Yannis Schumann
| Snapshot Date: 2026-02-11 13:40 -0500 (Wed, 11 Feb 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-12 11:32 -0500 (Thu, 12 Feb 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" | 4864 |
| 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 169/2352 | 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 | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-11 21:38:34 -0500 (Wed, 11 Feb 2026) |
| EndedAt: 2026-02-11 21:40:04 -0500 (Wed, 11 Feb 2026) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.594 1.164 16.921
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-11 21:39:25.413016 INFO::Formatting Data.
2026-02-11 21:39:25.414343 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:25.4253 INFO::Removing potential empty rows and columns
2026-02-11 21:39:25.664705 INFO::Found 0 missing values.
2026-02-11 21:39:25.668048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:25.668754 INFO::Done
2026-02-11 21:39:25.66932 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:25.680733 INFO::Starting hierarchical adjustment
2026-02-11 21:39:25.681609 INFO::Found 3 batches.
2026-02-11 21:39:25.682155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:25.683257 INFO::Using default BPPARAM
2026-02-11 21:39:25.683809 INFO::Processing subtree level 1
2026-02-11 21:39:25.782092 INFO::Adjusting the last 1 batches sequentially
2026-02-11 21:39:25.791503 INFO::Done
2026-02-11 21:39:25.792715 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:25.795789 INFO::ASW Batch was -0.0567793434591428 prior to batch effect correction and is now -0.0567793434591428 .
2026-02-11 21:39:25.797151 INFO::Total function execution time is 0.384760618209839 s and adjustment time is 0.109775304794312 s ( 28.53 )
2026-02-11 21:39:25.813182 INFO::Formatting Data.
2026-02-11 21:39:25.814064 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:25.815079 INFO::Removing potential empty rows and columns
2026-02-11 21:39:25.816354 INFO::Found 0 missing values.
2026-02-11 21:39:25.817375 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.
2026-02-11 21:39:25.82899 INFO::Formatting Data.
2026-02-11 21:39:25.82985 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:25.830792 INFO::Removing potential empty rows and columns
2026-02-11 21:39:25.831925 INFO::Found 0 missing values.
2026-02-11 21:39:25.832875 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.
2026-02-11 21:39:25.850118 INFO::Formatting Data.
2026-02-11 21:39:25.851025 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:25.851991 INFO::Removing potential empty rows and columns
2026-02-11 21:39:25.853101 INFO::Found 0 missing values.
2026-02-11 21:39:25.854115 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.
2026-02-11 21:39:25.859002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:25.859635 INFO::Done
2026-02-11 21:39:25.860204 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:25.862404 INFO::Starting hierarchical adjustment
2026-02-11 21:39:25.863139 INFO::Found 2 batches.
2026-02-11 21:39:25.863724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:25.864476 INFO::Using default BPPARAM
2026-02-11 21:39:25.865055 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:25.866007 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-11 21:39:25.889571 INFO::Done
2026-02-11 21:39:25.890359 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:25.892772 INFO::ASW Batch was 0.0144815280913121 prior to batch effect correction and is now -0.113625514497234 .
2026-02-11 21:39:25.893659 INFO::Total function execution time is 0.0436661243438721 s and adjustment time is 0.0265486240386963 s ( 60.8 )
2026-02-11 21:39:25.89677 INFO::Formatting Data.
2026-02-11 21:39:25.897441 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:25.906458 INFO::Formatting Data.
2026-02-11 21:39:25.907182 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:25.9081 INFO::Removing potential empty rows and columns
2026-02-11 21:39:25.909153 INFO::Found 0 missing values.
2026-02-11 21:39:25.912225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:25.912786 INFO::Done
2026-02-11 21:39:25.913324 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:25.915444 INFO::Starting hierarchical adjustment
2026-02-11 21:39:25.916167 INFO::Found 2 batches.
2026-02-11 21:39:25.916717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:25.91738 INFO::Using default BPPARAM
2026-02-11 21:39:25.917929 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:25.918912 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-11 21:39:25.970031 INFO::Done
2026-02-11 21:39:25.970766 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:25.972783 INFO::ASW Batch was 0.00680830014563774 prior to batch effect correction and is now -0.0924860219817975 .
2026-02-11 21:39:25.973664 INFO::Total function execution time is 0.0672359466552734 s and adjustment time is 0.0539877414703369 s ( 80.3 )
2026-02-11 21:39:25.974741 INFO::Formatting Data.
2026-02-11 21:39:25.975353 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:25.976228 INFO::Removing potential empty rows and columns
2026-02-11 21:39:25.977267 INFO::Found 0 missing values.
2026-02-11 21:39:25.980119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:25.980681 INFO::Done
2026-02-11 21:39:25.981207 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:25.983175 INFO::Starting hierarchical adjustment
2026-02-11 21:39:25.983879 INFO::Found 2 batches.
2026-02-11 21:39:25.984399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:25.984995 INFO::Using default BPPARAM
2026-02-11 21:39:25.985514 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:25.986421 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-11 21:39:26.001185 INFO::Done
2026-02-11 21:39:26.00188 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:26.003902 INFO::ASW Batch was 0.00680830014563774 prior to batch effect correction and is now -0.0924860219817975 .
2026-02-11 21:39:26.004723 INFO::Total function execution time is 0.0299782752990723 s and adjustment time is 0.017427921295166 s ( 58.14 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-11 21:39:29.230742 INFO::Formatting Data.
2026-02-11 21:39:29.231521 INFO::Recognized SummarizedExperiment
2026-02-11 21:39:29.232076 INFO::Typecasting input to dataframe.
2026-02-11 21:39:29.265023 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:29.266425 INFO::Removing potential empty rows and columns
2026-02-11 21:39:29.270875 INFO::Found 0 missing values.
2026-02-11 21:39:29.278634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:29.279354 INFO::Done
2026-02-11 21:39:29.279936 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:29.283719 INFO::Starting hierarchical adjustment
2026-02-11 21:39:29.284456 INFO::Found 2 batches.
2026-02-11 21:39:29.284996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:29.286147 INFO::Using default BPPARAM
2026-02-11 21:39:29.28673 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:29.287734 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-11 21:39:29.347003 INFO::Done
2026-02-11 21:39:29.347781 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:29.351483 INFO::ASW Batch was 0.00106679933287584 prior to batch effect correction and is now -0.0955019203655663 .
2026-02-11 21:39:29.352395 INFO::Total function execution time is 0.121974945068359 s and adjustment time is 0.0626730918884277 s ( 51.38 )
Warning: stack imbalance in '{', 73 then 75
2026-02-11 21:39:29.371739 INFO::Formatting Data.
2026-02-11 21:39:29.37253 INFO::Recognized SummarizedExperiment
2026-02-11 21:39:29.373113 INFO::Typecasting input to dataframe.
2026-02-11 21:39:29.382629 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:29.383813 INFO::Removing potential empty rows and columns
2026-02-11 21:39:29.387754 INFO::Found 0 missing values.
2026-02-11 21:39:29.395566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:29.396217 INFO::Done
2026-02-11 21:39:29.396784 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:29.400465 INFO::Starting hierarchical adjustment
2026-02-11 21:39:29.401198 INFO::Found 2 batches.
2026-02-11 21:39:29.401742 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:29.402391 INFO::Using default BPPARAM
2026-02-11 21:39:29.402924 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:29.403933 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-11 21:39:29.430933 INFO::Done
2026-02-11 21:39:29.431733 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:29.435539 INFO::ASW Batch was -0.010799483481971 prior to batch effect correction and is now -0.010799483481971 .
2026-02-11 21:39:29.436469 INFO::Total function execution time is 0.0646970272064209 s and adjustment time is 0.0298409461975098 s ( 46.12 )
2026-02-11 21:39:29.455852 INFO::Formatting Data.
2026-02-11 21:39:29.456738 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:29.45769 INFO::Removing potential empty rows and columns
2026-02-11 21:39:29.458766 INFO::Found 0 missing values.
2026-02-11 21:39:29.461852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:29.462408 INFO::Done
2026-02-11 21:39:29.462926 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:29.46508 INFO::Starting hierarchical adjustment
2026-02-11 21:39:29.46582 INFO::Found 3 batches.
2026-02-11 21:39:29.466343 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:29.466973 INFO::Using default BPPARAM
2026-02-11 21:39:29.46752 INFO::Processing subtree level 1
2026-02-11 21:39:29.617745 INFO::Adjusting the last 1 batches sequentially
2026-02-11 21:39:29.620041 INFO::Done
2026-02-11 21:39:29.620847 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:29.62362 INFO::ASW Batch was -0.0485744971358696 prior to batch effect correction and is now -0.13193866393218 .
2026-02-11 21:39:29.624662 INFO::Total function execution time is 0.168847322463989 s and adjustment time is 0.154328107833862 s ( 91.4 )
2026-02-11 21:39:29.640544 INFO::Skipping initial DF formatting
2026-02-11 21:39:29.641348 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:29.645891 INFO::Starting hierarchical adjustment
2026-02-11 21:39:29.646782 INFO::Found 5 batches.
2026-02-11 21:39:29.647384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:29.648048 INFO::Using default BPPARAM
2026-02-11 21:39:29.648619 INFO::Processing subtree level 1
2026-02-11 21:39:29.976351 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:29.978231 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-11 21:39:29.99881 INFO::Done
2026-02-11 21:39:29.999674 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:30.057058 INFO::ASW Batch was 0.520214676012953 prior to batch effect correction and is now 0.520214676012953 .
2026-02-11 21:39:30.058701 INFO::ASW Label was 0.365725400969506 prior to batch effect correction and is now 0.365725400969506 .
2026-02-11 21:39:30.059696 INFO::Total function execution time is 0.419275999069214 s and adjustment time is 0.352185249328613 s ( 84 )
2026-02-11 21:39:30.080473 INFO::Formatting Data.
2026-02-11 21:39:30.081506 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:30.082657 INFO::Removing potential empty rows and columns
2026-02-11 21:39:30.083982 INFO::Found 0 missing values.
2026-02-11 21:39:30.089199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:30.089852 INFO::Done
2026-02-11 21:39:30.090465 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:30.094603 INFO::Starting hierarchical adjustment
2026-02-11 21:39:30.095452 INFO::Found 5 batches.
2026-02-11 21:39:30.096075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:30.096792 INFO::Using default BPPARAM
2026-02-11 21:39:30.097441 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.
2026-02-11 21:39:30.268071 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:30.269955 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-11 21:39:30.289404 INFO::Done
2026-02-11 21:39:30.290347 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:30.29455 INFO::ASW Batch was 0.317744447167639 prior to batch effect correction and is now -0.110456881807941 .
2026-02-11 21:39:30.295303 INFO::ASW Label was 0.270230224796561 prior to batch effect correction and is now 0.871837896001916 .
2026-02-11 21:39:30.296258 INFO::Total function execution time is 0.215953588485718 s and adjustment time is 0.194110631942749 s ( 89.89 )
2026-02-11 21:39:30.297197 INFO::Formatting Data.
2026-02-11 21:39:30.297965 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:30.299 INFO::Removing potential empty rows and columns
2026-02-11 21:39:30.300229 INFO::Found 0 missing values.
2026-02-11 21:39:30.305017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:30.305661 INFO::Done
2026-02-11 21:39:30.30626 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:30.309781 INFO::Starting hierarchical adjustment
2026-02-11 21:39:30.310554 INFO::Found 5 batches.
2026-02-11 21:39:30.3111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:30.311775 INFO::Using default BPPARAM
2026-02-11 21:39:30.312323 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.
2026-02-11 21:39:30.454126 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:30.456017 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-11 21:39:30.474461 INFO::Done
2026-02-11 21:39:30.475342 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:30.4793 INFO::ASW Batch was 0.317744447167639 prior to batch effect correction and is now -0.110456881807941 .
2026-02-11 21:39:30.479997 INFO::ASW Label was 0.270230224796561 prior to batch effect correction and is now 0.871837896001916 .
2026-02-11 21:39:30.480991 INFO::Total function execution time is 0.183790922164917 s and adjustment time is 0.163986921310425 s ( 89.22 )
2026-02-11 21:39:30.497041 INFO::Formatting Data.
2026-02-11 21:39:30.497979 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:30.498988 INFO::Removing potential empty rows and columns
2026-02-11 21:39:30.500105 INFO::Found 0 missing values.
2026-02-11 21:39:30.504689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:30.505314 INFO::Done
2026-02-11 21:39:30.505871 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:30.509136 INFO::Starting hierarchical adjustment
2026-02-11 21:39:30.509913 INFO::Found 5 batches.
2026-02-11 21:39:30.51047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:30.511117 INFO::Using default BPPARAM
2026-02-11 21:39:30.511697 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.
2026-02-11 21:39:30.651294 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:30.653039 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-11 21:39:30.670315 INFO::Done
2026-02-11 21:39:30.671115 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:30.674834 INFO::ASW Batch was 0.493943977023395 prior to batch effect correction and is now -0.0715746331683515 .
2026-02-11 21:39:30.67557 INFO::ASW Label was 0.283184460884387 prior to batch effect correction and is now 0.775027138798126 .
2026-02-11 21:39:30.676461 INFO::Total function execution time is 0.179548263549805 s and adjustment time is 0.160514354705811 s ( 89.4 )
2026-02-11 21:39:30.677344 INFO::Formatting Data.
2026-02-11 21:39:30.678038 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:30.678988 INFO::Removing potential empty rows and columns
2026-02-11 21:39:30.680069 INFO::Found 0 missing values.
2026-02-11 21:39:30.684468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:30.685112 INFO::Done
2026-02-11 21:39:30.685793 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:30.689156 INFO::Starting hierarchical adjustment
2026-02-11 21:39:30.689932 INFO::Found 5 batches.
2026-02-11 21:39:30.690516 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:30.691181 INFO::Using default BPPARAM
2026-02-11 21:39:30.691761 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.
2026-02-11 21:39:30.842356 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:30.844204 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-11 21:39:30.862531 INFO::Done
2026-02-11 21:39:30.863418 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:30.867591 INFO::ASW Batch was 0.493943977023395 prior to batch effect correction and is now -0.0715746331683515 .
2026-02-11 21:39:30.868229 INFO::ASW Label was 0.283184460884387 prior to batch effect correction and is now 0.775027138798126 .
2026-02-11 21:39:30.86913 INFO::Total function execution time is 0.191778898239136 s and adjustment time is 0.172712087631226 s ( 90.06 )
2026-02-11 21:39:30.883161 INFO::Formatting Data.
2026-02-11 21:39:30.883967 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:30.88491 INFO::Removing potential empty rows and columns
2026-02-11 21:39:30.885934 INFO::Found 0 missing values.
2026-02-11 21:39:30.888707 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:30.889265 INFO::Done
2026-02-11 21:39:30.889797 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:30.893019 INFO::Starting hierarchical adjustment
2026-02-11 21:39:30.89375 INFO::Found 2 batches.
2026-02-11 21:39:30.894276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:30.894917 INFO::Using default BPPARAM
2026-02-11 21:39:30.895482 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:30.896424 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-11 21:39:30.913346 INFO::Done
2026-02-11 21:39:30.914215 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:30.918159 INFO::ASW Batch was 0.527435695862471 prior to batch effect correction and is now -0.0264140434931781 .
2026-02-11 21:39:30.918931 INFO::ASW Label was 0.544048740705668 prior to batch effect correction and is now 0.917772148291342 .
2026-02-11 21:39:30.919977 INFO::Total function execution time is 0.0368809700012207 s and adjustment time is 0.0196988582611084 s ( 53.41 )
2026-02-11 21:39:30.921011 INFO::Formatting Data.
2026-02-11 21:39:30.921805 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:30.922912 INFO::Removing potential empty rows and columns
2026-02-11 21:39:30.92418 INFO::Found 0 missing values.
2026-02-11 21:39:30.927977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:30.928692 INFO::Done
2026-02-11 21:39:30.929361 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:30.933209 INFO::Starting hierarchical adjustment
2026-02-11 21:39:30.93413 INFO::Found 2 batches.
2026-02-11 21:39:30.934808 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:30.935563 INFO::Using default BPPARAM
2026-02-11 21:39:30.93627 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:30.93742 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-11 21:39:30.957451 INFO::Done
2026-02-11 21:39:30.958423 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:30.962848 INFO::ASW Batch was 0.527435695862471 prior to batch effect correction and is now -0.0264140434931781 .
2026-02-11 21:39:30.963753 INFO::ASW Label was 0.544048740705668 prior to batch effect correction and is now 0.917772148291342 .
2026-02-11 21:39:30.964803 INFO::Total function execution time is 0.0438034534454346 s and adjustment time is 0.023451566696167 s ( 53.54 )
2026-02-11 21:39:30.979882 INFO::Formatting Data.
2026-02-11 21:39:30.980883 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:30.98201 INFO::Removing potential empty rows and columns
2026-02-11 21:39:30.983223 INFO::Found 0 missing values.
2026-02-11 21:39:30.986015 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:30.986679 INFO::Done
2026-02-11 21:39:30.987324 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:30.989783 INFO::Starting hierarchical adjustment
2026-02-11 21:39:30.990668 INFO::Found 2 batches.
2026-02-11 21:39:30.991306 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:30.992048 INFO::Using default BPPARAM
2026-02-11 21:39:30.992721 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:30.993814 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-11 21:39:31.061711 INFO::Done
2026-02-11 21:39:31.063122 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:31.06642 INFO::ASW Batch was -0.0449148930757144 prior to batch effect correction and is now -0.126220487849738 .
2026-02-11 21:39:31.067686 INFO::Total function execution time is 0.0878691673278809 s and adjustment time is 0.0711057186126709 s ( 80.92 )
2026-02-11 21:39:31.088868 INFO::Formatting Data.
2026-02-11 21:39:31.08985 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:31.091025 INFO::Removing potential empty rows and columns
2026-02-11 21:39:31.092272 INFO::Found 0 missing values.
2026-02-11 21:39:31.093794 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.
2026-02-11 21:39:31.099896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:31.100581 INFO::Done
2026-02-11 21:39:31.10124 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:31.105273 INFO::Starting hierarchical adjustment
2026-02-11 21:39:31.106118 INFO::Found 2 batches.
2026-02-11 21:39:31.106754 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:31.107518 INFO::Using default BPPARAM
2026-02-11 21:39:31.108163 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:31.109288 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-11 21:39:31.132039 INFO::Done
2026-02-11 21:39:31.132869 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:31.13656 INFO::ASW Batch was 0.64916387981111 prior to batch effect correction and is now -0.0137405940142278 .
2026-02-11 21:39:31.137329 INFO::ASW Label was 0.306086326291051 prior to batch effect correction and is now 0.895686599832631 .
2026-02-11 21:39:31.138332 INFO::Total function execution time is 0.0495727062225342 s and adjustment time is 0.0260710716247559 s ( 52.59 )
2026-02-11 21:39:31.139397 INFO::Formatting Data.
2026-02-11 21:39:31.140178 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:31.141781 INFO::Removing potential empty rows and columns
2026-02-11 21:39:31.143042 INFO::Found 0 missing values.
2026-02-11 21:39:31.144159 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.
2026-02-11 21:39:31.149918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:31.150604 INFO::Done
2026-02-11 21:39:31.151491 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:31.155219 INFO::Starting hierarchical adjustment
2026-02-11 21:39:31.15608 INFO::Found 2 batches.
2026-02-11 21:39:31.156767 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:31.157526 INFO::Using default BPPARAM
2026-02-11 21:39:31.158171 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:31.15934 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-11 21:39:31.180304 INFO::Done
2026-02-11 21:39:31.181129 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:31.184812 INFO::ASW Batch was 0.64916387981111 prior to batch effect correction and is now -0.0137405940142278 .
2026-02-11 21:39:31.185552 INFO::ASW Label was 0.306086326291051 prior to batch effect correction and is now 0.895686599832631 .
2026-02-11 21:39:31.186513 INFO::Total function execution time is 0.0471515655517578 s and adjustment time is 0.0243792533874512 s ( 51.7 )
2026-02-11 21:39:31.4239 INFO::Formatting Data.
2026-02-11 21:39:31.424752 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:31.425735 INFO::Removing potential empty rows and columns
2026-02-11 21:39:31.42684 INFO::Found 0 missing values.
2026-02-11 21:39:31.429895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:31.430455 INFO::Done
2026-02-11 21:39:31.430986 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:31.433088 INFO::Starting hierarchical adjustment
2026-02-11 21:39:31.433816 INFO::Found 3 batches.
2026-02-11 21:39:31.434375 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:31.435019 INFO::Using default BPPARAM
2026-02-11 21:39:31.435573 INFO::Processing subtree level 1
2026-02-11 21:39:31.532926 INFO::Adjusting the last 1 batches sequentially
2026-02-11 21:39:31.534724 INFO::Done
2026-02-11 21:39:31.535403 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:31.537941 INFO::ASW Batch was -0.0738108129680049 prior to batch effect correction and is now -0.0738108129680049 .
2026-02-11 21:39:31.53896 INFO::Total function execution time is 0.115101337432861 s and adjustment time is 0.101039171218872 s ( 87.78 )
2026-02-11 21:39:31.540095 INFO::Formatting Data.
2026-02-11 21:39:31.540786 INFO::Typecasting input to dataframe.
2026-02-11 21:39:31.541562 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:31.542511 INFO::Removing potential empty rows and columns
2026-02-11 21:39:31.543673 INFO::Found 0 missing values.
2026-02-11 21:39:31.546772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:31.547403 INFO::Done
2026-02-11 21:39:31.547959 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:31.550149 INFO::Starting hierarchical adjustment
2026-02-11 21:39:31.550901 INFO::Found 3 batches.
2026-02-11 21:39:31.55146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:31.552122 INFO::Using default BPPARAM
2026-02-11 21:39:31.552728 INFO::Processing subtree level 1
2026-02-11 21:39:31.64694 INFO::Adjusting the last 1 batches sequentially
2026-02-11 21:39:31.648778 INFO::Done
2026-02-11 21:39:31.649487 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:31.652095 INFO::ASW Batch was -0.0738108129680049 prior to batch effect correction and is now -0.0738108129680049 .
2026-02-11 21:39:31.6531 INFO::Total function execution time is 0.112974166870117 s and adjustment time is 0.0980105400085449 s ( 86.75 )
2026-02-11 21:39:31.666777 INFO::Formatting Data.
2026-02-11 21:39:31.667643 INFO::Typecasting input to dataframe.
2026-02-11 21:39:31.668541 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:31.669729 INFO::Removing potential empty rows and columns
2026-02-11 21:39:31.670881 INFO::Found 0 missing values.
2026-02-11 21:39:31.673986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:31.674588 INFO::Done
2026-02-11 21:39:31.675145 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:31.677291 INFO::Starting hierarchical adjustment
2026-02-11 21:39:31.678033 INFO::Found 3 batches.
2026-02-11 21:39:31.678607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:31.679268 INFO::Using default BPPARAM
2026-02-11 21:39:31.679852 INFO::Processing subtree level 1
2026-02-11 21:39:31.771825 INFO::Adjusting the last 1 batches sequentially
2026-02-11 21:39:31.773691 INFO::Done
2026-02-11 21:39:31.774429 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:31.777277 INFO::ASW Batch was -0.0304144990740742 prior to batch effect correction and is now -0.0304144990740742 .
2026-02-11 21:39:31.778301 INFO::Total function execution time is 0.111557483673096 s and adjustment time is 0.0957851409912109 s ( 85.86 )
2026-02-11 21:39:31.926276 INFO::Formatting Data.
2026-02-11 21:39:31.927185 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:31.928355 INFO::Removing potential empty rows and columns
2026-02-11 21:39:31.931319 INFO::Found 1000 missing values.
2026-02-11 21:39:31.951192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:31.952033 INFO::Done
2026-02-11 21:39:31.952631 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:31.958294 INFO::Starting hierarchical adjustment
2026-02-11 21:39:31.95911 INFO::Found 10 batches.
2026-02-11 21:39:31.959696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:31.960342 INFO::Using default BPPARAM
2026-02-11 21:39:31.960923 INFO::Processing subtree level 1
2026-02-11 21:39:32.108886 INFO::Processing subtree level 2
2026-02-11 21:39:32.256126 INFO::Adjusting the last 1 batches sequentially
2026-02-11 21:39:32.258128 INFO::Done
2026-02-11 21:39:32.258811 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:32.264442 INFO::ASW Batch was 0.461250167941402 prior to batch effect correction and is now 0.461250167941402 .
2026-02-11 21:39:32.265135 INFO::ASW Label was 0.370988549854944 prior to batch effect correction and is now 0.370988549854944 .
2026-02-11 21:39:32.266131 INFO::Total function execution time is 0.339881181716919 s and adjustment time is 0.299166440963745 s ( 88.02 )
2026-02-11 21:39:32.267043 INFO::Formatting Data.
2026-02-11 21:39:32.267719 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:32.268977 INFO::Removing potential empty rows and columns
2026-02-11 21:39:32.27191 INFO::Found 1000 missing values.
2026-02-11 21:39:32.291714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:32.292481 INFO::Done
2026-02-11 21:39:32.293071 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:32.298751 INFO::Starting hierarchical adjustment
2026-02-11 21:39:32.299554 INFO::Found 10 batches.
2026-02-11 21:39:33.639771 INFO::Set up parallel execution backend with 2 workers
2026-02-11 21:39:33.642268 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-11 21:39:34.967179 INFO::Adjusting the last 2 batches sequentially
2026-02-11 21:39:34.969152 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-11 21:39:34.985929 INFO::Done
2026-02-11 21:39:34.986659 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:34.991272 INFO::ASW Batch was 0.461250167941402 prior to batch effect correction and is now 0.461250167941402 .
2026-02-11 21:39:34.991927 INFO::ASW Label was 0.370988549854944 prior to batch effect correction and is now 0.370988549854944 .
2026-02-11 21:39:34.992688 INFO::Total function execution time is 2.72568035125732 s and adjustment time is 2.68648481369019 s ( 98.56 )
2026-02-11 21:39:35.135278 INFO::Formatting Data.
2026-02-11 21:39:35.136096 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.136998 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.138053 INFO::Found 0 missing values.
2026-02-11 21:39:35.141651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.142209 INFO::Done
2026-02-11 21:39:35.142724 INFO::Acquiring quality metrics before batch effect correction.
2026-02-11 21:39:35.145357 INFO::Starting hierarchical adjustment
2026-02-11 21:39:35.146074 INFO::Found 3 batches.
2026-02-11 21:39:35.146604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-11 21:39:35.147246 INFO::Using default BPPARAM
2026-02-11 21:39:35.147774 INFO::Processing subtree level 1
2026-02-11 21:39:35.254005 INFO::Adjusting the last 1 batches sequentially
2026-02-11 21:39:35.25594 INFO::Done
2026-02-11 21:39:35.256662 INFO::Acquiring quality metrics after batch effect correction.
2026-02-11 21:39:35.26006 INFO::ASW Batch was 0.255255247432166 prior to batch effect correction and is now -0.151089034004133 .
2026-02-11 21:39:35.260747 INFO::ASW Label was -0.183861507525848 prior to batch effect correction and is now 0.0663733429640277 .
2026-02-11 21:39:35.261735 INFO::Total function execution time is 0.126510620117188 s and adjustment time is 0.109974145889282 s ( 86.93 )
2026-02-11 21:39:35.383951 INFO::Formatting Data.
2026-02-11 21:39:35.384835 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.385793 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.38687 INFO::Found 2 missing values.
2026-02-11 21:39:35.389713 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.390306 INFO::Done
2026-02-11 21:39:35.418274 INFO::Found NA in Reference column
2026-02-11 21:39:35.427752 INFO::Require at least two references per batch.
2026-02-11 21:39:35.448216 INFO::Formatting Data.
2026-02-11 21:39:35.449116 INFO::Recognized SummarizedExperiment
2026-02-11 21:39:35.449722 INFO::Typecasting input to dataframe.
2026-02-11 21:39:35.460158 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.461548 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.465241 INFO::Found 0 missing values.
2026-02-11 21:39:35.472234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.472961 INFO::Done
2026-02-11 21:39:35.489176 INFO::Formatting Data.
2026-02-11 21:39:35.490049 INFO::Recognized SummarizedExperiment
2026-02-11 21:39:35.490625 INFO::Typecasting input to dataframe.
2026-02-11 21:39:35.508262 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.509669 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.513427 INFO::Found 0 missing values.
2026-02-11 21:39:35.524731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.525481 INFO::Done
2026-02-11 21:39:35.541957 INFO::Formatting Data.
2026-02-11 21:39:35.542744 INFO::Recognized SummarizedExperiment
2026-02-11 21:39:35.543269 INFO::Typecasting input to dataframe.
2026-02-11 21:39:35.560507 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.56168 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.56286 INFO::Found 0 missing values.
2026-02-11 21:39:35.563839 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.
2026-02-11 21:39:35.568305 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.568955 INFO::Done
2026-02-11 21:39:35.578944 INFO::Formatting Data.
2026-02-11 21:39:35.588305 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.58949 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.59059 INFO::Found 0 missing values.
2026-02-11 21:39:35.593522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.594088 INFO::Done
2026-02-11 21:39:35.60665 INFO::Formatting Data.
2026-02-11 21:39:35.607497 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.608451 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.609524 INFO::Found 0 missing values.
2026-02-11 21:39:35.612597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.613166 INFO::Done
2026-02-11 21:39:35.645597 INFO::Formatting Data.
2026-02-11 21:39:35.64656 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.647691 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.648895 INFO::Found 1 missing values.
2026-02-11 21:39:35.651635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.652252 INFO::Done
2026-02-11 21:39:35.6736 INFO::Formatting Data.
2026-02-11 21:39:35.674543 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.675509 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.676516 INFO::Found 2 missing values.
2026-02-11 21:39:35.677482 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.
2026-02-11 21:39:35.680061 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.680624 INFO::Done
2026-02-11 21:39:35.691804 INFO::Formatting Data.
2026-02-11 21:39:35.692724 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.693673 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.694633 INFO::Found 2 missing values.
2026-02-11 21:39:35.696306 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.696886 INFO::Done
2026-02-11 21:39:35.7081 INFO::Formatting Data.
2026-02-11 21:39:35.709002 INFO::Typecasting input to dataframe.
2026-02-11 21:39:35.709873 INFO::Replacing NaNs with NAs.
2026-02-11 21:39:35.710788 INFO::Removing potential empty rows and columns
2026-02-11 21:39:35.711841 INFO::Found 0 missing values.
2026-02-11 21:39:35.714878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-11 21:39:35.715472 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.578 4.933 22.102
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.594 | 1.164 | 16.921 | |
| compute_asw | 0.023 | 0.000 | 0.025 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |