Yannis Schumann
| Snapshot Date: 2026-02-19 13:40 -0500 (Thu, 19 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-20 11:32 -0500 (Fri, 20 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4869 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 169/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-19 21:30:44 -0500 (Thu, 19 Feb 2026) |
| EndedAt: 2026-02-19 21:32:16 -0500 (Thu, 19 Feb 2026) |
| EllapsedTime: 92.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.17 1.402 16.959
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-19 21:31:34.96267 INFO::Formatting Data.
2026-02-19 21:31:34.963925 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:34.975097 INFO::Removing potential empty rows and columns
2026-02-19 21:31:35.211741 INFO::Found 0 missing values.
2026-02-19 21:31:35.214939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:35.215578 INFO::Done
2026-02-19 21:31:35.216101 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:35.226967 INFO::Starting hierarchical adjustment
2026-02-19 21:31:35.227844 INFO::Found 3 batches.
2026-02-19 21:31:35.228389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:35.229466 INFO::Using default BPPARAM
2026-02-19 21:31:35.230003 INFO::Processing subtree level 1
2026-02-19 21:31:35.322234 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:31:35.323957 INFO::Done
2026-02-19 21:31:35.324638 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:35.327199 INFO::ASW Batch was -0.079242975219886 prior to batch effect correction and is now -0.079242975219886 .
2026-02-19 21:31:35.328287 INFO::Total function execution time is 0.366208076477051 s and adjustment time is 0.0962896347045898 s ( 26.29 )
2026-02-19 21:31:35.341463 INFO::Formatting Data.
2026-02-19 21:31:35.342204 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:35.343135 INFO::Removing potential empty rows and columns
2026-02-19 21:31:35.344264 INFO::Found 0 missing values.
2026-02-19 21:31:35.3452 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-19 21:31:35.355723 INFO::Formatting Data.
2026-02-19 21:31:35.35646 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:35.357352 INFO::Removing potential empty rows and columns
2026-02-19 21:31:35.358418 INFO::Found 0 missing values.
2026-02-19 21:31:35.35931 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-19 21:31:35.375027 INFO::Formatting Data.
2026-02-19 21:31:35.375784 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:35.376655 INFO::Removing potential empty rows and columns
2026-02-19 21:31:35.377687 INFO::Found 0 missing values.
2026-02-19 21:31:35.378602 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-19 21:31:35.383013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:35.383588 INFO::Done
2026-02-19 21:31:35.384109 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:35.386142 INFO::Starting hierarchical adjustment
2026-02-19 21:31:35.386861 INFO::Found 2 batches.
2026-02-19 21:31:35.387416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:35.388065 INFO::Using default BPPARAM
2026-02-19 21:31:35.388612 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:35.389537 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:31:35.410013 INFO::Done
2026-02-19 21:31:35.410746 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:35.412999 INFO::ASW Batch was -0.0613756952251756 prior to batch effect correction and is now -0.134525237567883 .
2026-02-19 21:31:35.413844 INFO::Total function execution time is 0.038862943649292 s and adjustment time is 0.023266077041626 s ( 59.87 )
2026-02-19 21:31:35.416672 INFO::Formatting Data.
2026-02-19 21:31:35.41731 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:35.426188 INFO::Formatting Data.
2026-02-19 21:31:35.426965 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:35.427875 INFO::Removing potential empty rows and columns
2026-02-19 21:31:35.428928 INFO::Found 0 missing values.
2026-02-19 21:31:35.431927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:35.432488 INFO::Done
2026-02-19 21:31:35.433018 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:35.43505 INFO::Starting hierarchical adjustment
2026-02-19 21:31:35.435774 INFO::Found 2 batches.
2026-02-19 21:31:35.436313 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:35.436961 INFO::Using default BPPARAM
2026-02-19 21:31:35.437521 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:35.438478 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:35.47395 INFO::Done
2026-02-19 21:31:35.474611 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:35.476539 INFO::ASW Batch was -0.0726695845007072 prior to batch effect correction and is now -0.120996249398042 .
2026-02-19 21:31:35.477296 INFO::Total function execution time is 0.0511641502380371 s and adjustment time is 0.0382936000823975 s ( 74.84 )
2026-02-19 21:31:35.478291 INFO::Formatting Data.
2026-02-19 21:31:35.478861 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:35.479669 INFO::Removing potential empty rows and columns
2026-02-19 21:31:35.48062 INFO::Found 0 missing values.
2026-02-19 21:31:35.483196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:35.483723 INFO::Done
2026-02-19 21:31:35.484215 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:35.486087 INFO::Starting hierarchical adjustment
2026-02-19 21:31:35.486755 INFO::Found 2 batches.
2026-02-19 21:31:35.487247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:35.487825 INFO::Using default BPPARAM
2026-02-19 21:31:35.48831 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:35.489187 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:35.50295 INFO::Done
2026-02-19 21:31:35.503605 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:35.505497 INFO::ASW Batch was -0.0726695845007072 prior to batch effect correction and is now -0.120996249398042 .
2026-02-19 21:31:35.506236 INFO::Total function execution time is 0.0279326438903809 s and adjustment time is 0.0163192749023438 s ( 58.42 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-19 21:31:38.301582 INFO::Formatting Data.
2026-02-19 21:31:38.302237 INFO::Recognized SummarizedExperiment
2026-02-19 21:31:38.302723 INFO::Typecasting input to dataframe.
2026-02-19 21:31:38.331445 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:38.332629 INFO::Removing potential empty rows and columns
2026-02-19 21:31:38.336633 INFO::Found 0 missing values.
2026-02-19 21:31:38.344264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:38.344974 INFO::Done
2026-02-19 21:31:38.345538 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:38.349142 INFO::Starting hierarchical adjustment
2026-02-19 21:31:38.349906 INFO::Found 2 batches.
2026-02-19 21:31:38.350446 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:38.351555 INFO::Using default BPPARAM
2026-02-19 21:31:38.352102 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:38.353106 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:31:38.410187 INFO::Done
2026-02-19 21:31:38.410934 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:38.414613 INFO::ASW Batch was 0.0279343542259878 prior to batch effect correction and is now -0.0933498704795872 .
2026-02-19 21:31:38.415523 INFO::Total function execution time is 0.114195346832275 s and adjustment time is 0.0604062080383301 s ( 52.9 )
Warning: stack imbalance in '{', 73 then 75
2026-02-19 21:31:38.434576 INFO::Formatting Data.
2026-02-19 21:31:38.435349 INFO::Recognized SummarizedExperiment
2026-02-19 21:31:38.435922 INFO::Typecasting input to dataframe.
2026-02-19 21:31:38.445326 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:38.446582 INFO::Removing potential empty rows and columns
2026-02-19 21:31:38.45116 INFO::Found 0 missing values.
2026-02-19 21:31:38.459815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:38.460566 INFO::Done
2026-02-19 21:31:38.461164 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:38.465038 INFO::Starting hierarchical adjustment
2026-02-19 21:31:38.466286 INFO::Found 2 batches.
2026-02-19 21:31:38.466886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:38.467564 INFO::Using default BPPARAM
2026-02-19 21:31:38.468138 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:38.4692 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:31:38.498153 INFO::Done
2026-02-19 21:31:38.498923 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:38.502584 INFO::ASW Batch was -0.0122954414353945 prior to batch effect correction and is now -0.0122954414353945 .
2026-02-19 21:31:38.503495 INFO::Total function execution time is 0.0688812732696533 s and adjustment time is 0.0320091247558594 s ( 46.47 )
2026-02-19 21:31:38.522827 INFO::Formatting Data.
2026-02-19 21:31:38.523693 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:38.524668 INFO::Removing potential empty rows and columns
2026-02-19 21:31:38.525779 INFO::Found 0 missing values.
2026-02-19 21:31:38.529007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:38.529614 INFO::Done
2026-02-19 21:31:38.530171 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:38.53238 INFO::Starting hierarchical adjustment
2026-02-19 21:31:38.533144 INFO::Found 3 batches.
2026-02-19 21:31:38.533728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:38.534377 INFO::Using default BPPARAM
2026-02-19 21:31:38.534953 INFO::Processing subtree level 1
2026-02-19 21:31:38.676517 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:31:38.678355 INFO::Done
2026-02-19 21:31:38.679046 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:38.681507 INFO::ASW Batch was 0.0116545755878582 prior to batch effect correction and is now -0.158333421484738 .
2026-02-19 21:31:38.68246 INFO::Total function execution time is 0.159667730331421 s and adjustment time is 0.145368099212646 s ( 91.04 )
2026-02-19 21:31:38.696802 INFO::Skipping initial DF formatting
2026-02-19 21:31:38.697556 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:38.701735 INFO::Starting hierarchical adjustment
2026-02-19 21:31:38.702584 INFO::Found 5 batches.
2026-02-19 21:31:38.703159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:38.703807 INFO::Using default BPPARAM
2026-02-19 21:31:38.704345 INFO::Processing subtree level 1
2026-02-19 21:31:38.945051 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:38.946692 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:31:38.967131 INFO::Done
2026-02-19 21:31:38.967941 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.014071 INFO::ASW Batch was 0.526857194248806 prior to batch effect correction and is now 0.526857194248806 .
2026-02-19 21:31:39.015279 INFO::ASW Label was 0.384309092778848 prior to batch effect correction and is now 0.384309092778848 .
2026-02-19 21:31:39.01612 INFO::Total function execution time is 0.319394588470459 s and adjustment time is 0.264701128005981 s ( 82.88 )
2026-02-19 21:31:39.033055 INFO::Formatting Data.
2026-02-19 21:31:39.033809 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.034718 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.035729 INFO::Found 0 missing values.
2026-02-19 21:31:39.039938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.0405 INFO::Done
2026-02-19 21:31:39.04102 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.043995 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.044704 INFO::Found 5 batches.
2026-02-19 21:31:39.045227 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.045838 INFO::Using default BPPARAM
2026-02-19 21:31:39.046416 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.191166 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.192953 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.210461 INFO::Done
2026-02-19 21:31:39.211256 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.214742 INFO::ASW Batch was 0.411432104905274 prior to batch effect correction and is now -0.0418266197989154 .
2026-02-19 21:31:39.215477 INFO::ASW Label was 0.226650676668281 prior to batch effect correction and is now 0.761513643513331 .
2026-02-19 21:31:39.216339 INFO::Total function execution time is 0.183332443237305 s and adjustment time is 0.165857076644897 s ( 90.47 )
2026-02-19 21:31:39.217233 INFO::Formatting Data.
2026-02-19 21:31:39.217953 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.218943 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.22014 INFO::Found 0 missing values.
2026-02-19 21:31:39.224587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.225198 INFO::Done
2026-02-19 21:31:39.225762 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.228996 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.229727 INFO::Found 5 batches.
2026-02-19 21:31:39.230248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.230907 INFO::Using default BPPARAM
2026-02-19 21:31:39.231438 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.354864 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.356651 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.374119 INFO::Done
2026-02-19 21:31:39.374881 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.378312 INFO::ASW Batch was 0.411432104905274 prior to batch effect correction and is now -0.0418266197989154 .
2026-02-19 21:31:39.378981 INFO::ASW Label was 0.226650676668281 prior to batch effect correction and is now 0.761513643513331 .
2026-02-19 21:31:39.379889 INFO::Total function execution time is 0.162659645080566 s and adjustment time is 0.144499778747559 s ( 88.84 )
2026-02-19 21:31:39.394278 INFO::Formatting Data.
2026-02-19 21:31:39.395104 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.396058 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.397114 INFO::Found 0 missing values.
2026-02-19 21:31:39.401223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.401813 INFO::Done
2026-02-19 21:31:39.402329 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.405226 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.405952 INFO::Found 5 batches.
2026-02-19 21:31:39.406473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.407074 INFO::Using default BPPARAM
2026-02-19 21:31:39.407622 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.522427 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.524238 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.545173 INFO::Done
2026-02-19 21:31:39.545965 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.549482 INFO::ASW Batch was 0.44346187237054 prior to batch effect correction and is now -0.0436557777783751 .
2026-02-19 21:31:39.550159 INFO::ASW Label was 0.279848870062796 prior to batch effect correction and is now 0.808661223004745 .
2026-02-19 21:31:39.550995 INFO::Total function execution time is 0.156784057617188 s and adjustment time is 0.139315128326416 s ( 88.86 )
2026-02-19 21:31:39.551879 INFO::Formatting Data.
2026-02-19 21:31:39.552582 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.553494 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.554576 INFO::Found 0 missing values.
2026-02-19 21:31:39.558846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.559514 INFO::Done
2026-02-19 21:31:39.560151 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.563282 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.56403 INFO::Found 5 batches.
2026-02-19 21:31:39.564603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.565219 INFO::Using default BPPARAM
2026-02-19 21:31:39.565767 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.686904 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.688505 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.705118 INFO::Done
2026-02-19 21:31:39.705902 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.709662 INFO::ASW Batch was 0.44346187237054 prior to batch effect correction and is now -0.0436557777783751 .
2026-02-19 21:31:39.7103 INFO::ASW Label was 0.279848870062796 prior to batch effect correction and is now 0.808661223004745 .
2026-02-19 21:31:39.711178 INFO::Total function execution time is 0.159301280975342 s and adjustment time is 0.141212224960327 s ( 88.64 )
2026-02-19 21:31:39.725234 INFO::Formatting Data.
2026-02-19 21:31:39.726074 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.727052 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.728128 INFO::Found 0 missing values.
2026-02-19 21:31:39.731035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.731641 INFO::Done
2026-02-19 21:31:39.732204 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.735346 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.736105 INFO::Found 2 batches.
2026-02-19 21:31:39.736664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.737324 INFO::Using default BPPARAM
2026-02-19 21:31:39.737937 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.73891 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.75562 INFO::Done
2026-02-19 21:31:39.756312 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.759432 INFO::ASW Batch was 0.6532395797031 prior to batch effect correction and is now -0.0270795004551046 .
2026-02-19 21:31:39.760041 INFO::ASW Label was 0.419423016541732 prior to batch effect correction and is now 0.917059919747287 .
2026-02-19 21:31:39.760871 INFO::Total function execution time is 0.0357222557067871 s and adjustment time is 0.0196409225463867 s ( 54.98 )
2026-02-19 21:31:39.761712 INFO::Formatting Data.
2026-02-19 21:31:39.762352 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.763251 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.764289 INFO::Found 0 missing values.
2026-02-19 21:31:39.767074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.767676 INFO::Done
2026-02-19 21:31:39.768218 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.771214 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.771955 INFO::Found 2 batches.
2026-02-19 21:31:39.772529 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.773155 INFO::Using default BPPARAM
2026-02-19 21:31:39.773733 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.774676 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-19 21:31:39.789725 INFO::Done
2026-02-19 21:31:39.790411 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.793485 INFO::ASW Batch was 0.6532395797031 prior to batch effect correction and is now -0.0270795004551046 .
2026-02-19 21:31:39.794154 INFO::ASW Label was 0.419423016541732 prior to batch effect correction and is now 0.917059919747287 .
2026-02-19 21:31:39.794989 INFO::Total function execution time is 0.0332908630371094 s and adjustment time is 0.0178985595703125 s ( 53.76 )
2026-02-19 21:31:39.808543 INFO::Formatting Data.
2026-02-19 21:31:39.809507 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.810531 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.811558 INFO::Found 0 missing values.
2026-02-19 21:31:39.813998 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.814606 INFO::Done
2026-02-19 21:31:39.815192 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.817365 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.818138 INFO::Found 2 batches.
2026-02-19 21:31:39.81874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.819427 INFO::Using default BPPARAM
2026-02-19 21:31:39.82003 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.821042 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:31:39.855598 INFO::Done
2026-02-19 21:31:39.8565 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.858937 INFO::ASW Batch was -0.0933226589579173 prior to batch effect correction and is now -0.135641304269586 .
2026-02-19 21:31:39.859948 INFO::Total function execution time is 0.0515141487121582 s and adjustment time is 0.0375723838806152 s ( 72.94 )
2026-02-19 21:31:39.875416 INFO::Formatting Data.
2026-02-19 21:31:39.876374 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.877605 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.878803 INFO::Found 0 missing values.
2026-02-19 21:31:39.880131 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-19 21:31:39.885894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.886643 INFO::Done
2026-02-19 21:31:39.887281 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.890746 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.891632 INFO::Found 2 batches.
2026-02-19 21:31:39.892293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.89306 INFO::Using default BPPARAM
2026-02-19 21:31:39.89372 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.895215 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:31:39.915421 INFO::Done
2026-02-19 21:31:39.91625 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.919849 INFO::ASW Batch was 0.602722875780297 prior to batch effect correction and is now 0.0194383470688126 .
2026-02-19 21:31:39.920556 INFO::ASW Label was 0.457621479862308 prior to batch effect correction and is now 0.877850966934497 .
2026-02-19 21:31:39.921504 INFO::Total function execution time is 0.0462052822113037 s and adjustment time is 0.0239462852478027 s ( 51.83 )
2026-02-19 21:31:39.922472 INFO::Formatting Data.
2026-02-19 21:31:39.923213 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:39.924268 INFO::Removing potential empty rows and columns
2026-02-19 21:31:39.925428 INFO::Found 0 missing values.
2026-02-19 21:31:39.926437 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-19 21:31:39.931083 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:39.931673 INFO::Done
2026-02-19 21:31:39.932205 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:39.935191 INFO::Starting hierarchical adjustment
2026-02-19 21:31:39.935913 INFO::Found 2 batches.
2026-02-19 21:31:39.936483 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:39.937097 INFO::Using default BPPARAM
2026-02-19 21:31:39.93765 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:39.938608 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:31:39.95783 INFO::Done
2026-02-19 21:31:39.958671 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:39.962134 INFO::ASW Batch was 0.602722875780297 prior to batch effect correction and is now 0.0194383470688126 .
2026-02-19 21:31:39.962904 INFO::ASW Label was 0.457621479862308 prior to batch effect correction and is now 0.877850966934497 .
2026-02-19 21:31:39.963846 INFO::Total function execution time is 0.0414118766784668 s and adjustment time is 0.0220177173614502 s ( 53.17 )
2026-02-19 21:31:40.188242 INFO::Formatting Data.
2026-02-19 21:31:40.189125 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:40.190089 INFO::Removing potential empty rows and columns
2026-02-19 21:31:40.191257 INFO::Found 0 missing values.
2026-02-19 21:31:40.194637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:40.195218 INFO::Done
2026-02-19 21:31:40.196116 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:40.198195 INFO::Starting hierarchical adjustment
2026-02-19 21:31:40.198906 INFO::Found 3 batches.
2026-02-19 21:31:40.199459 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:40.200086 INFO::Using default BPPARAM
2026-02-19 21:31:40.200632 INFO::Processing subtree level 1
2026-02-19 21:31:40.285416 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:31:40.287347 INFO::Done
2026-02-19 21:31:40.288062 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:40.290566 INFO::ASW Batch was -0.0702840492073099 prior to batch effect correction and is now -0.0702840492073099 .
2026-02-19 21:31:40.2916 INFO::Total function execution time is 0.103388071060181 s and adjustment time is 0.0885508060455322 s ( 85.65 )
2026-02-19 21:31:40.292662 INFO::Formatting Data.
2026-02-19 21:31:40.293329 INFO::Typecasting input to dataframe.
2026-02-19 21:31:40.294139 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:40.295109 INFO::Removing potential empty rows and columns
2026-02-19 21:31:40.296256 INFO::Found 0 missing values.
2026-02-19 21:31:40.299529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:40.300179 INFO::Done
2026-02-19 21:31:40.300744 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:40.302952 INFO::Starting hierarchical adjustment
2026-02-19 21:31:40.303715 INFO::Found 3 batches.
2026-02-19 21:31:40.304275 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:40.304944 INFO::Using default BPPARAM
2026-02-19 21:31:40.305548 INFO::Processing subtree level 1
2026-02-19 21:31:40.390223 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:31:40.39221 INFO::Done
2026-02-19 21:31:40.392964 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:40.395865 INFO::ASW Batch was -0.0702840492073099 prior to batch effect correction and is now -0.0702840492073099 .
2026-02-19 21:31:40.396937 INFO::Total function execution time is 0.104257822036743 s and adjustment time is 0.0886061191558838 s ( 84.99 )
2026-02-19 21:31:40.410521 INFO::Formatting Data.
2026-02-19 21:31:40.411385 INFO::Typecasting input to dataframe.
2026-02-19 21:31:40.412287 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:40.413246 INFO::Removing potential empty rows and columns
2026-02-19 21:31:40.414357 INFO::Found 0 missing values.
2026-02-19 21:31:40.417479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:40.418058 INFO::Done
2026-02-19 21:31:40.418603 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:40.420719 INFO::Starting hierarchical adjustment
2026-02-19 21:31:40.421463 INFO::Found 3 batches.
2026-02-19 21:31:40.421996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:40.422658 INFO::Using default BPPARAM
2026-02-19 21:31:40.4232 INFO::Processing subtree level 1
2026-02-19 21:31:40.506958 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:31:40.508845 INFO::Done
2026-02-19 21:31:40.509522 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:40.51202 INFO::ASW Batch was -0.100172769790893 prior to batch effect correction and is now -0.100172769790893 .
2026-02-19 21:31:40.512984 INFO::Total function execution time is 0.1025550365448 s and adjustment time is 0.0875241756439209 s ( 85.34 )
2026-02-19 21:31:40.645594 INFO::Formatting Data.
2026-02-19 21:31:40.646427 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:40.647606 INFO::Removing potential empty rows and columns
2026-02-19 21:31:40.650529 INFO::Found 1000 missing values.
2026-02-19 21:31:40.670841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:40.671671 INFO::Done
2026-02-19 21:31:40.67226 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:40.677884 INFO::Starting hierarchical adjustment
2026-02-19 21:31:40.678689 INFO::Found 10 batches.
2026-02-19 21:31:40.679238 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:40.679937 INFO::Using default BPPARAM
2026-02-19 21:31:40.68049 INFO::Processing subtree level 1
2026-02-19 21:31:40.816668 INFO::Processing subtree level 2
2026-02-19 21:31:40.959343 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:31:40.961729 INFO::Done
2026-02-19 21:31:40.962574 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:40.969653 INFO::ASW Batch was 0.479159860985665 prior to batch effect correction and is now 0.479159860985665 .
2026-02-19 21:31:40.970513 INFO::ASW Label was 0.357610179705613 prior to batch effect correction and is now 0.357610179705613 .
2026-02-19 21:31:40.971642 INFO::Total function execution time is 0.326066493988037 s and adjustment time is 0.283177137374878 s ( 86.85 )
2026-02-19 21:31:40.972674 INFO::Formatting Data.
2026-02-19 21:31:40.973465 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:40.974864 INFO::Removing potential empty rows and columns
2026-02-19 21:31:40.978396 INFO::Found 1000 missing values.
2026-02-19 21:31:41.004254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:41.005139 INFO::Done
2026-02-19 21:31:41.005832 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:41.012252 INFO::Starting hierarchical adjustment
2026-02-19 21:31:41.013142 INFO::Found 10 batches.
2026-02-19 21:31:41.888093 INFO::Set up parallel execution backend with 2 workers
2026-02-19 21:31:41.890043 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-19 21:31:42.896427 INFO::Adjusting the last 2 batches sequentially
2026-02-19 21:31:42.900759 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-19 21:31:42.918766 INFO::Done
2026-02-19 21:31:42.919425 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:42.924148 INFO::ASW Batch was 0.479159860985665 prior to batch effect correction and is now 0.479159860985665 .
2026-02-19 21:31:42.924737 INFO::ASW Label was 0.357610179705613 prior to batch effect correction and is now 0.357610179705613 .
2026-02-19 21:31:42.92549 INFO::Total function execution time is 1.95290565490723 s and adjustment time is 1.90580606460571 s ( 97.59 )
2026-02-19 21:31:43.07411 INFO::Formatting Data.
2026-02-19 21:31:43.074861 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.075761 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.076828 INFO::Found 0 missing values.
2026-02-19 21:31:43.080612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.081151 INFO::Done
2026-02-19 21:31:43.08168 INFO::Acquiring quality metrics before batch effect correction.
2026-02-19 21:31:43.084436 INFO::Starting hierarchical adjustment
2026-02-19 21:31:43.08514 INFO::Found 3 batches.
2026-02-19 21:31:43.085675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-19 21:31:43.086328 INFO::Using default BPPARAM
2026-02-19 21:31:43.086883 INFO::Processing subtree level 1
2026-02-19 21:31:43.191635 INFO::Adjusting the last 1 batches sequentially
2026-02-19 21:31:43.193442 INFO::Done
2026-02-19 21:31:43.1941 INFO::Acquiring quality metrics after batch effect correction.
2026-02-19 21:31:43.197386 INFO::ASW Batch was 0.142401583129742 prior to batch effect correction and is now -0.140312024246463 .
2026-02-19 21:31:43.198002 INFO::ASW Label was -0.180505585370907 prior to batch effect correction and is now 0.00330565683720817 .
2026-02-19 21:31:43.198934 INFO::Total function execution time is 0.124862432479858 s and adjustment time is 0.108405590057373 s ( 86.82 )
2026-02-19 21:31:43.322159 INFO::Formatting Data.
2026-02-19 21:31:43.323057 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.324039 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.325128 INFO::Found 2 missing values.
2026-02-19 21:31:43.328175 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.32878 INFO::Done
2026-02-19 21:31:43.35608 INFO::Found NA in Reference column
2026-02-19 21:31:43.365628 INFO::Require at least two references per batch.
2026-02-19 21:31:43.386503 INFO::Formatting Data.
2026-02-19 21:31:43.387302 INFO::Recognized SummarizedExperiment
2026-02-19 21:31:43.387874 INFO::Typecasting input to dataframe.
2026-02-19 21:31:43.397386 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.398503 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.402236 INFO::Found 0 missing values.
2026-02-19 21:31:43.409378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.409971 INFO::Done
2026-02-19 21:31:43.425759 INFO::Formatting Data.
2026-02-19 21:31:43.426524 INFO::Recognized SummarizedExperiment
2026-02-19 21:31:43.427067 INFO::Typecasting input to dataframe.
2026-02-19 21:31:43.444185 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.445464 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.44927 INFO::Found 0 missing values.
2026-02-19 21:31:43.461095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.461823 INFO::Done
2026-02-19 21:31:43.477546 INFO::Formatting Data.
2026-02-19 21:31:43.478334 INFO::Recognized SummarizedExperiment
2026-02-19 21:31:43.478892 INFO::Typecasting input to dataframe.
2026-02-19 21:31:43.495609 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.49666 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.497788 INFO::Found 0 missing values.
2026-02-19 21:31:43.498708 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-19 21:31:43.503142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.503739 INFO::Done
2026-02-19 21:31:43.513928 INFO::Formatting Data.
2026-02-19 21:31:43.514775 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.515671 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.516663 INFO::Found 0 missing values.
2026-02-19 21:31:43.519491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.519996 INFO::Done
2026-02-19 21:31:43.531265 INFO::Formatting Data.
2026-02-19 21:31:43.532053 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.532944 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.533925 INFO::Found 0 missing values.
2026-02-19 21:31:43.536804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.537317 INFO::Done
2026-02-19 21:31:43.566915 INFO::Formatting Data.
2026-02-19 21:31:43.567738 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.568757 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.569864 INFO::Found 1 missing values.
2026-02-19 21:31:43.572331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.572889 INFO::Done
2026-02-19 21:31:43.591301 INFO::Formatting Data.
2026-02-19 21:31:43.59212 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.593004 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.593927 INFO::Found 2 missing values.
2026-02-19 21:31:43.594799 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-02-19 21:31:43.597162 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.597685 INFO::Done
2026-02-19 21:31:43.607428 INFO::Formatting Data.
2026-02-19 21:31:43.608217 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.609089 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.609972 INFO::Found 2 missing values.
2026-02-19 21:31:43.611482 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.612014 INFO::Done
2026-02-19 21:31:43.622064 INFO::Formatting Data.
2026-02-19 21:31:43.622836 INFO::Typecasting input to dataframe.
2026-02-19 21:31:43.623626 INFO::Replacing NaNs with NAs.
2026-02-19 21:31:43.624461 INFO::Removing potential empty rows and columns
2026-02-19 21:31:43.625415 INFO::Found 0 missing values.
2026-02-19 21:31:43.628215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-19 21:31:43.628742 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.782 3.273 19.879
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.170 | 1.402 | 16.959 | |
| compute_asw | 0.023 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.013 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.011 | |