Yannis Schumann
| Snapshot Date: 2026-01-12 13:45 -0500 (Mon, 12 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-15 11:58 -0500 (Thu, 15 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4886 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4672 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-01-12 21:53:20 -0500 (Mon, 12 Jan 2026) |
| EndedAt: 2026-01-12 21:54:47 -0500 (Mon, 12 Jan 2026) |
| EllapsedTime: 87.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.6.0’
* 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 23.132 1.203 16.73
* 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-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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")
2026-01-12 21:54:10.8112 INFO::Formatting Data.
2026-01-12 21:54:10.812486 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:10.823278 INFO::Removing potential empty rows and columns
2026-01-12 21:54:11.08674 INFO::Found 0 missing values.
2026-01-12 21:54:11.090278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:11.090969 INFO::Done
2026-01-12 21:54:11.091589 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:11.103774 INFO::Starting hierarchical adjustment
2026-01-12 21:54:11.104776 INFO::Found 3 batches.
2026-01-12 21:54:11.10539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:11.106669 INFO::Using default BPPARAM
2026-01-12 21:54:11.107281 INFO::Processing subtree level 1
2026-01-12 21:54:11.233901 INFO::Adjusting the last 1 batches sequentially
2026-01-12 21:54:11.236721 INFO::Done
2026-01-12 21:54:11.237734 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:11.241325 INFO::ASW Batch was -0.0377487136301315 prior to batch effect correction and is now -0.0377487136301315 .
2026-01-12 21:54:11.242677 INFO::Total function execution time is 0.432056427001953 s and adjustment time is 0.132134914398193 s ( 30.58 )
2026-01-12 21:54:11.261054 INFO::Formatting Data.
2026-01-12 21:54:11.26214 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:11.263376 INFO::Removing potential empty rows and columns
2026-01-12 21:54:11.264817 INFO::Found 0 missing values.
2026-01-12 21:54:11.266018 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.
2026-01-12 21:54:11.280319 INFO::Formatting Data.
2026-01-12 21:54:11.281524 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:11.28288 INFO::Removing potential empty rows and columns
2026-01-12 21:54:11.284196 INFO::Found 0 missing values.
2026-01-12 21:54:11.285336 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.
2026-01-12 21:54:11.304885 INFO::Formatting Data.
2026-01-12 21:54:11.305884 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:11.306932 INFO::Removing potential empty rows and columns
2026-01-12 21:54:11.3081 INFO::Found 0 missing values.
2026-01-12 21:54:11.309142 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.
2026-01-12 21:54:11.3141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:11.314709 INFO::Done
2026-01-12 21:54:11.315273 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:11.317597 INFO::Starting hierarchical adjustment
2026-01-12 21:54:11.318352 INFO::Found 2 batches.
2026-01-12 21:54:11.318923 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:11.319613 INFO::Using default BPPARAM
2026-01-12 21:54:11.320186 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:11.321184 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-12 21:54:11.343782 INFO::Done
2026-01-12 21:54:11.344528 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:11.346818 INFO::ASW Batch was -0.0213163935114964 prior to batch effect correction and is now -0.128157456490641 .
2026-01-12 21:54:11.347787 INFO::Total function execution time is 0.0430605411529541 s and adjustment time is 0.0255439281463623 s ( 59.32 )
2026-01-12 21:54:11.350911 INFO::Formatting Data.
2026-01-12 21:54:11.351572 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:11.360914 INFO::Formatting Data.
2026-01-12 21:54:11.361696 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:11.362634 INFO::Removing potential empty rows and columns
2026-01-12 21:54:11.363711 INFO::Found 0 missing values.
2026-01-12 21:54:11.366838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:11.367406 INFO::Done
2026-01-12 21:54:11.367966 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:11.398156 INFO::Starting hierarchical adjustment
2026-01-12 21:54:11.399574 INFO::Found 2 batches.
2026-01-12 21:54:11.400136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:11.400719 INFO::Using default BPPARAM
2026-01-12 21:54:11.40123 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:11.402142 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-12 21:54:11.416822 INFO::Done
2026-01-12 21:54:11.417479 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:11.419542 INFO::ASW Batch was 0.0469415833749517 prior to batch effect correction and is now -0.121508392804249 .
2026-01-12 21:54:11.420294 INFO::Total function execution time is 0.059453010559082 s and adjustment time is 0.0174360275268555 s ( 29.33 )
2026-01-12 21:54:11.421341 INFO::Formatting Data.
2026-01-12 21:54:11.421952 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:11.422797 INFO::Removing potential empty rows and columns
2026-01-12 21:54:11.423782 INFO::Found 0 missing values.
2026-01-12 21:54:11.426557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:11.427085 INFO::Done
2026-01-12 21:54:11.427596 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:11.429631 INFO::Starting hierarchical adjustment
2026-01-12 21:54:11.430327 INFO::Found 2 batches.
2026-01-12 21:54:11.430852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:11.431451 INFO::Using default BPPARAM
2026-01-12 21:54:11.43199 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:11.432889 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-12 21:54:11.447777 INFO::Done
2026-01-12 21:54:11.448447 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:11.45046 INFO::ASW Batch was 0.0469415833749517 prior to batch effect correction and is now -0.121508392804249 .
2026-01-12 21:54:11.451237 INFO::Total function execution time is 0.0298862457275391 s and adjustment time is 0.0175731182098389 s ( 58.8 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-12 21:54:14.422555 INFO::Formatting Data.
2026-01-12 21:54:14.423311 INFO::Recognized SummarizedExperiment
2026-01-12 21:54:14.423847 INFO::Typecasting input to dataframe.
2026-01-12 21:54:14.456131 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:14.457479 INFO::Removing potential empty rows and columns
2026-01-12 21:54:14.46149 INFO::Found 0 missing values.
2026-01-12 21:54:14.469113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:14.469866 INFO::Done
2026-01-12 21:54:14.470426 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:14.474257 INFO::Starting hierarchical adjustment
2026-01-12 21:54:14.475098 INFO::Found 2 batches.
2026-01-12 21:54:14.47568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:14.476827 INFO::Using default BPPARAM
2026-01-12 21:54:14.477397 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:14.478419 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-12 21:54:14.538259 INFO::Done
2026-01-12 21:54:14.539107 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:14.543014 INFO::ASW Batch was 0.0192210278969142 prior to batch effect correction and is now -0.0979416522470661 .
2026-01-12 21:54:14.544002 INFO::Total function execution time is 0.121736288070679 s and adjustment time is 0.0632719993591309 s ( 51.97 )
Warning: stack imbalance in '{', 73 then 75
2026-01-12 21:54:14.563996 INFO::Formatting Data.
2026-01-12 21:54:14.564837 INFO::Recognized SummarizedExperiment
2026-01-12 21:54:14.565394 INFO::Typecasting input to dataframe.
2026-01-12 21:54:14.575412 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:14.576768 INFO::Removing potential empty rows and columns
2026-01-12 21:54:14.580698 INFO::Found 0 missing values.
2026-01-12 21:54:14.588269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:14.58907 INFO::Done
2026-01-12 21:54:14.589665 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:14.593516 INFO::Starting hierarchical adjustment
2026-01-12 21:54:14.594337 INFO::Found 2 batches.
2026-01-12 21:54:14.594934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:14.595562 INFO::Using default BPPARAM
2026-01-12 21:54:14.596102 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:14.597144 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-12 21:54:14.623829 INFO::Done
2026-01-12 21:54:14.624683 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:14.628597 INFO::ASW Batch was 0.00975677426873425 prior to batch effect correction and is now 0.00975677426873425 .
2026-01-12 21:54:14.629573 INFO::Total function execution time is 0.0655426979064941 s and adjustment time is 0.0295884609222412 s ( 45.14 )
2026-01-12 21:54:14.650113 INFO::Formatting Data.
2026-01-12 21:54:14.651045 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:14.652042 INFO::Removing potential empty rows and columns
2026-01-12 21:54:14.653138 INFO::Found 0 missing values.
2026-01-12 21:54:14.656296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:14.656884 INFO::Done
2026-01-12 21:54:14.657412 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:14.659627 INFO::Starting hierarchical adjustment
2026-01-12 21:54:14.660367 INFO::Found 3 batches.
2026-01-12 21:54:14.660925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:14.661561 INFO::Using default BPPARAM
2026-01-12 21:54:14.662101 INFO::Processing subtree level 1
2026-01-12 21:54:14.800904 INFO::Adjusting the last 1 batches sequentially
2026-01-12 21:54:14.802712 INFO::Done
2026-01-12 21:54:14.803358 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:14.805992 INFO::ASW Batch was -0.0752380031943171 prior to batch effect correction and is now -0.158074830672607 .
2026-01-12 21:54:14.807037 INFO::Total function execution time is 0.156966686248779 s and adjustment time is 0.142492771148682 s ( 90.78 )
2026-01-12 21:54:14.821814 INFO::Skipping initial DF formatting
2026-01-12 21:54:14.822575 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:14.826719 INFO::Starting hierarchical adjustment
2026-01-12 21:54:14.827551 INFO::Found 5 batches.
2026-01-12 21:54:14.828118 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:14.828765 INFO::Using default BPPARAM
2026-01-12 21:54:14.8293 INFO::Processing subtree level 1
2026-01-12 21:54:15.083032 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:15.08488 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-12 21:54:15.105475 INFO::Done
2026-01-12 21:54:15.106352 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:15.167555 INFO::ASW Batch was 0.48509056672016 prior to batch effect correction and is now 0.48509056672016 .
2026-01-12 21:54:15.168351 INFO::ASW Label was 0.36077082059418 prior to batch effect correction and is now 0.36077082059418 .
2026-01-12 21:54:15.169239 INFO::Total function execution time is 0.347506999969482 s and adjustment time is 0.278026103973389 s ( 80.01 )
2026-01-12 21:54:15.188229 INFO::Formatting Data.
2026-01-12 21:54:15.189251 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:15.190349 INFO::Removing potential empty rows and columns
2026-01-12 21:54:15.19147 INFO::Found 0 missing values.
2026-01-12 21:54:15.195843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:15.19646 INFO::Done
2026-01-12 21:54:15.196997 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:15.200178 INFO::Starting hierarchical adjustment
2026-01-12 21:54:15.20095 INFO::Found 5 batches.
2026-01-12 21:54:15.20148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:15.202109 INFO::Using default BPPARAM
2026-01-12 21:54:15.202665 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.
2026-01-12 21:54:15.344985 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:15.346899 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-12 21:54:15.367358 INFO::Done
2026-01-12 21:54:15.368287 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:15.372334 INFO::ASW Batch was 0.513921520975661 prior to batch effect correction and is now -0.0948414478370072 .
2026-01-12 21:54:15.373113 INFO::ASW Label was 0.219615133649111 prior to batch effect correction and is now 0.821141046918127 .
2026-01-12 21:54:15.374135 INFO::Total function execution time is 0.186034202575684 s and adjustment time is 0.166468381881714 s ( 89.48 )
2026-01-12 21:54:15.375227 INFO::Formatting Data.
2026-01-12 21:54:15.375966 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:15.377043 INFO::Removing potential empty rows and columns
2026-01-12 21:54:15.378284 INFO::Found 0 missing values.
2026-01-12 21:54:15.383191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:15.383889 INFO::Done
2026-01-12 21:54:15.384477 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:15.38799 INFO::Starting hierarchical adjustment
2026-01-12 21:54:15.388849 INFO::Found 5 batches.
2026-01-12 21:54:15.389454 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:15.390141 INFO::Using default BPPARAM
2026-01-12 21:54:15.390743 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.
2026-01-12 21:54:15.52242 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:15.52401 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-12 21:54:15.540115 INFO::Done
2026-01-12 21:54:15.540884 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:15.544174 INFO::ASW Batch was 0.513921520975661 prior to batch effect correction and is now -0.0948414478370072 .
2026-01-12 21:54:15.544809 INFO::ASW Label was 0.219615133649111 prior to batch effect correction and is now 0.821141046918127 .
2026-01-12 21:54:15.545615 INFO::Total function execution time is 0.17041802406311 s and adjustment time is 0.151433706283569 s ( 88.86 )
2026-01-12 21:54:15.559314 INFO::Formatting Data.
2026-01-12 21:54:15.56011 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:15.561025 INFO::Removing potential empty rows and columns
2026-01-12 21:54:15.562044 INFO::Found 0 missing values.
2026-01-12 21:54:15.56616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:15.566778 INFO::Done
2026-01-12 21:54:15.567349 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:15.570468 INFO::Starting hierarchical adjustment
2026-01-12 21:54:15.571207 INFO::Found 5 batches.
2026-01-12 21:54:15.57175 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:15.572358 INFO::Using default BPPARAM
2026-01-12 21:54:15.572892 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.
2026-01-12 21:54:15.698433 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:15.700113 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-12 21:54:15.717198 INFO::Done
2026-01-12 21:54:15.717945 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:15.721247 INFO::ASW Batch was 0.506506511679716 prior to batch effect correction and is now -0.0897214018542932 .
2026-01-12 21:54:15.72192 INFO::ASW Label was 0.224602552710172 prior to batch effect correction and is now 0.822935155111461 .
2026-01-12 21:54:15.722758 INFO::Total function execution time is 0.163506984710693 s and adjustment time is 0.146097898483276 s ( 89.35 )
2026-01-12 21:54:15.723627 INFO::Formatting Data.
2026-01-12 21:54:15.724292 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:15.725229 INFO::Removing potential empty rows and columns
2026-01-12 21:54:15.726296 INFO::Found 0 missing values.
2026-01-12 21:54:15.730472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:15.731101 INFO::Done
2026-01-12 21:54:15.731653 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:15.734798 INFO::Starting hierarchical adjustment
2026-01-12 21:54:15.735595 INFO::Found 5 batches.
2026-01-12 21:54:15.73616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:15.736815 INFO::Using default BPPARAM
2026-01-12 21:54:15.737385 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.
2026-01-12 21:54:15.866623 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:15.869308 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-12 21:54:15.894824 INFO::Done
2026-01-12 21:54:15.895998 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:15.900578 INFO::ASW Batch was 0.506506511679716 prior to batch effect correction and is now -0.0897214018542932 .
2026-01-12 21:54:15.90145 INFO::ASW Label was 0.224602552710172 prior to batch effect correction and is now 0.822935155111461 .
2026-01-12 21:54:15.902437 INFO::Total function execution time is 0.178787708282471 s and adjustment time is 0.159253835678101 s ( 89.07 )
2026-01-12 21:54:15.92001 INFO::Formatting Data.
2026-01-12 21:54:15.921006 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:15.922093 INFO::Removing potential empty rows and columns
2026-01-12 21:54:15.923301 INFO::Found 0 missing values.
2026-01-12 21:54:15.926449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:15.927135 INFO::Done
2026-01-12 21:54:15.927735 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:15.931257 INFO::Starting hierarchical adjustment
2026-01-12 21:54:15.932165 INFO::Found 2 batches.
2026-01-12 21:54:15.932786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:15.933474 INFO::Using default BPPARAM
2026-01-12 21:54:15.934078 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:15.935139 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-12 21:54:15.95156 INFO::Done
2026-01-12 21:54:15.952279 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:15.955361 INFO::ASW Batch was 0.433609136779196 prior to batch effect correction and is now 0.100180302918799 .
2026-01-12 21:54:15.956056 INFO::ASW Label was 0.679223444802353 prior to batch effect correction and is now 0.861394130630693 .
2026-01-12 21:54:15.956936 INFO::Total function execution time is 0.0371081829071045 s and adjustment time is 0.019536018371582 s ( 52.65 )
2026-01-12 21:54:15.957791 INFO::Formatting Data.
2026-01-12 21:54:15.958445 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:15.959373 INFO::Removing potential empty rows and columns
2026-01-12 21:54:15.960449 INFO::Found 0 missing values.
2026-01-12 21:54:15.963403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:15.964012 INFO::Done
2026-01-12 21:54:15.964566 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:15.967751 INFO::Starting hierarchical adjustment
2026-01-12 21:54:15.968541 INFO::Found 2 batches.
2026-01-12 21:54:15.969097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:15.969719 INFO::Using default BPPARAM
2026-01-12 21:54:15.970239 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:15.971188 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-12 21:54:15.986012 INFO::Done
2026-01-12 21:54:15.986789 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:15.989864 INFO::ASW Batch was 0.433609136779196 prior to batch effect correction and is now 0.100180302918799 .
2026-01-12 21:54:15.990496 INFO::ASW Label was 0.679223444802353 prior to batch effect correction and is now 0.861394130630693 .
2026-01-12 21:54:15.991327 INFO::Total function execution time is 0.0335524082183838 s and adjustment time is 0.0176169872283936 s ( 52.51 )
2026-01-12 21:54:16.003289 INFO::Formatting Data.
2026-01-12 21:54:16.00411 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:16.005024 INFO::Removing potential empty rows and columns
2026-01-12 21:54:16.005949 INFO::Found 0 missing values.
2026-01-12 21:54:16.008089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:16.008654 INFO::Done
2026-01-12 21:54:16.00916 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:16.011097 INFO::Starting hierarchical adjustment
2026-01-12 21:54:16.011824 INFO::Found 2 batches.
2026-01-12 21:54:16.012344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:16.012957 INFO::Using default BPPARAM
2026-01-12 21:54:16.01349 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:16.014455 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-12 21:54:16.046651 INFO::Done
2026-01-12 21:54:16.047443 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:16.049584 INFO::ASW Batch was -0.0631658874970691 prior to batch effect correction and is now -0.123705529775271 .
2026-01-12 21:54:16.050454 INFO::Total function execution time is 0.0472469329833984 s and adjustment time is 0.0349133014678955 s ( 73.9 )
2026-01-12 21:54:16.063055 INFO::Formatting Data.
2026-01-12 21:54:16.063923 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:16.064897 INFO::Removing potential empty rows and columns
2026-01-12 21:54:16.065923 INFO::Found 0 missing values.
2026-01-12 21:54:16.067129 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.
2026-01-12 21:54:16.071953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:16.072655 INFO::Done
2026-01-12 21:54:16.073195 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:16.076223 INFO::Starting hierarchical adjustment
2026-01-12 21:54:16.077034 INFO::Found 2 batches.
2026-01-12 21:54:16.077598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:16.078206 INFO::Using default BPPARAM
2026-01-12 21:54:16.078765 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:16.079748 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-12 21:54:16.096713 INFO::Done
2026-01-12 21:54:16.097493 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:16.100581 INFO::ASW Batch was 0.639584269171193 prior to batch effect correction and is now -0.0294370583574545 .
2026-01-12 21:54:16.101219 INFO::ASW Label was 0.428192640472179 prior to batch effect correction and is now 0.90233192313764 .
2026-01-12 21:54:16.102011 INFO::Total function execution time is 0.0390548706054688 s and adjustment time is 0.0197911262512207 s ( 50.68 )
2026-01-12 21:54:16.102812 INFO::Formatting Data.
2026-01-12 21:54:16.10343 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:16.104398 INFO::Removing potential empty rows and columns
2026-01-12 21:54:16.105407 INFO::Found 0 missing values.
2026-01-12 21:54:16.106326 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.
2026-01-12 21:54:16.110967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:16.111627 INFO::Done
2026-01-12 21:54:16.112177 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:16.115374 INFO::Starting hierarchical adjustment
2026-01-12 21:54:16.116237 INFO::Found 2 batches.
2026-01-12 21:54:16.116823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:16.117449 INFO::Using default BPPARAM
2026-01-12 21:54:16.118006 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:16.118989 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-12 21:54:16.135909 INFO::Done
2026-01-12 21:54:16.136675 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:16.139755 INFO::ASW Batch was 0.639584269171193 prior to batch effect correction and is now -0.0294370583574545 .
2026-01-12 21:54:16.140435 INFO::ASW Label was 0.428192640472179 prior to batch effect correction and is now 0.90233192313764 .
2026-01-12 21:54:16.141263 INFO::Total function execution time is 0.0384633541107178 s and adjustment time is 0.0198214054107666 s ( 51.53 )
2026-01-12 21:54:16.360977 INFO::Formatting Data.
2026-01-12 21:54:16.361835 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:16.362784 INFO::Removing potential empty rows and columns
2026-01-12 21:54:16.363866 INFO::Found 0 missing values.
2026-01-12 21:54:16.367012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:16.367615 INFO::Done
2026-01-12 21:54:16.368145 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:16.370277 INFO::Starting hierarchical adjustment
2026-01-12 21:54:16.371026 INFO::Found 3 batches.
2026-01-12 21:54:16.371567 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:16.372183 INFO::Using default BPPARAM
2026-01-12 21:54:16.372734 INFO::Processing subtree level 1
2026-01-12 21:54:16.461778 INFO::Adjusting the last 1 batches sequentially
2026-01-12 21:54:16.463699 INFO::Done
2026-01-12 21:54:16.464373 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:16.467068 INFO::ASW Batch was 0.0347735890918648 prior to batch effect correction and is now 0.0347735890918648 .
2026-01-12 21:54:16.468083 INFO::Total function execution time is 0.107157707214355 s and adjustment time is 0.0928094387054443 s ( 86.61 )
2026-01-12 21:54:16.469248 INFO::Formatting Data.
2026-01-12 21:54:16.469959 INFO::Typecasting input to dataframe.
2026-01-12 21:54:16.470763 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:16.471748 INFO::Removing potential empty rows and columns
2026-01-12 21:54:16.472915 INFO::Found 0 missing values.
2026-01-12 21:54:16.47616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:16.476738 INFO::Done
2026-01-12 21:54:16.477278 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:16.479455 INFO::Starting hierarchical adjustment
2026-01-12 21:54:16.480194 INFO::Found 3 batches.
2026-01-12 21:54:16.480741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:16.48138 INFO::Using default BPPARAM
2026-01-12 21:54:16.481933 INFO::Processing subtree level 1
2026-01-12 21:54:16.571939 INFO::Adjusting the last 1 batches sequentially
2026-01-12 21:54:16.573873 INFO::Done
2026-01-12 21:54:16.574587 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:16.577281 INFO::ASW Batch was 0.0347735890918648 prior to batch effect correction and is now 0.0347735890918648 .
2026-01-12 21:54:16.578313 INFO::Total function execution time is 0.109048366546631 s and adjustment time is 0.0937807559967041 s ( 86 )
2026-01-12 21:54:16.592609 INFO::Formatting Data.
2026-01-12 21:54:16.593529 INFO::Typecasting input to dataframe.
2026-01-12 21:54:16.594416 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:16.595387 INFO::Removing potential empty rows and columns
2026-01-12 21:54:16.596523 INFO::Found 0 missing values.
2026-01-12 21:54:16.599685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:16.600235 INFO::Done
2026-01-12 21:54:16.600769 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:16.602966 INFO::Starting hierarchical adjustment
2026-01-12 21:54:16.603692 INFO::Found 3 batches.
2026-01-12 21:54:16.604223 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:16.604879 INFO::Using default BPPARAM
2026-01-12 21:54:16.605412 INFO::Processing subtree level 1
2026-01-12 21:54:16.696917 INFO::Adjusting the last 1 batches sequentially
2026-01-12 21:54:16.698946 INFO::Done
2026-01-12 21:54:16.699649 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:16.70233 INFO::ASW Batch was -0.058065613414535 prior to batch effect correction and is now -0.058065613414535 .
2026-01-12 21:54:16.703365 INFO::Total function execution time is 0.110933065414429 s and adjustment time is 0.0953879356384277 s ( 85.99 )
2026-01-12 21:54:16.853965 INFO::Formatting Data.
2026-01-12 21:54:16.854946 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:16.856166 INFO::Removing potential empty rows and columns
2026-01-12 21:54:16.859052 INFO::Found 1000 missing values.
2026-01-12 21:54:16.878232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:16.879073 INFO::Done
2026-01-12 21:54:16.879653 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:16.885376 INFO::Starting hierarchical adjustment
2026-01-12 21:54:16.886193 INFO::Found 10 batches.
2026-01-12 21:54:16.886746 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:16.887365 INFO::Using default BPPARAM
2026-01-12 21:54:16.887923 INFO::Processing subtree level 1
2026-01-12 21:54:17.032912 INFO::Processing subtree level 2
2026-01-12 21:54:17.177652 INFO::Adjusting the last 1 batches sequentially
2026-01-12 21:54:17.17981 INFO::Done
2026-01-12 21:54:17.180586 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:17.186521 INFO::ASW Batch was 0.497371729280163 prior to batch effect correction and is now 0.497371729280163 .
2026-01-12 21:54:17.187254 INFO::ASW Label was 0.317578688506603 prior to batch effect correction and is now 0.317578688506603 .
2026-01-12 21:54:17.188238 INFO::Total function execution time is 0.334381103515625 s and adjustment time is 0.293755531311035 s ( 87.85 )
2026-01-12 21:54:17.189146 INFO::Formatting Data.
2026-01-12 21:54:17.189852 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:17.191195 INFO::Removing potential empty rows and columns
2026-01-12 21:54:17.194044 INFO::Found 1000 missing values.
2026-01-12 21:54:17.21309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:17.213931 INFO::Done
2026-01-12 21:54:17.21454 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:17.220298 INFO::Starting hierarchical adjustment
2026-01-12 21:54:17.221149 INFO::Found 10 batches.
2026-01-12 21:54:18.289266 INFO::Set up parallel execution backend with 2 workers
2026-01-12 21:54:18.291478 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-12 21:54:19.525384 INFO::Adjusting the last 2 batches sequentially
2026-01-12 21:54:19.527349 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-12 21:54:19.554553 INFO::Done
2026-01-12 21:54:19.555435 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:19.561411 INFO::ASW Batch was 0.497371729280163 prior to batch effect correction and is now 0.497371729280163 .
2026-01-12 21:54:19.562092 INFO::ASW Label was 0.317578688506603 prior to batch effect correction and is now 0.317578688506603 .
2026-01-12 21:54:19.562924 INFO::Total function execution time is 2.37380957603455 s and adjustment time is 2.33348846435547 s ( 98.3 )
2026-01-12 21:54:19.714685 INFO::Formatting Data.
2026-01-12 21:54:19.715538 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:19.716483 INFO::Removing potential empty rows and columns
2026-01-12 21:54:19.717626 INFO::Found 0 missing values.
2026-01-12 21:54:19.721479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:19.722056 INFO::Done
2026-01-12 21:54:19.722592 INFO::Acquiring quality metrics before batch effect correction.
2026-01-12 21:54:19.725471 INFO::Starting hierarchical adjustment
2026-01-12 21:54:19.726215 INFO::Found 3 batches.
2026-01-12 21:54:19.726768 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-12 21:54:19.727409 INFO::Using default BPPARAM
2026-01-12 21:54:19.727974 INFO::Processing subtree level 1
2026-01-12 21:54:19.835626 INFO::Adjusting the last 1 batches sequentially
2026-01-12 21:54:19.837459 INFO::Done
2026-01-12 21:54:19.838141 INFO::Acquiring quality metrics after batch effect correction.
2026-01-12 21:54:19.841434 INFO::ASW Batch was 0.159280381115454 prior to batch effect correction and is now -0.145422859636098 .
2026-01-12 21:54:19.842102 INFO::ASW Label was -0.196128994302469 prior to batch effect correction and is now 0.02284089238189 .
2026-01-12 21:54:19.843057 INFO::Total function execution time is 0.12844705581665 s and adjustment time is 0.111378192901611 s ( 86.71 )
2026-01-12 21:54:19.97465 INFO::Formatting Data.
2026-01-12 21:54:19.975542 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:19.976559 INFO::Removing potential empty rows and columns
2026-01-12 21:54:19.977727 INFO::Found 2 missing values.
2026-01-12 21:54:19.980723 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:19.981295 INFO::Done
2026-01-12 21:54:20.01088 INFO::Found NA in Reference column
2026-01-12 21:54:20.02147 INFO::Require at least two references per batch.
2026-01-12 21:54:20.04386 INFO::Formatting Data.
2026-01-12 21:54:20.044699 INFO::Recognized SummarizedExperiment
2026-01-12 21:54:20.045242 INFO::Typecasting input to dataframe.
2026-01-12 21:54:20.055764 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.057067 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.060869 INFO::Found 0 missing values.
2026-01-12 21:54:20.068259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.069028 INFO::Done
2026-01-12 21:54:20.08695 INFO::Formatting Data.
2026-01-12 21:54:20.087815 INFO::Recognized SummarizedExperiment
2026-01-12 21:54:20.088376 INFO::Typecasting input to dataframe.
2026-01-12 21:54:20.107122 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.108418 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.112144 INFO::Found 0 missing values.
2026-01-12 21:54:20.123822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.124577 INFO::Done
2026-01-12 21:54:20.141001 INFO::Formatting Data.
2026-01-12 21:54:20.141841 INFO::Recognized SummarizedExperiment
2026-01-12 21:54:20.142385 INFO::Typecasting input to dataframe.
2026-01-12 21:54:20.159997 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.161133 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.162263 INFO::Found 0 missing values.
2026-01-12 21:54:20.16322 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.
2026-01-12 21:54:20.167944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.168552 INFO::Done
2026-01-12 21:54:20.179395 INFO::Formatting Data.
2026-01-12 21:54:20.180244 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.181188 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.182235 INFO::Found 0 missing values.
2026-01-12 21:54:20.185311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.18589 INFO::Done
2026-01-12 21:54:20.19794 INFO::Formatting Data.
2026-01-12 21:54:20.198787 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.199817 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.200899 INFO::Found 0 missing values.
2026-01-12 21:54:20.203689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.204225 INFO::Done
2026-01-12 21:54:20.233997 INFO::Formatting Data.
2026-01-12 21:54:20.234875 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.235936 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.237101 INFO::Found 1 missing values.
2026-01-12 21:54:20.239748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.240277 INFO::Done
2026-01-12 21:54:20.259643 INFO::Formatting Data.
2026-01-12 21:54:20.261544 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.262689 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.263724 INFO::Found 2 missing values.
2026-01-12 21:54:20.264677 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.
2026-01-12 21:54:20.266995 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.267559 INFO::Done
2026-01-12 21:54:20.27783 INFO::Formatting Data.
2026-01-12 21:54:20.27859 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.279438 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.28044 INFO::Found 2 missing values.
2026-01-12 21:54:20.282072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.282629 INFO::Done
2026-01-12 21:54:20.292991 INFO::Formatting Data.
2026-01-12 21:54:20.293779 INFO::Typecasting input to dataframe.
2026-01-12 21:54:20.294587 INFO::Replacing NaNs with NAs.
2026-01-12 21:54:20.295419 INFO::Removing potential empty rows and columns
2026-01-12 21:54:20.296388 INFO::Found 0 missing values.
2026-01-12 21:54:20.299268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-12 21:54:20.299805 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.392 4.167 21.123
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.132 | 1.203 | 16.730 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.000 | 0.013 | |
| generate_data_covariables | 0.011 | 0.000 | 0.012 | |
| generate_dataset | 0.010 | 0.001 | 0.011 | |