Yannis Schumann
| Snapshot Date: 2026-05-06 13:40 -0400 (Wed, 06 May 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_23 |
| git_last_commit: 0c9135c |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-07 11:35 -0400 (Thu, 07 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4990 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4723 |
| 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 172/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.8.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2026-05-06 21:53:42 -0400 (Wed, 06 May 2026) |
| EndedAt: 2026-05-06 21:55:12 -0400 (Wed, 06 May 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-07 01:53:42 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.356 1.167 17.259
* 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 ‘1.8.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-05-06 21:54:33.752956 INFO::Formatting Data.
2026-05-06 21:54:33.754324 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:33.766013 INFO::Removing potential empty rows and columns
2026-05-06 21:54:34.012994 INFO::Found 0 missing values.
2026-05-06 21:54:34.016417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:34.017102 INFO::Done
2026-05-06 21:54:34.017689 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:34.030282 INFO::Starting hierarchical adjustment
2026-05-06 21:54:34.031184 INFO::Found 3 batches.
2026-05-06 21:54:34.031811 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:34.032958 INFO::Using default BPPARAM
2026-05-06 21:54:34.033562 INFO::Processing subtree level 1
2026-05-06 21:54:34.131083 INFO::Adjusting the last 1 batches sequentially
2026-05-06 21:54:34.132957 INFO::Done
2026-05-06 21:54:34.133662 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:34.136195 INFO::ASW Batch was -0.0989930872685538 prior to batch effect correction and is now -0.0989930872685538 .
2026-05-06 21:54:34.137287 INFO::Total function execution time is 0.384994268417358 s and adjustment time is 0.101940631866455 s ( 26.48 )
2026-05-06 21:54:34.150949 INFO::Formatting Data.
2026-05-06 21:54:34.151761 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:34.152706 INFO::Removing potential empty rows and columns
2026-05-06 21:54:34.153816 INFO::Found 0 missing values.
2026-05-06 21:54:34.154831 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 21:54:34.166067 INFO::Formatting Data.
2026-05-06 21:54:34.166833 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:34.167798 INFO::Removing potential empty rows and columns
2026-05-06 21:54:34.169005 INFO::Found 0 missing values.
2026-05-06 21:54:34.169981 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 21:54:34.185909 INFO::Formatting Data.
2026-05-06 21:54:34.186706 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:34.187606 INFO::Removing potential empty rows and columns
2026-05-06 21:54:34.188682 INFO::Found 0 missing values.
2026-05-06 21:54:34.189604 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 21:54:34.194161 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:34.19475 INFO::Done
2026-05-06 21:54:34.195312 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:34.197368 INFO::Starting hierarchical adjustment
2026-05-06 21:54:34.198136 INFO::Found 2 batches.
2026-05-06 21:54:34.198771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:34.199485 INFO::Using default BPPARAM
2026-05-06 21:54:34.200097 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:34.20109 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 21:54:34.222462 INFO::Done
2026-05-06 21:54:34.223211 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:34.225233 INFO::ASW Batch was -0.028861929866392 prior to batch effect correction and is now -0.110661702840326 .
2026-05-06 21:54:34.22608 INFO::Total function execution time is 0.0402305126190186 s and adjustment time is 0.0244629383087158 s ( 60.81 )
2026-05-06 21:54:34.228972 INFO::Formatting Data.
2026-05-06 21:54:34.229666 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:34.238389 INFO::Formatting Data.
2026-05-06 21:54:34.239132 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:34.240058 INFO::Removing potential empty rows and columns
2026-05-06 21:54:34.241173 INFO::Found 0 missing values.
2026-05-06 21:54:34.244163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:34.244749 INFO::Done
2026-05-06 21:54:34.245308 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:34.247332 INFO::Starting hierarchical adjustment
2026-05-06 21:54:34.248122 INFO::Found 2 batches.
2026-05-06 21:54:34.248702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:34.249357 INFO::Using default BPPARAM
2026-05-06 21:54:34.249942 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:34.250889 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:34.266843 INFO::Done
2026-05-06 21:54:34.267635 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:34.269791 INFO::ASW Batch was 0.0634545359929717 prior to batch effect correction and is now -0.131068734463987 .
2026-05-06 21:54:34.270738 INFO::Total function execution time is 0.0323562622070312 s and adjustment time is 0.0188357830047607 s ( 58.21 )
2026-05-06 21:54:34.271893 INFO::Formatting Data.
2026-05-06 21:54:34.272564 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:34.273489 INFO::Removing potential empty rows and columns
2026-05-06 21:54:34.27459 INFO::Found 0 missing values.
2026-05-06 21:54:34.277605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:34.278232 INFO::Done
2026-05-06 21:54:34.278814 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:34.280939 INFO::Starting hierarchical adjustment
2026-05-06 21:54:34.281733 INFO::Found 2 batches.
2026-05-06 21:54:34.282327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:34.282995 INFO::Using default BPPARAM
2026-05-06 21:54:34.283583 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:34.284577 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:34.299583 INFO::Done
2026-05-06 21:54:34.300341 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:34.302382 INFO::ASW Batch was 0.0634545359929717 prior to batch effect correction and is now -0.131068734463987 .
2026-05-06 21:54:34.3032 INFO::Total function execution time is 0.0313034057617188 s and adjustment time is 0.0179941654205322 s ( 57.48 )
2026-05-06 21:54:37.482409 INFO::Formatting Data.
2026-05-06 21:54:37.483299 INFO::Recognized SummarizedExperiment
2026-05-06 21:54:37.48388 INFO::Typecasting input to dataframe.
2026-05-06 21:54:37.51425 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:37.515658 INFO::Removing potential empty rows and columns
2026-05-06 21:54:37.519139 INFO::Found 0 missing values.
2026-05-06 21:54:37.525497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:37.52618 INFO::Done
2026-05-06 21:54:37.526744 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:37.530026 INFO::Starting hierarchical adjustment
2026-05-06 21:54:37.530741 INFO::Found 2 batches.
2026-05-06 21:54:37.531251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:37.532329 INFO::Using default BPPARAM
2026-05-06 21:54:37.532892 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:37.533885 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 21:54:37.586574 INFO::Done
2026-05-06 21:54:37.587371 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:37.590695 INFO::ASW Batch was -0.00104259223496755 prior to batch effect correction and is now -0.0950287762668757 .
2026-05-06 21:54:37.591529 INFO::Total function execution time is 0.109421253204346 s and adjustment time is 0.0559537410736084 s ( 51.14 )
2026-05-06 21:54:37.608809 INFO::Formatting Data.
2026-05-06 21:54:37.609586 INFO::Recognized SummarizedExperiment
2026-05-06 21:54:37.610162 INFO::Typecasting input to dataframe.
2026-05-06 21:54:37.618838 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:37.620033 INFO::Removing potential empty rows and columns
2026-05-06 21:54:37.623352 INFO::Found 0 missing values.
2026-05-06 21:54:37.629802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:37.630469 INFO::Done
2026-05-06 21:54:37.631069 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:37.634722 INFO::Starting hierarchical adjustment
2026-05-06 21:54:37.635477 INFO::Found 2 batches.
2026-05-06 21:54:37.636036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:37.636641 INFO::Using default BPPARAM
2026-05-06 21:54:37.637178 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:37.638236 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 21:54:37.663722 INFO::Done
2026-05-06 21:54:37.664621 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:37.668451 INFO::ASW Batch was -0.000741774282842758 prior to batch effect correction and is now -0.000741774282842758 .
2026-05-06 21:54:37.66939 INFO::Total function execution time is 0.0605623722076416 s and adjustment time is 0.0283575057983398 s ( 46.82 )
2026-05-06 21:54:37.688428 INFO::Formatting Data.
2026-05-06 21:54:37.689354 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:37.690314 INFO::Removing potential empty rows and columns
2026-05-06 21:54:37.691399 INFO::Found 0 missing values.
2026-05-06 21:54:37.694608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:37.695211 INFO::Done
2026-05-06 21:54:37.695789 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:37.697902 INFO::Starting hierarchical adjustment
2026-05-06 21:54:37.698662 INFO::Found 3 batches.
2026-05-06 21:54:37.699244 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:37.6999 INFO::Using default BPPARAM
2026-05-06 21:54:37.700452 INFO::Processing subtree level 1
2026-05-06 21:54:37.837096 INFO::Adjusting the last 1 batches sequentially
2026-05-06 21:54:37.839068 INFO::Done
2026-05-06 21:54:37.839827 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:37.842526 INFO::ASW Batch was -0.0858385637870441 prior to batch effect correction and is now -0.1469826720996 .
2026-05-06 21:54:37.843535 INFO::Total function execution time is 0.155139923095703 s and adjustment time is 0.140531063079834 s ( 90.58 )
2026-05-06 21:54:37.858178 INFO::Skipping initial DF formatting
2026-05-06 21:54:37.858981 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:37.863112 INFO::Starting hierarchical adjustment
2026-05-06 21:54:37.863947 INFO::Found 5 batches.
2026-05-06 21:54:37.864568 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:37.865251 INFO::Using default BPPARAM
2026-05-06 21:54:37.865848 INFO::Processing subtree level 1
2026-05-06 21:54:37.988104 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:37.990165 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 21:54:38.011871 INFO::Done
2026-05-06 21:54:38.012935 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.019045 INFO::ASW Batch was 0.558959404777174 prior to batch effect correction and is now 0.558959404777174 .
2026-05-06 21:54:38.019984 INFO::ASW Label was 0.313529557762632 prior to batch effect correction and is now 0.313529557762632 .
2026-05-06 21:54:38.021106 INFO::Total function execution time is 0.162960529327393 s and adjustment time is 0.147966861724854 s ( 90.8 )
2026-05-06 21:54:38.043283 INFO::Formatting Data.
2026-05-06 21:54:38.044324 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.045449 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.046582 INFO::Found 0 missing values.
2026-05-06 21:54:38.051205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.051869 INFO::Done
2026-05-06 21:54:38.052455 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.055856 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.056666 INFO::Found 5 batches.
2026-05-06 21:54:38.057289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.058002 INFO::Using default BPPARAM
2026-05-06 21:54:38.058598 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.179829 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.181744 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.198556 INFO::Done
2026-05-06 21:54:38.199424 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.203111 INFO::ASW Batch was 0.497207955232116 prior to batch effect correction and is now 0.00355735335867224 .
2026-05-06 21:54:38.203858 INFO::ASW Label was 0.350237255209228 prior to batch effect correction and is now 0.700619021742194 .
2026-05-06 21:54:38.204901 INFO::Total function execution time is 0.161714792251587 s and adjustment time is 0.142026662826538 s ( 87.83 )
2026-05-06 21:54:38.205832 INFO::Formatting Data.
2026-05-06 21:54:38.206515 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.207508 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.208599 INFO::Found 0 missing values.
2026-05-06 21:54:38.212951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.213572 INFO::Done
2026-05-06 21:54:38.214157 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.217411 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.218217 INFO::Found 5 batches.
2026-05-06 21:54:38.218811 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.219496 INFO::Using default BPPARAM
2026-05-06 21:54:38.220157 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.341069 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.343211 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.363528 INFO::Done
2026-05-06 21:54:38.36464 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.369059 INFO::ASW Batch was 0.497207955232116 prior to batch effect correction and is now 0.00355735335867224 .
2026-05-06 21:54:38.369852 INFO::ASW Label was 0.350237255209228 prior to batch effect correction and is now 0.700619021742194 .
2026-05-06 21:54:38.37087 INFO::Total function execution time is 0.165022134780884 s and adjustment time is 0.145361423492432 s ( 88.09 )
2026-05-06 21:54:38.387995 INFO::Formatting Data.
2026-05-06 21:54:38.389132 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.390306 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.391489 INFO::Found 0 missing values.
2026-05-06 21:54:38.396181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.396874 INFO::Done
2026-05-06 21:54:38.397509 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.401116 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.402008 INFO::Found 5 batches.
2026-05-06 21:54:38.402696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.403403 INFO::Using default BPPARAM
2026-05-06 21:54:38.404019 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.531465 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.53347 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.551733 INFO::Done
2026-05-06 21:54:38.552746 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.556731 INFO::ASW Batch was 0.300964084285784 prior to batch effect correction and is now -0.0216360634658597 .
2026-05-06 21:54:38.557456 INFO::ASW Label was 0.516395721338838 prior to batch effect correction and is now 0.76568694415008 .
2026-05-06 21:54:38.558443 INFO::Total function execution time is 0.170634984970093 s and adjustment time is 0.149824857711792 s ( 87.8 )
2026-05-06 21:54:38.559443 INFO::Formatting Data.
2026-05-06 21:54:38.560172 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.561204 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.562341 INFO::Found 0 missing values.
2026-05-06 21:54:38.566847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.567462 INFO::Done
2026-05-06 21:54:38.568054 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.571418 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.572224 INFO::Found 5 batches.
2026-05-06 21:54:38.572822 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.573541 INFO::Using default BPPARAM
2026-05-06 21:54:38.574156 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.69631 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.698308 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.716666 INFO::Done
2026-05-06 21:54:38.717654 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.721518 INFO::ASW Batch was 0.300964084285784 prior to batch effect correction and is now -0.0216360634658597 .
2026-05-06 21:54:38.72224 INFO::ASW Label was 0.516395721338838 prior to batch effect correction and is now 0.76568694415008 .
2026-05-06 21:54:38.723188 INFO::Total function execution time is 0.163758039474487 s and adjustment time is 0.144526243209839 s ( 88.26 )
2026-05-06 21:54:38.738552 INFO::Formatting Data.
2026-05-06 21:54:38.739564 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.74072 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.741902 INFO::Found 0 missing values.
2026-05-06 21:54:38.744933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.745539 INFO::Done
2026-05-06 21:54:38.746133 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.749559 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.750363 INFO::Found 2 batches.
2026-05-06 21:54:38.750965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.751673 INFO::Using default BPPARAM
2026-05-06 21:54:38.752277 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.753354 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.770804 INFO::Done
2026-05-06 21:54:38.771703 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.775232 INFO::ASW Batch was 0.188642949256461 prior to batch effect correction and is now -0.0348242834702377 .
2026-05-06 21:54:38.775906 INFO::ASW Label was 0.769612802276846 prior to batch effect correction and is now 0.932196956896665 .
2026-05-06 21:54:38.776826 INFO::Total function execution time is 0.0384440422058105 s and adjustment time is 0.0205392837524414 s ( 53.43 )
2026-05-06 21:54:38.777802 INFO::Formatting Data.
2026-05-06 21:54:38.778496 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.779472 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.780542 INFO::Found 0 missing values.
2026-05-06 21:54:38.783442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.784034 INFO::Done
2026-05-06 21:54:38.784626 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.78784 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.788598 INFO::Found 2 batches.
2026-05-06 21:54:38.789194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.789865 INFO::Using default BPPARAM
2026-05-06 21:54:38.790432 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.791438 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-05-06 21:54:38.807327 INFO::Done
2026-05-06 21:54:38.808137 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.811361 INFO::ASW Batch was 0.188642949256461 prior to batch effect correction and is now -0.0348242834702377 .
2026-05-06 21:54:38.812026 INFO::ASW Label was 0.769612802276846 prior to batch effect correction and is now 0.932196956896665 .
2026-05-06 21:54:38.812912 INFO::Total function execution time is 0.0351512432098389 s and adjustment time is 0.0188488960266113 s ( 53.62 )
2026-05-06 21:54:38.825126 INFO::Formatting Data.
2026-05-06 21:54:38.825994 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.826988 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.82798 INFO::Found 0 missing values.
2026-05-06 21:54:38.830239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.830823 INFO::Done
2026-05-06 21:54:38.831429 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.833601 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.834356 INFO::Found 2 batches.
2026-05-06 21:54:38.834937 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.835598 INFO::Using default BPPARAM
2026-05-06 21:54:38.836181 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.83716 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 21:54:38.871844 INFO::Done
2026-05-06 21:54:38.872754 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.875158 INFO::ASW Batch was 0.16410938850607 prior to batch effect correction and is now -0.0312277518350963 .
2026-05-06 21:54:38.876103 INFO::Total function execution time is 0.0510694980621338 s and adjustment time is 0.0375821590423584 s ( 73.59 )
2026-05-06 21:54:38.889468 INFO::Formatting Data.
2026-05-06 21:54:38.890442 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.891468 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.892576 INFO::Found 0 missing values.
2026-05-06 21:54:38.893881 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 21:54:38.898815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.899436 INFO::Done
2026-05-06 21:54:38.900028 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.903486 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.904256 INFO::Found 2 batches.
2026-05-06 21:54:38.904841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.905491 INFO::Using default BPPARAM
2026-05-06 21:54:38.906086 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.907097 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 21:54:38.924723 INFO::Done
2026-05-06 21:54:38.925509 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.928767 INFO::ASW Batch was 0.663513955429894 prior to batch effect correction and is now 0.101949442849357 .
2026-05-06 21:54:38.929412 INFO::ASW Label was 0.432002824097348 prior to batch effect correction and is now 0.829980346901719 .
2026-05-06 21:54:38.930268 INFO::Total function execution time is 0.0409281253814697 s and adjustment time is 0.020576000213623 s ( 50.27 )
2026-05-06 21:54:38.93119 INFO::Formatting Data.
2026-05-06 21:54:38.931883 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:38.932878 INFO::Removing potential empty rows and columns
2026-05-06 21:54:38.933932 INFO::Found 0 missing values.
2026-05-06 21:54:38.934884 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 21:54:38.93987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:38.940459 INFO::Done
2026-05-06 21:54:38.941029 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:38.944194 INFO::Starting hierarchical adjustment
2026-05-06 21:54:38.944944 INFO::Found 2 batches.
2026-05-06 21:54:38.945521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:38.946204 INFO::Using default BPPARAM
2026-05-06 21:54:38.94679 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:38.947798 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 21:54:38.965858 INFO::Done
2026-05-06 21:54:38.966766 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:38.970388 INFO::ASW Batch was 0.663513955429894 prior to batch effect correction and is now 0.101949442849357 .
2026-05-06 21:54:38.971089 INFO::ASW Label was 0.432002824097348 prior to batch effect correction and is now 0.829980346901719 .
2026-05-06 21:54:38.972028 INFO::Total function execution time is 0.0408682823181152 s and adjustment time is 0.021000862121582 s ( 51.39 )
2026-05-06 21:54:39.198771 INFO::Formatting Data.
2026-05-06 21:54:39.199815 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:39.200871 INFO::Removing potential empty rows and columns
2026-05-06 21:54:39.202043 INFO::Found 0 missing values.
2026-05-06 21:54:39.205256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:39.205873 INFO::Done
2026-05-06 21:54:39.206443 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:39.208744 INFO::Starting hierarchical adjustment
2026-05-06 21:54:39.209503 INFO::Found 3 batches.
2026-05-06 21:54:39.210091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:39.210776 INFO::Using default BPPARAM
2026-05-06 21:54:39.211388 INFO::Processing subtree level 1
2026-05-06 21:54:39.305249 INFO::Adjusting the last 1 batches sequentially
2026-05-06 21:54:39.30746 INFO::Done
2026-05-06 21:54:39.308565 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:39.311622 INFO::ASW Batch was -0.0415170547696097 prior to batch effect correction and is now -0.0415170547696097 .
2026-05-06 21:54:39.312775 INFO::Total function execution time is 0.114103317260742 s and adjustment time is 0.0980620384216309 s ( 85.94 )
2026-05-06 21:54:39.314044 INFO::Formatting Data.
2026-05-06 21:54:39.314814 INFO::Typecasting input to dataframe.
2026-05-06 21:54:39.315673 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:39.316881 INFO::Removing potential empty rows and columns
2026-05-06 21:54:39.318114 INFO::Found 0 missing values.
2026-05-06 21:54:39.321487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:39.322123 INFO::Done
2026-05-06 21:54:39.322726 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:39.32511 INFO::Starting hierarchical adjustment
2026-05-06 21:54:39.325916 INFO::Found 3 batches.
2026-05-06 21:54:39.326523 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:39.327237 INFO::Using default BPPARAM
2026-05-06 21:54:39.327853 INFO::Processing subtree level 1
2026-05-06 21:54:39.424107 INFO::Adjusting the last 1 batches sequentially
2026-05-06 21:54:39.426206 INFO::Done
2026-05-06 21:54:39.427014 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:39.429802 INFO::ASW Batch was -0.0415170547696097 prior to batch effect correction and is now -0.0415170547696097 .
2026-05-06 21:54:39.430883 INFO::Total function execution time is 0.116824150085449 s and adjustment time is 0.10043478012085 s ( 85.97 )
2026-05-06 21:54:39.445002 INFO::Formatting Data.
2026-05-06 21:54:39.445922 INFO::Typecasting input to dataframe.
2026-05-06 21:54:39.44691 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:39.447921 INFO::Removing potential empty rows and columns
2026-05-06 21:54:39.449106 INFO::Found 0 missing values.
2026-05-06 21:54:39.452228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:39.452898 INFO::Done
2026-05-06 21:54:39.453479 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:39.45569 INFO::Starting hierarchical adjustment
2026-05-06 21:54:39.456485 INFO::Found 3 batches.
2026-05-06 21:54:39.45707 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:39.457758 INFO::Using default BPPARAM
2026-05-06 21:54:39.458335 INFO::Processing subtree level 1
2026-05-06 21:54:39.551291 INFO::Adjusting the last 1 batches sequentially
2026-05-06 21:54:39.553564 INFO::Done
2026-05-06 21:54:39.554337 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:39.557165 INFO::ASW Batch was 0.0943463185576815 prior to batch effect correction and is now 0.0943463185576815 .
2026-05-06 21:54:39.558258 INFO::Total function execution time is 0.113337278366089 s and adjustment time is 0.0969674587249756 s ( 85.56 )
2026-05-06 21:54:39.705038 INFO::Formatting Data.
2026-05-06 21:54:39.706083 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:39.707341 INFO::Removing potential empty rows and columns
2026-05-06 21:54:39.710298 INFO::Found 1000 missing values.
2026-05-06 21:54:39.730633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:39.731552 INFO::Done
2026-05-06 21:54:39.732237 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:39.738116 INFO::Starting hierarchical adjustment
2026-05-06 21:54:39.738969 INFO::Found 10 batches.
2026-05-06 21:54:39.739559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:39.740269 INFO::Using default BPPARAM
2026-05-06 21:54:39.740902 INFO::Processing subtree level 1
2026-05-06 21:54:39.893437 INFO::Processing subtree level 2
2026-05-06 21:54:40.044759 INFO::Adjusting the last 1 batches sequentially
2026-05-06 21:54:40.047151 INFO::Done
2026-05-06 21:54:40.048054 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:40.05452 INFO::ASW Batch was 0.511919590566251 prior to batch effect correction and is now 0.511919590566251 .
2026-05-06 21:54:40.055337 INFO::ASW Label was 0.314382357283122 prior to batch effect correction and is now 0.314382357283122 .
2026-05-06 21:54:40.056454 INFO::Total function execution time is 0.351543426513672 s and adjustment time is 0.308302402496338 s ( 87.7 )
2026-05-06 21:54:40.057429 INFO::Formatting Data.
2026-05-06 21:54:40.058198 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:40.059784 INFO::Removing potential empty rows and columns
2026-05-06 21:54:40.062956 INFO::Found 1000 missing values.
2026-05-06 21:54:40.084593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:40.085574 INFO::Done
2026-05-06 21:54:40.086323 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:40.09252 INFO::Starting hierarchical adjustment
2026-05-06 21:54:40.093421 INFO::Found 10 batches.
2026-05-06 21:54:41.447401 INFO::Set up parallel execution backend with 2 workers
2026-05-06 21:54:41.450873 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-05-06 21:54:42.894508 INFO::Adjusting the last 2 batches sequentially
2026-05-06 21:54:42.897953 INFO::Adjusting sequential tree level 1 with 2 batches
2026-05-06 21:54:42.914494 INFO::Done
2026-05-06 21:54:42.915287 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:42.919983 INFO::ASW Batch was 0.511919590566251 prior to batch effect correction and is now 0.511919590566251 .
2026-05-06 21:54:42.920651 INFO::ASW Label was 0.314382357283122 prior to batch effect correction and is now 0.314382357283122 .
2026-05-06 21:54:42.921487 INFO::Total function execution time is 2.86411476135254 s and adjustment time is 2.82121276855469 s ( 98.5 )
2026-05-06 21:54:43.069499 INFO::Formatting Data.
2026-05-06 21:54:43.070519 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.071538 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.072652 INFO::Found 0 missing values.
2026-05-06 21:54:43.076337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.077031 INFO::Done
2026-05-06 21:54:43.077609 INFO::Acquiring quality metrics before batch effect correction.
2026-05-06 21:54:43.080529 INFO::Starting hierarchical adjustment
2026-05-06 21:54:43.081341 INFO::Found 3 batches.
2026-05-06 21:54:43.081933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-05-06 21:54:43.082606 INFO::Using default BPPARAM
2026-05-06 21:54:43.083187 INFO::Processing subtree level 1
2026-05-06 21:54:43.206512 INFO::Adjusting the last 1 batches sequentially
2026-05-06 21:54:43.209623 INFO::Done
2026-05-06 21:54:43.210432 INFO::Acquiring quality metrics after batch effect correction.
2026-05-06 21:54:43.214789 INFO::ASW Batch was 0.152500772118406 prior to batch effect correction and is now -0.139289412741005 .
2026-05-06 21:54:43.215642 INFO::ASW Label was -0.188546516266248 prior to batch effect correction and is now -0.0553556912092542 .
2026-05-06 21:54:43.216779 INFO::Total function execution time is 0.14733624458313 s and adjustment time is 0.128408670425415 s ( 87.15 )
2026-05-06 21:54:43.351313 INFO::Formatting Data.
2026-05-06 21:54:43.352356 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.353493 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.354789 INFO::Found 2 missing values.
2026-05-06 21:54:43.357992 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.35858 INFO::Done
2026-05-06 21:54:43.387823 INFO::Found NA in Reference column
2026-05-06 21:54:43.397996 INFO::Require at least two references per batch.
2026-05-06 21:54:43.419472 INFO::Formatting Data.
2026-05-06 21:54:43.420428 INFO::Recognized SummarizedExperiment
2026-05-06 21:54:43.421044 INFO::Typecasting input to dataframe.
2026-05-06 21:54:43.431572 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.433041 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.436849 INFO::Found 0 missing values.
2026-05-06 21:54:43.443969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.444857 INFO::Done
2026-05-06 21:54:43.461329 INFO::Formatting Data.
2026-05-06 21:54:43.462318 INFO::Recognized SummarizedExperiment
2026-05-06 21:54:43.462962 INFO::Typecasting input to dataframe.
2026-05-06 21:54:43.480963 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.482398 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.486149 INFO::Found 0 missing values.
2026-05-06 21:54:43.497411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.49826 INFO::Done
2026-05-06 21:54:43.514365 INFO::Formatting Data.
2026-05-06 21:54:43.515264 INFO::Recognized SummarizedExperiment
2026-05-06 21:54:43.515885 INFO::Typecasting input to dataframe.
2026-05-06 21:54:43.532769 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.533949 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.535103 INFO::Found 0 missing values.
2026-05-06 21:54:43.536062 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 21:54:43.540619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.541238 INFO::Done
2026-05-06 21:54:43.551738 INFO::Formatting Data.
2026-05-06 21:54:43.552556 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.553503 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.554592 INFO::Found 0 missing values.
2026-05-06 21:54:43.557479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.558059 INFO::Done
2026-05-06 21:54:43.569479 INFO::Formatting Data.
2026-05-06 21:54:43.5703 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.571195 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.572242 INFO::Found 0 missing values.
2026-05-06 21:54:43.575121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.575756 INFO::Done
2026-05-06 21:54:43.608262 INFO::Formatting Data.
2026-05-06 21:54:43.609435 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.610772 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.612172 INFO::Found 1 missing values.
2026-05-06 21:54:43.615165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.615826 INFO::Done
2026-05-06 21:54:43.636447 INFO::Formatting Data.
2026-05-06 21:54:43.637506 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.638529 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.639625 INFO::Found 2 missing values.
2026-05-06 21:54:43.640614 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-05-06 21:54:43.643016 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.643649 INFO::Done
2026-05-06 21:54:43.654153 INFO::Formatting Data.
2026-05-06 21:54:43.655003 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.655957 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.656975 INFO::Found 2 missing values.
2026-05-06 21:54:43.658718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.659347 INFO::Done
2026-05-06 21:54:43.670687 INFO::Formatting Data.
2026-05-06 21:54:43.671501 INFO::Typecasting input to dataframe.
2026-05-06 21:54:43.672343 INFO::Replacing NaNs with NAs.
2026-05-06 21:54:43.673241 INFO::Removing potential empty rows and columns
2026-05-06 21:54:43.674265 INFO::Found 0 missing values.
2026-05-06 21:54:43.677083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-05-06 21:54:43.677635 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.979 3.731 21.334
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.356 | 1.167 | 17.259 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.013 | |
| generate_data_covariables | 0.009 | 0.003 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.011 | |