37.736113 INFO::Total function execution time is 0.019582986831665 s and adjustment time is 0.00886297225952148 s ( 45.26 )
2026-01-04 18:37:37.74431 INFO::Formatting Data.
2026-01-04 18:37:37.744562 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:37.74491 INFO::Removing potential empty rows and columns
2026-01-04 18:37:37.745299 INFO::Found 0 missing values.
2026-01-04 18:37:37.746365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:37.746582 INFO::Done
2026-01-04 18:37:37.746761 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:37.747516 INFO::Starting hierarchical adjustment
2026-01-04 18:37:37.747764 INFO::Found 3 batches.
2026-01-04 18:37:37.747958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:37.748188 INFO::Using default BPPARAM
2026-01-04 18:37:37.748384 INFO::Processing subtree level 1
2026-01-04 18:37:37.810038 INFO::Adjusting the last 1 batches sequentially
2026-01-04 18:37:37.813459 INFO::Done
2026-01-04 18:37:37.814244 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:37.816733 INFO::ASW Batch was 0.0165862807867286 prior to batch effect correction and is now -0.149979923030571 .
2026-01-04 18:37:37.817663 INFO::Total function execution time is 0.0733621120452881 s and adjustment time is 0.0657188892364502 s ( 89.58 )
2026-01-04 18:37:37.8253 INFO::Skipping initial DF formatting
2026-01-04 18:37:37.825605 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:37.827233 INFO::Starting hierarchical adjustment
2026-01-04 18:37:37.827524 INFO::Found 5 batches.
2026-01-04 18:37:37.827704 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:37.827949 INFO::Using default BPPARAM
2026-01-04 18:37:37.828123 INFO::Processing subtree level 1
2026-01-04 18:37:37.884716 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:37.885922 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-04 18:37:37.893747 INFO::Done
2026-01-04 18:37:37.894277 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:37.896352 INFO::ASW Batch was 0.505111380297568 prior to batch effect correction and is now 0.505111380297568 .
2026-01-04 18:37:37.896549 INFO::ASW Label was 0.381196212338154 prior to batch effect correction and is now 0.381196212338154 .
2026-01-04 18:37:37.897175 INFO::Total function execution time is 0.0719120502471924 s and adjustment time is 0.0662920475006104 s ( 92.18 )
2026-01-04 18:37:37.90758 INFO::Formatting Data.
2026-01-04 18:37:37.907969 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:37.908405 INFO::Removing potential empty rows and columns
2026-01-04 18:37:37.908843 INFO::Found 0 missing values.
2026-01-04 18:37:37.910433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:37.910644 INFO::Done
2026-01-04 18:37:37.910865 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:37.912141 INFO::Starting hierarchical adjustment
2026-01-04 18:37:37.912447 INFO::Found 5 batches.
2026-01-04 18:37:37.912633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:37.912896 INFO::Using default BPPARAM
2026-01-04 18:37:37.913084 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.
2026-01-04 18:37:37.97116 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:37.973278 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-04 18:37:37.981318 INFO::Done
2026-01-04 18:37:37.981653 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:37.983259 INFO::ASW Batch was 0.408737842120121 prior to batch effect correction and is now -0.0973136247232524 .
2026-01-04 18:37:37.983473 INFO::ASW Label was 0.383881134756657 prior to batch effect correction and is now 0.828332071915725 .
2026-01-04 18:37:37.983931 INFO::Total function execution time is 0.0764288902282715 s and adjustment time is 0.0689358711242676 s ( 90.2 )
2026-01-04 18:37:37.985235 INFO::Formatting Data.
2026-01-04 18:37:37.985447 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:37.985735 INFO::Removing potential empty rows and columns
2026-01-04 18:37:37.986042 INFO::Found 0 missing values.
2026-01-04 18:37:37.987187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:37.987346 INFO::Done
2026-01-04 18:37:37.987496 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:37.988368 INFO::Starting hierarchical adjustment
2026-01-04 18:37:37.988605 INFO::Found 5 batches.
2026-01-04 18:37:37.98876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:37.988986 INFO::Using default BPPARAM
2026-01-04 18:37:37.989487 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.
2026-01-04 18:37:38.042227 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:38.044942 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-04 18:37:38.053125 INFO::Done
2026-01-04 18:37:38.053516 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.055038 INFO::ASW Batch was 0.408737842120121 prior to batch effect correction and is now -0.0973136247232524 .
2026-01-04 18:37:38.055243 INFO::ASW Label was 0.383881134756657 prior to batch effect correction and is now 0.828332071915725 .
2026-01-04 18:37:38.055715 INFO::Total function execution time is 0.070465087890625 s and adjustment time is 0.06455397605896 s ( 91.61 )
2026-01-04 18:37:38.064639 INFO::Formatting Data.
2026-01-04 18:37:38.064907 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.065238 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.065595 INFO::Found 0 missing values.
2026-01-04 18:37:38.06686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.067039 INFO::Done
2026-01-04 18:37:38.067204 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.06835 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.068701 INFO::Found 5 batches.
2026-01-04 18:37:38.068894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.069121 INFO::Using default BPPARAM
2026-01-04 18:37:38.069289 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.
2026-01-04 18:37:38.133723 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:38.136289 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-04 18:37:38.145614 INFO::Done
2026-01-04 18:37:38.146214 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.147911 INFO::ASW Batch was 0.264043592525811 prior to batch effect correction and is now -0.0577768337473714 .
2026-01-04 18:37:38.148133 INFO::ASW Label was 0.523429800070043 prior to batch effect correction and is now 0.804642812461008 .
2026-01-04 18:37:38.148637 INFO::Total function execution time is 0.0840258598327637 s and adjustment time is 0.0769760608673096 s ( 91.61 )
2026-01-04 18:37:38.149011 INFO::Formatting Data.
2026-01-04 18:37:38.149224 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.149524 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.149854 INFO::Found 0 missing values.
2026-01-04 18:37:38.151057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.151236 INFO::Done
2026-01-04 18:37:38.151432 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.152543 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.152972 INFO::Found 5 batches.
2026-01-04 18:37:38.153154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.153375 INFO::Using default BPPARAM
2026-01-04 18:37:38.153662 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.
2026-01-04 18:37:38.212476 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:38.214702 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-04 18:37:38.22276 INFO::Done
2026-01-04 18:37:38.223137 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.22447 INFO::ASW Batch was 0.264043592525811 prior to batch effect correction and is now -0.0577768337473714 .
2026-01-04 18:37:38.224673 INFO::ASW Label was 0.523429800070043 prior to batch effect correction and is now 0.804642812461008 .
2026-01-04 18:37:38.225091 INFO::Total function execution time is 0.076092004776001 s and adjustment time is 0.0700130462646484 s ( 92.01 )
2026-01-04 18:37:38.231277 INFO::Formatting Data.
2026-01-04 18:37:38.231497 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.231806 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.232141 INFO::Found 0 missing values.
2026-01-04 18:37:38.232965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.233134 INFO::Done
2026-01-04 18:37:38.233293 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.234307 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.234593 INFO::Found 2 batches.
2026-01-04 18:37:38.234791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.235042 INFO::Using default BPPARAM
2026-01-04 18:37:38.235238 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:38.235557 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-04 18:37:38.241114 INFO::Done
2026-01-04 18:37:38.241362 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.242421 INFO::ASW Batch was 0.472947841274275 prior to batch effect correction and is now 0.00313499413487497 .
2026-01-04 18:37:38.242649 INFO::ASW Label was 0.526686702495056 prior to batch effect correction and is now 0.924275314284692 .
2026-01-04 18:37:38.242935 INFO::Total function execution time is 0.0116739273071289 s and adjustment time is 0.00657916069030762 s ( 56.36 )
2026-01-04 18:37:38.243209 INFO::Formatting Data.
2026-01-04 18:37:38.243427 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.243745 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.244094 INFO::Found 0 missing values.
2026-01-04 18:37:38.245048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.245254 INFO::Done
2026-01-04 18:37:38.245451 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.246473 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.246738 INFO::Found 2 batches.
2026-01-04 18:37:38.246934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.247162 INFO::Using default BPPARAM
2026-01-04 18:37:38.247358 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:38.247675 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-04 18:37:38.252881 INFO::Done
2026-01-04 18:37:38.2531 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.254067 INFO::ASW Batch was 0.472947841274275 prior to batch effect correction and is now 0.00313499413487497 .
2026-01-04 18:37:38.254266 INFO::ASW Label was 0.526686702495056 prior to batch effect correction and is now 0.924275314284692 .
2026-01-04 18:37:38.254508 INFO::Total function execution time is 0.0113050937652588 s and adjustment time is 0.00618910789489746 s ( 54.75 )
2026-01-04 18:37:38.259266 INFO::Formatting Data.
2026-01-04 18:37:38.259508 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.259792 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.260079 INFO::Found 0 missing values.
2026-01-04 18:37:38.260763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.260935 INFO::Done
2026-01-04 18:37:38.261107 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.261755 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.261976 INFO::Found 2 batches.
2026-01-04 18:37:38.262152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.26237 INFO::Using default BPPARAM
2026-01-04 18:37:38.262527 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:38.262771 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-04 18:37:38.27678 INFO::Done
2026-01-04 18:37:38.277061 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.277804 INFO::ASW Batch was -0.124019363649494 prior to batch effect correction and is now -0.17590584444394 .
2026-01-04 18:37:38.278241 INFO::Total function execution time is 0.0189480781555176 s and adjustment time is 0.0148279666900635 s ( 78.26 )
2026-01-04 18:37:38.283074 INFO::Formatting Data.
2026-01-04 18:37:38.283342 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.28364 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.283989 INFO::Found 0 missing values.
2026-01-04 18:37:38.284414 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.
2026-01-04 18:37:38.285808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.285988 INFO::Done
2026-01-04 18:37:38.286155 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.287073 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.287295 INFO::Found 2 batches.
2026-01-04 18:37:38.287453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.287648 INFO::Using default BPPARAM
2026-01-04 18:37:38.287799 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:38.288077 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-04 18:37:38.293437 INFO::Done
2026-01-04 18:37:38.293666 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.294573 INFO::ASW Batch was 0.398882536759363 prior to batch effect correction and is now -0.0362469975690976 .
2026-01-04 18:37:38.294772 INFO::ASW Label was 0.632621254943327 prior to batch effect correction and is now 0.943545859652085 .
2026-01-04 18:37:38.295023 INFO::Total function execution time is 0.01204514503479 s and adjustment time is 0.00617504119873047 s ( 51.27 )
2026-01-04 18:37:38.295255 INFO::Formatting Data.
2026-01-04 18:37:38.295439 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.295715 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.296021 INFO::Found 0 missing values.
2026-01-04 18:37:38.296306 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.
2026-01-04 18:37:38.297592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.297762 INFO::Done
2026-01-04 18:37:38.297915 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.298789 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.299006 INFO::Found 2 batches.
2026-01-04 18:37:38.299178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.299353 INFO::Using default BPPARAM
2026-01-04 18:37:38.299519 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:38.299799 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-04 18:37:38.304869 INFO::Done
2026-01-04 18:37:38.30508 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.305969 INFO::ASW Batch was 0.398882536759363 prior to batch effect correction and is now -0.0362469975690976 .
2026-01-04 18:37:38.306141 INFO::ASW Label was 0.632621254943327 prior to batch effect correction and is now 0.943545859652085 .
2026-01-04 18:37:38.306375 INFO::Total function execution time is 0.011113166809082 s and adjustment time is 0.00589489936828613 s ( 53.04 )
2026-01-04 18:37:38.376401 INFO::Formatting Data.
2026-01-04 18:37:38.376742 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.377064 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.377395 INFO::Found 0 missing values.
2026-01-04 18:37:38.378411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.378616 INFO::Done
2026-01-04 18:37:38.378802 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.379688 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.379954 INFO::Found 3 batches.
2026-01-04 18:37:38.380122 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.38031 INFO::Using default BPPARAM
2026-01-04 18:37:38.38059 INFO::Processing subtree level 1
2026-01-04 18:37:38.424754 INFO::Adjusting the last 1 batches sequentially
2026-01-04 18:37:38.426526 INFO::Done
2026-01-04 18:37:38.42752 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.4313 INFO::ASW Batch was 0.0143699211550902 prior to batch effect correction and is now 0.0143699211550902 .
2026-01-04 18:37:38.432703 INFO::Total function execution time is 0.0562889575958252 s and adjustment time is 0.0466201305389404 s ( 82.82 )
2026-01-04 18:37:38.433354 INFO::Formatting Data.
2026-01-04 18:37:38.433592 INFO::Typecasting input to dataframe.
2026-01-04 18:37:38.434098 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.434465 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.434871 INFO::Found 0 missing values.
2026-01-04 18:37:38.435809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.435984 INFO::Done
2026-01-04 18:37:38.43615 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.43682 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.437047 INFO::Found 3 batches.
2026-01-04 18:37:38.437372 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.437642 INFO::Using default BPPARAM
2026-01-04 18:37:38.437811 INFO::Processing subtree level 1
2026-01-04 18:37:38.482311 INFO::Adjusting the last 1 batches sequentially
2026-01-04 18:37:38.48353 INFO::Done
2026-01-04 18:37:38.483774 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.485323 INFO::ASW Batch was 0.0143699211550902 prior to batch effect correction and is now 0.0143699211550902 .
2026-01-04 18:37:38.48591 INFO::Total function execution time is 0.0525588989257812 s and adjustment time is 0.0465190410614014 s ( 88.51 )
2026-01-04 18:37:38.492515 INFO::Formatting Data.
2026-01-04 18:37:38.492785 INFO::Typecasting input to dataframe.
2026-01-04 18:37:38.493096 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.49343 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.493841 INFO::Found 0 missing values.
2026-01-04 18:37:38.494822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.495033 INFO::Done
2026-01-04 18:37:38.495239 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.495976 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.496218 INFO::Found 3 batches.
2026-01-04 18:37:38.49639 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.496635 INFO::Using default BPPARAM
2026-01-04 18:37:38.49681 INFO::Processing subtree level 1
2026-01-04 18:37:38.542895 INFO::Adjusting the last 1 batches sequentially
2026-01-04 18:37:38.544395 INFO::Done
2026-01-04 18:37:38.544621 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.546299 INFO::ASW Batch was -0.0918907327337102 prior to batch effect correction and is now -0.0918907327337102 .
2026-01-04 18:37:38.546784 INFO::Total function execution time is 0.0542941093444824 s and adjustment time is 0.0482299327850342 s ( 88.83 )
2026-01-04 18:37:38.631213 INFO::Formatting Data.
2026-01-04 18:37:38.631516 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.631977 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.633092 INFO::Found 1000 missing values.
2026-01-04 18:37:38.639457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.639717 INFO::Done
2026-01-04 18:37:38.639903 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.64228 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.642543 INFO::Found 10 batches.
2026-01-04 18:37:38.642728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:38.644005 INFO::Using default BPPARAM
2026-01-04 18:37:38.644372 INFO::Processing subtree level 1
2026-01-04 18:37:38.710013 INFO::Processing subtree level 2
2026-01-04 18:37:38.854733 INFO::Adjusting the last 1 batches sequentially
2026-01-04 18:37:38.856408 INFO::Done
2026-01-04 18:37:38.85666 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:38.904309 INFO::ASW Batch was 0.496064896869554 prior to batch effect correction and is now 0.496064896869554 .
2026-01-04 18:37:38.9049 INFO::ASW Label was 0.358474640976501 prior to batch effect correction and is now 0.358474640976501 .
2026-01-04 18:37:38.905854 INFO::Total function execution time is 0.274656057357788 s and adjustment time is 0.21391487121582 s ( 77.88 )
2026-01-04 18:37:38.906362 INFO::Formatting Data.
2026-01-04 18:37:38.906591 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:38.907095 INFO::Removing potential empty rows and columns
2026-01-04 18:37:38.908184 INFO::Found 1000 missing values.
2026-01-04 18:37:38.917269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:38.917697 INFO::Done
2026-01-04 18:37:38.91794 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:38.921026 INFO::Starting hierarchical adjustment
2026-01-04 18:37:38.921585 INFO::Found 10 batches.
2026-01-04 18:37:39.437974 INFO::Set up parallel execution backend with 2 workers
2026-01-04 18:37:39.438326 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-04 18:37:40.056859 INFO::Adjusting the last 2 batches sequentially
2026-01-04 18:37:40.057534 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-04 18:37:40.063486 INFO::Done
2026-01-04 18:37:40.063715 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:40.06564 INFO::ASW Batch was 0.496064896869554 prior to batch effect correction and is now 0.496064896869554 .
2026-01-04 18:37:40.065835 INFO::ASW Label was 0.358474640976501 prior to batch effect correction and is now 0.358474640976501 .
2026-01-04 18:37:40.066106 INFO::Total function execution time is 1.15975904464722 s and adjustment time is 1.14203786849976 s ( 98.47 )
2026-01-04 18:37:40.13775 INFO::Formatting Data.
2026-01-04 18:37:40.138045 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.138412 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.138874 INFO::Found 0 missing values.
2026-01-04 18:37:40.14022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.140435 INFO::Done
2026-01-04 18:37:40.140748 INFO::Acquiring quality metrics before batch effect correction.
2026-01-04 18:37:40.14179 INFO::Starting hierarchical adjustment
2026-01-04 18:37:40.142072 INFO::Found 3 batches.
2026-01-04 18:37:40.142256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-04 18:37:40.142506 INFO::Using default BPPARAM
2026-01-04 18:37:40.142687 INFO::Processing subtree level 1
2026-01-04 18:37:40.202837 INFO::Adjusting the last 1 batches sequentially
2026-01-04 18:37:40.208285 INFO::Done
2026-01-04 18:37:40.20863 INFO::Acquiring quality metrics after batch effect correction.
2026-01-04 18:37:40.211031 INFO::ASW Batch was 0.250528500432659 prior to batch effect correction and is now -0.157067229921832 .
2026-01-04 18:37:40.211302 INFO::ASW Label was -0.198754741427516 prior to batch effect correction and is now -0.110542941546434 .
2026-01-04 18:37:40.211895 INFO::Total function execution time is 0.0741720199584961 s and adjustment time is 0.0662391185760498 s ( 89.3 )
2026-01-04 18:37:40.269704 INFO::Formatting Data.
2026-01-04 18:37:40.270096 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.270527 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.271044 INFO::Found 2 missing values.
2026-01-04 18:37:40.272264 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.272489 INFO::Done
2026-01-04 18:37:40.286842 INFO::Found NA in Reference column
2026-01-04 18:37:40.291094 INFO::Require at least two references per batch.
2026-01-04 18:37:40.299923 INFO::Formatting Data.
2026-01-04 18:37:40.300237 INFO::Recognized SummarizedExperiment
2026-01-04 18:37:40.300423 INFO::Typecasting input to dataframe.
2026-01-04 18:37:40.304364 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.304789 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.306108 INFO::Found 0 missing values.
2026-01-04 18:37:40.308589 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.308785 INFO::Done
2026-01-04 18:37:40.314466 INFO::Formatting Data.
2026-01-04 18:37:40.314703 INFO::Recognized SummarizedExperiment
2026-01-04 18:37:40.314898 INFO::Typecasting input to dataframe.
2026-01-04 18:37:40.320774 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.321246 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.322669 INFO::Found 0 missing values.
2026-01-04 18:37:40.327522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.327751 INFO::Done
2026-01-04 18:37:40.334497 INFO::Formatting Data.
2026-01-04 18:37:40.33479 INFO::Recognized SummarizedExperiment
2026-01-04 18:37:40.334993 INFO::Typecasting input to dataframe.
2026-01-04 18:37:40.342259 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.342679 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.34313 INFO::Found 0 missing values.
2026-01-04 18:37:40.343519 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.
2026-01-04 18:37:40.345382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.345604 INFO::Done
2026-01-04 18:37:40.350743 INFO::Formatting Data.
2026-01-04 18:37:40.351075 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.351424 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.351816 INFO::Found 0 missing values.
2026-01-04 18:37:40.352936 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.353162 INFO::Done
2026-01-04 18:37:40.358826 INFO::Formatting Data.
2026-01-04 18:37:40.359268 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.359655 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.360067 INFO::Found 0 missing values.
2026-01-04 18:37:40.361123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.361323 INFO::Done
2026-01-04 18:37:40.374985 INFO::Formatting Data.
2026-01-04 18:37:40.375293 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.375684 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.376122 INFO::Found 1 missing values.
2026-01-04 18:37:40.37705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.377242 INFO::Done
2026-01-04 18:37:40.385218 INFO::Formatting Data.
2026-01-04 18:37:40.385498 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.385809 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.386136 INFO::Found 2 missing values.
2026-01-04 18:37:40.386456 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.
2026-01-04 18:37:40.387272 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.387457 INFO::Done
2026-01-04 18:37:40.392544 INFO::Formatting Data.
2026-01-04 18:37:40.392969 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.393355 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.393704 INFO::Found 2 missing values.
2026-01-04 18:37:40.394327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.394515 INFO::Done
2026-01-04 18:37:40.399173 INFO::Formatting Data.
2026-01-04 18:37:40.399499 INFO::Typecasting input to dataframe.
2026-01-04 18:37:40.399842 INFO::Replacing NaNs with NAs.
2026-01-04 18:37:40.400164 INFO::Removing potential empty rows and columns
2026-01-04 18:37:40.400553 INFO::Found 0 missing values.
2026-01-04 18:37:40.401572 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-04 18:37:40.401758 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.248 1.677 9.493
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.236 | 0.423 | 7.562 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.006 | 0.001 | 0.006 | |
| generate_data_covariables | 0.004 | 0.001 | 0.005 | |
| generate_dataset | 0.005 | 0.000 | 0.005 | |