Yannis Schumann
| Snapshot Date: 2026-04-23 13:45 -0400 (Thu, 23 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-04-24 11:32 -0400 (Fri, 24 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4800 |
| 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 165/2351 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-04-23 21:24:51 -0400 (Thu, 23 Apr 2026) |
| EndedAt: 2026-04-23 21:26:29 -0400 (Thu, 23 Apr 2026) |
| EllapsedTime: 98.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-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: 2026-04-24 01:24:52 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.591 1.631 18.287
* 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-3.24-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R 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")
2026-04-23 21:25:46.01144 INFO::Formatting Data.
2026-04-23 21:25:46.012816 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:46.024097 INFO::Removing potential empty rows and columns
2026-04-23 21:25:46.301469 INFO::Found 0 missing values.
2026-04-23 21:25:46.305254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:46.305962 INFO::Done
2026-04-23 21:25:46.306539 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:46.320498 INFO::Starting hierarchical adjustment
2026-04-23 21:25:46.321434 INFO::Found 3 batches.
2026-04-23 21:25:46.322059 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:46.323293 INFO::Using default BPPARAM
2026-04-23 21:25:46.323878 INFO::Processing subtree level 1
2026-04-23 21:25:46.431992 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:25:46.434307 INFO::Done
2026-04-23 21:25:46.435284 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:46.438318 INFO::ASW Batch was -0.0256544739360786 prior to batch effect correction and is now -0.0256544739360786 .
2026-04-23 21:25:46.439553 INFO::Total function execution time is 0.428705215454102 s and adjustment time is 0.113031387329102 s ( 26.37 )
2026-04-23 21:25:46.455998 INFO::Formatting Data.
2026-04-23 21:25:46.456955 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:46.458112 INFO::Removing potential empty rows and columns
2026-04-23 21:25:46.459412 INFO::Found 0 missing values.
2026-04-23 21:25:46.460513 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.
2026-04-23 21:25:46.472988 INFO::Formatting Data.
2026-04-23 21:25:46.473882 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:46.474983 INFO::Removing potential empty rows and columns
2026-04-23 21:25:46.476274 INFO::Found 0 missing values.
2026-04-23 21:25:46.47732 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.
2026-04-23 21:25:46.49488 INFO::Formatting Data.
2026-04-23 21:25:46.495758 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:46.496778 INFO::Removing potential empty rows and columns
2026-04-23 21:25:46.497903 INFO::Found 0 missing values.
2026-04-23 21:25:46.498876 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.
2026-04-23 21:25:46.503622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:46.504241 INFO::Done
2026-04-23 21:25:46.504795 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:46.507046 INFO::Starting hierarchical adjustment
2026-04-23 21:25:46.507789 INFO::Found 2 batches.
2026-04-23 21:25:46.50839 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:46.509107 INFO::Using default BPPARAM
2026-04-23 21:25:46.509691 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:46.51071 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:25:46.533762 INFO::Done
2026-04-23 21:25:46.534564 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:46.536769 INFO::ASW Batch was -0.0195070120763764 prior to batch effect correction and is now -0.105203678913596 .
2026-04-23 21:25:46.537617 INFO::Total function execution time is 0.0428361892700195 s and adjustment time is 0.0260894298553467 s ( 60.91 )
2026-04-23 21:25:46.540714 INFO::Formatting Data.
2026-04-23 21:25:46.541434 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:46.55074 INFO::Formatting Data.
2026-04-23 21:25:46.551536 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:46.55251 INFO::Removing potential empty rows and columns
2026-04-23 21:25:46.553659 INFO::Found 0 missing values.
2026-04-23 21:25:46.556752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:46.557352 INFO::Done
2026-04-23 21:25:46.557909 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:46.560153 INFO::Starting hierarchical adjustment
2026-04-23 21:25:46.56094 INFO::Found 2 batches.
2026-04-23 21:25:46.56155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:46.562241 INFO::Using default BPPARAM
2026-04-23 21:25:46.562829 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:46.563845 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:25:46.581882 INFO::Done
2026-04-23 21:25:46.582806 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:46.58543 INFO::ASW Batch was 0.0148697862771834 prior to batch effect correction and is now -0.137404175963837 .
2026-04-23 21:25:46.586424 INFO::Total function execution time is 0.0357167720794678 s and adjustment time is 0.0210576057434082 s ( 58.96 )
2026-04-23 21:25:46.587651 INFO::Formatting Data.
2026-04-23 21:25:46.588379 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:46.589384 INFO::Removing potential empty rows and columns
2026-04-23 21:25:46.590594 INFO::Found 0 missing values.
2026-04-23 21:25:46.593904 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:46.59454 INFO::Done
2026-04-23 21:25:46.595151 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:46.597517 INFO::Starting hierarchical adjustment
2026-04-23 21:25:46.59854 INFO::Found 2 batches.
2026-04-23 21:25:46.599186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:46.599878 INFO::Using default BPPARAM
2026-04-23 21:25:46.600525 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:46.601538 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:25:46.61777 INFO::Done
2026-04-23 21:25:46.618519 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:46.620737 INFO::ASW Batch was 0.0148697862771834 prior to batch effect correction and is now -0.137404175963837 .
2026-04-23 21:25:46.621599 INFO::Total function execution time is 0.0339498519897461 s and adjustment time is 0.0193836688995361 s ( 57.1 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-23 21:25:50.194062 INFO::Formatting Data.
2026-04-23 21:25:50.19489 INFO::Recognized SummarizedExperiment
2026-04-23 21:25:50.195457 INFO::Typecasting input to dataframe.
2026-04-23 21:25:50.22744 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:50.228881 INFO::Removing potential empty rows and columns
2026-04-23 21:25:50.23243 INFO::Found 0 missing values.
2026-04-23 21:25:50.23914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:50.239773 INFO::Done
2026-04-23 21:25:50.240355 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:50.244084 INFO::Starting hierarchical adjustment
2026-04-23 21:25:50.244831 INFO::Found 2 batches.
2026-04-23 21:25:50.245374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:50.246556 INFO::Using default BPPARAM
2026-04-23 21:25:50.247117 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:50.248116 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:25:50.30066 INFO::Done
2026-04-23 21:25:50.301522 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:50.305131 INFO::ASW Batch was -0.017253608268226 prior to batch effect correction and is now -0.0906861006560025 .
2026-04-23 21:25:50.306004 INFO::Total function execution time is 0.112233638763428 s and adjustment time is 0.0559391975402832 s ( 49.84 )
Warning: stack imbalance in '{', 73 then 75
2026-04-23 21:25:50.325073 INFO::Formatting Data.
2026-04-23 21:25:50.326062 INFO::Recognized SummarizedExperiment
2026-04-23 21:25:50.326647 INFO::Typecasting input to dataframe.
2026-04-23 21:25:50.336418 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:50.337738 INFO::Removing potential empty rows and columns
2026-04-23 21:25:50.341264 INFO::Found 0 missing values.
2026-04-23 21:25:50.348104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:50.348724 INFO::Done
2026-04-23 21:25:50.349303 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:50.352933 INFO::Starting hierarchical adjustment
2026-04-23 21:25:50.353668 INFO::Found 2 batches.
2026-04-23 21:25:50.354209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:50.354818 INFO::Using default BPPARAM
2026-04-23 21:25:50.355377 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:50.356395 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:25:50.383462 INFO::Done
2026-04-23 21:25:50.384476 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:50.38871 INFO::ASW Batch was -0.0132707897843964 prior to batch effect correction and is now -0.0132707897843964 .
2026-04-23 21:25:50.389734 INFO::Total function execution time is 0.0646798610687256 s and adjustment time is 0.0298409461975098 s ( 46.14 )
2026-04-23 21:25:50.412156 INFO::Formatting Data.
2026-04-23 21:25:50.413262 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:50.414365 INFO::Removing potential empty rows and columns
2026-04-23 21:25:50.415527 INFO::Found 0 missing values.
2026-04-23 21:25:50.418929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:50.419517 INFO::Done
2026-04-23 21:25:50.420093 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:50.422597 INFO::Starting hierarchical adjustment
2026-04-23 21:25:50.423389 INFO::Found 3 batches.
2026-04-23 21:25:50.423978 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:50.424636 INFO::Using default BPPARAM
2026-04-23 21:25:50.425222 INFO::Processing subtree level 1
2026-04-23 21:25:50.59054 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:25:50.592793 INFO::Done
2026-04-23 21:25:50.593633 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:50.59656 INFO::ASW Batch was -0.137088490815215 prior to batch effect correction and is now -0.178868041612663 .
2026-04-23 21:25:50.597683 INFO::Total function execution time is 0.185615301132202 s and adjustment time is 0.169517755508423 s ( 91.33 )
2026-04-23 21:25:50.614058 INFO::Skipping initial DF formatting
2026-04-23 21:25:50.615012 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:50.619455 INFO::Starting hierarchical adjustment
2026-04-23 21:25:50.620389 INFO::Found 5 batches.
2026-04-23 21:25:50.621015 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:50.621709 INFO::Using default BPPARAM
2026-04-23 21:25:50.622316 INFO::Processing subtree level 1
2026-04-23 21:25:50.766275 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:50.768556 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:25:50.78961 INFO::Done
2026-04-23 21:25:50.790447 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:50.795126 INFO::ASW Batch was 0.46434764983258 prior to batch effect correction and is now 0.46434764983258 .
2026-04-23 21:25:50.795835 INFO::ASW Label was 0.417140726943611 prior to batch effect correction and is now 0.417140726943611 .
2026-04-23 21:25:50.796821 INFO::Total function execution time is 0.182912111282349 s and adjustment time is 0.169398069381714 s ( 92.61 )
2026-04-23 21:25:50.816236 INFO::Formatting Data.
2026-04-23 21:25:50.817163 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:50.818194 INFO::Removing potential empty rows and columns
2026-04-23 21:25:50.819274 INFO::Found 0 missing values.
2026-04-23 21:25:50.823544 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:50.824158 INFO::Done
2026-04-23 21:25:50.824719 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:50.827964 INFO::Starting hierarchical adjustment
2026-04-23 21:25:50.828727 INFO::Found 5 batches.
2026-04-23 21:25:50.829322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:50.830008 INFO::Using default BPPARAM
2026-04-23 21:25:50.830598 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.
2026-04-23 21:25:50.975681 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:50.97786 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:25:51.000261 INFO::Done
2026-04-23 21:25:51.001276 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.005021 INFO::ASW Batch was 0.416305920036496 prior to batch effect correction and is now -0.0815397211546322 .
2026-04-23 21:25:51.005748 INFO::ASW Label was 0.39982726930012 prior to batch effect correction and is now 0.763536840651803 .
2026-04-23 21:25:51.00671 INFO::Total function execution time is 0.190525054931641 s and adjustment time is 0.171585321426392 s ( 90.06 )
2026-04-23 21:25:51.00762 INFO::Formatting Data.
2026-04-23 21:25:51.008308 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:51.009279 INFO::Removing potential empty rows and columns
2026-04-23 21:25:51.010435 INFO::Found 0 missing values.
2026-04-23 21:25:51.014821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:51.015424 INFO::Done
2026-04-23 21:25:51.015997 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:51.01921 INFO::Starting hierarchical adjustment
2026-04-23 21:25:51.019983 INFO::Found 5 batches.
2026-04-23 21:25:51.020555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:51.021245 INFO::Using default BPPARAM
2026-04-23 21:25:51.021807 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.
2026-04-23 21:25:51.153605 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:51.155579 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:25:51.173427 INFO::Done
2026-04-23 21:25:51.174434 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.178196 INFO::ASW Batch was 0.416305920036496 prior to batch effect correction and is now -0.0815397211546322 .
2026-04-23 21:25:51.178951 INFO::ASW Label was 0.39982726930012 prior to batch effect correction and is now 0.763536840651803 .
2026-04-23 21:25:51.17986 INFO::Total function execution time is 0.172240257263184 s and adjustment time is 0.153536796569824 s ( 89.14 )
2026-04-23 21:25:51.194944 INFO::Formatting Data.
2026-04-23 21:25:51.195891 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:51.196943 INFO::Removing potential empty rows and columns
2026-04-23 21:25:51.198063 INFO::Found 0 missing values.
2026-04-23 21:25:51.202656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:51.203325 INFO::Done
2026-04-23 21:25:51.20392 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:51.207286 INFO::Starting hierarchical adjustment
2026-04-23 21:25:51.208108 INFO::Found 5 batches.
2026-04-23 21:25:51.208686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:51.20938 INFO::Using default BPPARAM
2026-04-23 21:25:51.209967 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.
2026-04-23 21:25:51.339019 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:51.340871 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:25:51.357989 INFO::Done
2026-04-23 21:25:51.358862 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.362568 INFO::ASW Batch was 0.416792781644283 prior to batch effect correction and is now -0.00305042299378378 .
2026-04-23 21:25:51.363265 INFO::ASW Label was 0.249443790028661 prior to batch effect correction and is now 0.795205884912582 .
2026-04-23 21:25:51.364187 INFO::Total function execution time is 0.169372081756592 s and adjustment time is 0.149998426437378 s ( 88.56 )
2026-04-23 21:25:51.365156 INFO::Formatting Data.
2026-04-23 21:25:51.365848 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:51.366851 INFO::Removing potential empty rows and columns
2026-04-23 21:25:51.367997 INFO::Found 0 missing values.
2026-04-23 21:25:51.372393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:51.372999 INFO::Done
2026-04-23 21:25:51.37357 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:51.376824 INFO::Starting hierarchical adjustment
2026-04-23 21:25:51.377604 INFO::Found 5 batches.
2026-04-23 21:25:51.378196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:51.378859 INFO::Using default BPPARAM
2026-04-23 21:25:51.379468 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.
2026-04-23 21:25:51.5022 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:51.504222 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:25:51.523142 INFO::Done
2026-04-23 21:25:51.524173 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.52809 INFO::ASW Batch was 0.416792781644283 prior to batch effect correction and is now -0.00305042299378378 .
2026-04-23 21:25:51.528891 INFO::ASW Label was 0.249443790028661 prior to batch effect correction and is now 0.795205884912582 .
2026-04-23 21:25:51.5299 INFO::Total function execution time is 0.164730787277222 s and adjustment time is 0.145600557327271 s ( 88.39 )
2026-04-23 21:25:51.546492 INFO::Formatting Data.
2026-04-23 21:25:51.547611 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:51.548842 INFO::Removing potential empty rows and columns
2026-04-23 21:25:51.550201 INFO::Found 0 missing values.
2026-04-23 21:25:51.553766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:51.554444 INFO::Done
2026-04-23 21:25:51.555089 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:51.559083 INFO::Starting hierarchical adjustment
2026-04-23 21:25:51.56005 INFO::Found 2 batches.
2026-04-23 21:25:51.560708 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:51.561495 INFO::Using default BPPARAM
2026-04-23 21:25:51.562174 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:51.563281 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:25:51.582688 INFO::Done
2026-04-23 21:25:51.583729 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.587862 INFO::ASW Batch was 0.37167023599306 prior to batch effect correction and is now -0.0238304487286886 .
2026-04-23 21:25:51.588673 INFO::ASW Label was 0.597930473289281 prior to batch effect correction and is now 0.910670331097854 .
2026-04-23 21:25:51.58967 INFO::Total function execution time is 0.0433652400970459 s and adjustment time is 0.0227854251861572 s ( 52.54 )
2026-04-23 21:25:51.590633 INFO::Formatting Data.
2026-04-23 21:25:51.591359 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:51.592478 INFO::Removing potential empty rows and columns
2026-04-23 21:25:51.59367 INFO::Found 0 missing values.
2026-04-23 21:25:51.597126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:51.597821 INFO::Done
2026-04-23 21:25:51.598495 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:51.602273 INFO::Starting hierarchical adjustment
2026-04-23 21:25:51.603188 INFO::Found 2 batches.
2026-04-23 21:25:51.603816 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:51.604568 INFO::Using default BPPARAM
2026-04-23 21:25:51.605216 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:51.606406 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:25:51.625406 INFO::Done
2026-04-23 21:25:51.626392 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.630292 INFO::ASW Batch was 0.37167023599306 prior to batch effect correction and is now -0.0238304487286886 .
2026-04-23 21:25:51.631094 INFO::ASW Label was 0.597930473289281 prior to batch effect correction and is now 0.910670331097854 .
2026-04-23 21:25:51.632113 INFO::Total function execution time is 0.0414588451385498 s and adjustment time is 0.0223450660705566 s ( 53.9 )
2026-04-23 21:25:51.648382 INFO::Formatting Data.
2026-04-23 21:25:51.649484 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:51.650659 INFO::Removing potential empty rows and columns
2026-04-23 21:25:51.651758 INFO::Found 0 missing values.
2026-04-23 21:25:51.654493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:51.655167 INFO::Done
2026-04-23 21:25:51.655801 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:51.658329 INFO::Starting hierarchical adjustment
2026-04-23 21:25:51.659241 INFO::Found 2 batches.
2026-04-23 21:25:51.65995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:51.660769 INFO::Using default BPPARAM
2026-04-23 21:25:51.661468 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:51.662668 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:25:51.705932 INFO::Done
2026-04-23 21:25:51.706994 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.709743 INFO::ASW Batch was -0.120775520930313 prior to batch effect correction and is now -0.144307754989151 .
2026-04-23 21:25:51.710822 INFO::Total function execution time is 0.0626499652862549 s and adjustment time is 0.04679274559021 s ( 74.69 )
2026-04-23 21:25:51.726843 INFO::Formatting Data.
2026-04-23 21:25:51.728154 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:51.729413 INFO::Removing potential empty rows and columns
2026-04-23 21:25:51.730718 INFO::Found 0 missing values.
2026-04-23 21:25:51.732276 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.
2026-04-23 21:25:51.738189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:51.738991 INFO::Done
2026-04-23 21:25:51.739613 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:51.74337 INFO::Starting hierarchical adjustment
2026-04-23 21:25:51.744237 INFO::Found 2 batches.
2026-04-23 21:25:51.744866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:51.745652 INFO::Using default BPPARAM
2026-04-23 21:25:51.746303 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:51.747517 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:25:51.768975 INFO::Done
2026-04-23 21:25:51.769978 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.77403 INFO::ASW Batch was 0.435249673310931 prior to batch effect correction and is now 0.0341320215089126 .
2026-04-23 21:25:51.774893 INFO::ASW Label was 0.642419896675203 prior to batch effect correction and is now 0.928989603985788 .
2026-04-23 21:25:51.776016 INFO::Total function execution time is 0.049461841583252 s and adjustment time is 0.024808406829834 s ( 50.16 )
2026-04-23 21:25:51.777167 INFO::Formatting Data.
2026-04-23 21:25:51.778012 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:51.779312 INFO::Removing potential empty rows and columns
2026-04-23 21:25:51.780596 INFO::Found 0 missing values.
2026-04-23 21:25:51.782268 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.
2026-04-23 21:25:51.788742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:51.789647 INFO::Done
2026-04-23 21:25:51.790394 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:51.794644 INFO::Starting hierarchical adjustment
2026-04-23 21:25:51.795638 INFO::Found 2 batches.
2026-04-23 21:25:51.796392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:51.797209 INFO::Using default BPPARAM
2026-04-23 21:25:51.797861 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:51.799182 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:25:51.82296 INFO::Done
2026-04-23 21:25:51.824534 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:51.828869 INFO::ASW Batch was 0.435249673310931 prior to batch effect correction and is now 0.0341320215089126 .
2026-04-23 21:25:51.829774 INFO::ASW Label was 0.642419896675203 prior to batch effect correction and is now 0.928989603985788 .
2026-04-23 21:25:51.830874 INFO::Total function execution time is 0.053786039352417 s and adjustment time is 0.0274128913879395 s ( 50.97 )
2026-04-23 21:25:52.128403 INFO::Formatting Data.
2026-04-23 21:25:52.129431 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:52.130485 INFO::Removing potential empty rows and columns
2026-04-23 21:25:52.13185 INFO::Found 0 missing values.
2026-04-23 21:25:52.13518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:52.135795 INFO::Done
2026-04-23 21:25:52.136372 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:52.138732 INFO::Starting hierarchical adjustment
2026-04-23 21:25:52.139522 INFO::Found 3 batches.
2026-04-23 21:25:52.140099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:52.140761 INFO::Using default BPPARAM
2026-04-23 21:25:52.141341 INFO::Processing subtree level 1
2026-04-23 21:25:52.237617 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:25:52.239669 INFO::Done
2026-04-23 21:25:52.240522 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:52.243474 INFO::ASW Batch was -0.0926307196618249 prior to batch effect correction and is now -0.0926307196618249 .
2026-04-23 21:25:52.244698 INFO::Total function execution time is 0.116358280181885 s and adjustment time is 0.100270986557007 s ( 86.17 )
2026-04-23 21:25:52.245995 INFO::Formatting Data.
2026-04-23 21:25:52.246747 INFO::Typecasting input to dataframe.
2026-04-23 21:25:52.247654 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:52.248755 INFO::Removing potential empty rows and columns
2026-04-23 21:25:52.250008 INFO::Found 0 missing values.
2026-04-23 21:25:52.253501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:52.254181 INFO::Done
2026-04-23 21:25:52.254778 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:52.257509 INFO::Starting hierarchical adjustment
2026-04-23 21:25:52.258341 INFO::Found 3 batches.
2026-04-23 21:25:52.258949 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:52.259651 INFO::Using default BPPARAM
2026-04-23 21:25:52.260261 INFO::Processing subtree level 1
2026-04-23 21:25:52.356193 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:25:52.358216 INFO::Done
2026-04-23 21:25:52.359004 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:52.361725 INFO::ASW Batch was -0.0926307196618249 prior to batch effect correction and is now -0.0926307196618249 .
2026-04-23 21:25:52.36281 INFO::Total function execution time is 0.116829395294189 s and adjustment time is 0.100021362304688 s ( 85.61 )
2026-04-23 21:25:52.378996 INFO::Formatting Data.
2026-04-23 21:25:52.379994 INFO::Typecasting input to dataframe.
2026-04-23 21:25:52.38095 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:52.381994 INFO::Removing potential empty rows and columns
2026-04-23 21:25:52.383178 INFO::Found 0 missing values.
2026-04-23 21:25:52.386324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:52.386924 INFO::Done
2026-04-23 21:25:52.387511 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:52.389744 INFO::Starting hierarchical adjustment
2026-04-23 21:25:52.390519 INFO::Found 3 batches.
2026-04-23 21:25:52.391113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:52.391788 INFO::Using default BPPARAM
2026-04-23 21:25:52.39239 INFO::Processing subtree level 1
2026-04-23 21:25:52.493516 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:25:52.495797 INFO::Done
2026-04-23 21:25:52.49665 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:52.500258 INFO::ASW Batch was -0.0919872176072882 prior to batch effect correction and is now -0.0919872176072882 .
2026-04-23 21:25:52.501489 INFO::Total function execution time is 0.122589349746704 s and adjustment time is 0.105376720428467 s ( 85.96 )
2026-04-23 21:25:52.675492 INFO::Formatting Data.
2026-04-23 21:25:52.676638 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:52.678005 INFO::Removing potential empty rows and columns
2026-04-23 21:25:52.681341 INFO::Found 1000 missing values.
2026-04-23 21:25:52.702209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:52.703084 INFO::Done
2026-04-23 21:25:52.703712 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:52.709579 INFO::Starting hierarchical adjustment
2026-04-23 21:25:52.710473 INFO::Found 10 batches.
2026-04-23 21:25:52.711104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:52.711789 INFO::Using default BPPARAM
2026-04-23 21:25:52.712386 INFO::Processing subtree level 1
2026-04-23 21:25:52.883786 INFO::Processing subtree level 2
2026-04-23 21:25:53.053092 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:25:53.055758 INFO::Done
2026-04-23 21:25:53.056674 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:53.063291 INFO::ASW Batch was 0.469734717936826 prior to batch effect correction and is now 0.469734717936826 .
2026-04-23 21:25:53.064404 INFO::ASW Label was 0.356075717780153 prior to batch effect correction and is now 0.356075717780153 .
2026-04-23 21:25:53.065979 INFO::Total function execution time is 0.390508651733398 s and adjustment time is 0.345412015914917 s ( 88.45 )
2026-04-23 21:25:53.067384 INFO::Formatting Data.
2026-04-23 21:25:53.068439 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:53.070524 INFO::Removing potential empty rows and columns
2026-04-23 21:25:53.07542 INFO::Found 1000 missing values.
2026-04-23 21:25:53.10928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:53.110607 INFO::Done
2026-04-23 21:25:53.111651 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:53.12075 INFO::Starting hierarchical adjustment
2026-04-23 21:25:53.122067 INFO::Found 10 batches.
2026-04-23 21:25:54.650429 INFO::Set up parallel execution backend with 2 workers
2026-04-23 21:25:54.653287 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-23 21:25:56.190077 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:25:56.195088 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:25:56.215165 INFO::Done
2026-04-23 21:25:56.216073 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:56.221284 INFO::ASW Batch was 0.469734717936826 prior to batch effect correction and is now 0.469734717936826 .
2026-04-23 21:25:56.221889 INFO::ASW Label was 0.356075717780153 prior to batch effect correction and is now 0.356075717780153 .
2026-04-23 21:25:56.222687 INFO::Total function execution time is 3.15546751022339 s and adjustment time is 3.09337449073792 s ( 98.03 )
2026-04-23 21:25:56.388416 INFO::Formatting Data.
2026-04-23 21:25:56.389372 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.390388 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.391531 INFO::Found 0 missing values.
2026-04-23 21:25:56.395308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.395867 INFO::Done
2026-04-23 21:25:56.396429 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:25:56.399267 INFO::Starting hierarchical adjustment
2026-04-23 21:25:56.400002 INFO::Found 3 batches.
2026-04-23 21:25:56.40055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:25:56.401192 INFO::Using default BPPARAM
2026-04-23 21:25:56.401736 INFO::Processing subtree level 1
2026-04-23 21:25:56.522795 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:25:56.525342 INFO::Done
2026-04-23 21:25:56.526331 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:25:56.530811 INFO::ASW Batch was 0.252364122409087 prior to batch effect correction and is now -0.175603883076466 .
2026-04-23 21:25:56.531806 INFO::ASW Label was -0.191564088912352 prior to batch effect correction and is now -0.0359393252001586 .
2026-04-23 21:25:56.533095 INFO::Total function execution time is 0.144695520401001 s and adjustment time is 0.125419855117798 s ( 86.68 )
2026-04-23 21:25:56.662571 INFO::Formatting Data.
2026-04-23 21:25:56.663655 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.664764 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.665936 INFO::Found 2 missing values.
2026-04-23 21:25:56.668894 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.669474 INFO::Done
2026-04-23 21:25:56.698262 INFO::Found NA in Reference column
2026-04-23 21:25:56.708051 INFO::Require at least two references per batch.
2026-04-23 21:25:56.728596 INFO::Formatting Data.
2026-04-23 21:25:56.72958 INFO::Recognized SummarizedExperiment
2026-04-23 21:25:56.730207 INFO::Typecasting input to dataframe.
2026-04-23 21:25:56.740867 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.742398 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.746502 INFO::Found 0 missing values.
2026-04-23 21:25:56.754401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.755196 INFO::Done
2026-04-23 21:25:56.774443 INFO::Formatting Data.
2026-04-23 21:25:56.775459 INFO::Recognized SummarizedExperiment
2026-04-23 21:25:56.776153 INFO::Typecasting input to dataframe.
2026-04-23 21:25:56.796415 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.79795 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.801873 INFO::Found 0 missing values.
2026-04-23 21:25:56.813393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.814097 INFO::Done
2026-04-23 21:25:56.830749 INFO::Formatting Data.
2026-04-23 21:25:56.831519 INFO::Recognized SummarizedExperiment
2026-04-23 21:25:56.832122 INFO::Typecasting input to dataframe.
2026-04-23 21:25:56.849733 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.850907 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.852129 INFO::Found 0 missing values.
2026-04-23 21:25:56.85314 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.
2026-04-23 21:25:56.857957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.858548 INFO::Done
2026-04-23 21:25:56.869463 INFO::Formatting Data.
2026-04-23 21:25:56.870256 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.871172 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.872237 INFO::Found 0 missing values.
2026-04-23 21:25:56.875146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.875706 INFO::Done
2026-04-23 21:25:56.887058 INFO::Formatting Data.
2026-04-23 21:25:56.887823 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.888715 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.900956 INFO::Found 0 missing values.
2026-04-23 21:25:56.904496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.905123 INFO::Done
2026-04-23 21:25:56.937126 INFO::Formatting Data.
2026-04-23 21:25:56.938152 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.939269 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.940514 INFO::Found 1 missing values.
2026-04-23 21:25:56.943154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.943724 INFO::Done
2026-04-23 21:25:56.963847 INFO::Formatting Data.
2026-04-23 21:25:56.964973 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.966018 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.967157 INFO::Found 2 missing values.
2026-04-23 21:25:56.968162 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.
2026-04-23 21:25:56.970756 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.971394 INFO::Done
2026-04-23 21:25:56.981375 INFO::Formatting Data.
2026-04-23 21:25:56.982146 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.983021 INFO::Removing potential empty rows and columns
2026-04-23 21:25:56.98399 INFO::Found 2 missing values.
2026-04-23 21:25:56.985676 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:56.986325 INFO::Done
2026-04-23 21:25:56.997272 INFO::Formatting Data.
2026-04-23 21:25:56.998121 INFO::Typecasting input to dataframe.
2026-04-23 21:25:56.999007 INFO::Replacing NaNs with NAs.
2026-04-23 21:25:56.999935 INFO::Removing potential empty rows and columns
2026-04-23 21:25:57.001072 INFO::Found 0 missing values.
2026-04-23 21:25:57.00418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:25:57.004765 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.439 3.854 23.807
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.591 | 1.631 | 18.287 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.014 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.010 | 0.002 | 0.013 | |