Yannis Schumann
| Snapshot Date: 2026-02-12 13:40 -0500 (Thu, 12 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 2026-02-13 11:32 -0500 (Fri, 13 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" | 4863 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 169/2352 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-12 21:37:49 -0500 (Thu, 12 Feb 2026) |
| EndedAt: 2026-02-12 21:39:17 -0500 (Thu, 12 Feb 2026) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.26 1.117 16.525
* 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")
2026-02-12 21:38:39.782227 INFO::Formatting Data.
2026-02-12 21:38:39.783677 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:39.79533 INFO::Removing potential empty rows and columns
2026-02-12 21:38:40.035141 INFO::Found 0 missing values.
2026-02-12 21:38:40.038418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:40.039099 INFO::Done
2026-02-12 21:38:40.039674 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:40.05196 INFO::Starting hierarchical adjustment
2026-02-12 21:38:40.052922 INFO::Found 3 batches.
2026-02-12 21:38:40.0535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:40.054697 INFO::Using default BPPARAM
2026-02-12 21:38:40.055253 INFO::Processing subtree level 1
2026-02-12 21:38:40.174878 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:38:40.176936 INFO::Done
2026-02-12 21:38:40.177636 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:40.180537 INFO::ASW Batch was 0.0208785313088402 prior to batch effect correction and is now 0.0208785313088402 .
2026-02-12 21:38:40.181699 INFO::Total function execution time is 0.400134563446045 s and adjustment time is 0.124202489852905 s ( 31.04 )
2026-02-12 21:38:40.19625 INFO::Formatting Data.
2026-02-12 21:38:40.197098 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:40.198134 INFO::Removing potential empty rows and columns
2026-02-12 21:38:40.199388 INFO::Found 0 missing values.
2026-02-12 21:38:40.200411 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.
2026-02-12 21:38:40.212315 INFO::Formatting Data.
2026-02-12 21:38:40.21312 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:40.214084 INFO::Removing potential empty rows and columns
2026-02-12 21:38:40.215199 INFO::Found 0 missing values.
2026-02-12 21:38:40.216159 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.
2026-02-12 21:38:40.233153 INFO::Formatting Data.
2026-02-12 21:38:40.233999 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:40.234928 INFO::Removing potential empty rows and columns
2026-02-12 21:38:40.236025 INFO::Found 0 missing values.
2026-02-12 21:38:40.237002 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.
2026-02-12 21:38:40.241844 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:40.242506 INFO::Done
2026-02-12 21:38:40.243071 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:40.245221 INFO::Starting hierarchical adjustment
2026-02-12 21:38:40.246018 INFO::Found 2 batches.
2026-02-12 21:38:40.246616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:40.247311 INFO::Using default BPPARAM
2026-02-12 21:38:40.247896 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:40.248868 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:38:40.27098 INFO::Done
2026-02-12 21:38:40.27176 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:40.274245 INFO::ASW Batch was -0.0434265908349912 prior to batch effect correction and is now -0.116522427746578 .
2026-02-12 21:38:40.275143 INFO::Total function execution time is 0.0420572757720947 s and adjustment time is 0.0250809192657471 s ( 59.64 )
2026-02-12 21:38:40.27829 INFO::Formatting Data.
2026-02-12 21:38:40.279021 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:40.288318 INFO::Formatting Data.
2026-02-12 21:38:40.28914 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:40.290074 INFO::Removing potential empty rows and columns
2026-02-12 21:38:40.291143 INFO::Found 0 missing values.
2026-02-12 21:38:40.294266 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:40.29485 INFO::Done
2026-02-12 21:38:40.295406 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:40.297493 INFO::Starting hierarchical adjustment
2026-02-12 21:38:40.298232 INFO::Found 2 batches.
2026-02-12 21:38:40.298779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:40.299444 INFO::Using default BPPARAM
2026-02-12 21:38:40.299996 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:40.301015 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:38:40.346931 INFO::Done
2026-02-12 21:38:40.347618 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:40.349576 INFO::ASW Batch was 0.0163579011154438 prior to batch effect correction and is now -0.10381086545002 .
2026-02-12 21:38:40.350387 INFO::Total function execution time is 0.0621099472045898 s and adjustment time is 0.0488348007202148 s ( 78.63 )
2026-02-12 21:38:40.351393 INFO::Formatting Data.
2026-02-12 21:38:40.351988 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:40.352872 INFO::Removing potential empty rows and columns
2026-02-12 21:38:40.353878 INFO::Found 0 missing values.
2026-02-12 21:38:40.356602 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:40.357159 INFO::Done
2026-02-12 21:38:40.357683 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:40.359641 INFO::Starting hierarchical adjustment
2026-02-12 21:38:40.360345 INFO::Found 2 batches.
2026-02-12 21:38:40.360861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:40.361465 INFO::Using default BPPARAM
2026-02-12 21:38:40.361973 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:40.362911 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:38:40.377777 INFO::Done
2026-02-12 21:38:40.378463 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:40.380459 INFO::ASW Batch was 0.0163579011154438 prior to batch effect correction and is now -0.10381086545002 .
2026-02-12 21:38:40.381233 INFO::Total function execution time is 0.0298526287078857 s and adjustment time is 0.0175466537475586 s ( 58.78 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-12 21:38:43.292209 INFO::Formatting Data.
2026-02-12 21:38:43.292946 INFO::Recognized SummarizedExperiment
2026-02-12 21:38:43.293447 INFO::Typecasting input to dataframe.
2026-02-12 21:38:43.322826 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:43.324099 INFO::Removing potential empty rows and columns
2026-02-12 21:38:43.328188 INFO::Found 0 missing values.
2026-02-12 21:38:43.335788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:43.336511 INFO::Done
2026-02-12 21:38:43.337083 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:43.340813 INFO::Starting hierarchical adjustment
2026-02-12 21:38:43.341555 INFO::Found 2 batches.
2026-02-12 21:38:43.342098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:43.343219 INFO::Using default BPPARAM
2026-02-12 21:38:43.343884 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:43.344881 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:38:43.404025 INFO::Done
2026-02-12 21:38:43.404973 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:43.408996 INFO::ASW Batch was -0.00952611054624429 prior to batch effect correction and is now -0.0916485287690593 .
2026-02-12 21:38:43.410003 INFO::Total function execution time is 0.118027925491333 s and adjustment time is 0.062532901763916 s ( 52.98 )
Warning: stack imbalance in '{', 73 then 75
2026-02-12 21:38:43.430435 INFO::Formatting Data.
2026-02-12 21:38:43.431242 INFO::Recognized SummarizedExperiment
2026-02-12 21:38:43.431815 INFO::Typecasting input to dataframe.
2026-02-12 21:38:43.441417 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:43.442558 INFO::Removing potential empty rows and columns
2026-02-12 21:38:43.446479 INFO::Found 0 missing values.
2026-02-12 21:38:43.454187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:43.454839 INFO::Done
2026-02-12 21:38:43.455391 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:43.459108 INFO::Starting hierarchical adjustment
2026-02-12 21:38:43.459861 INFO::Found 2 batches.
2026-02-12 21:38:43.460403 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:43.46105 INFO::Using default BPPARAM
2026-02-12 21:38:43.461594 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:43.462594 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:38:43.488735 INFO::Done
2026-02-12 21:38:43.489532 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:43.493125 INFO::ASW Batch was -0.00613869821574018 prior to batch effect correction and is now -0.00613869821574018 .
2026-02-12 21:38:43.493997 INFO::Total function execution time is 0.0635724067687988 s and adjustment time is 0.0289816856384277 s ( 45.59 )
2026-02-12 21:38:43.512405 INFO::Formatting Data.
2026-02-12 21:38:43.513235 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:43.514173 INFO::Removing potential empty rows and columns
2026-02-12 21:38:43.515231 INFO::Found 0 missing values.
2026-02-12 21:38:43.518303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:43.518861 INFO::Done
2026-02-12 21:38:43.519397 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:43.521701 INFO::Starting hierarchical adjustment
2026-02-12 21:38:43.522456 INFO::Found 3 batches.
2026-02-12 21:38:43.52298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:43.523607 INFO::Using default BPPARAM
2026-02-12 21:38:43.524141 INFO::Processing subtree level 1
2026-02-12 21:38:43.660374 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:38:43.662253 INFO::Done
2026-02-12 21:38:43.662948 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:43.665475 INFO::ASW Batch was -0.0154038308337447 prior to batch effect correction and is now -0.189022398716196 .
2026-02-12 21:38:43.666408 INFO::Total function execution time is 0.154057264328003 s and adjustment time is 0.139935255050659 s ( 90.83 )
2026-02-12 21:38:43.680661 INFO::Skipping initial DF formatting
2026-02-12 21:38:43.681359 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:43.685463 INFO::Starting hierarchical adjustment
2026-02-12 21:38:43.686315 INFO::Found 5 batches.
2026-02-12 21:38:43.686899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:43.687551 INFO::Using default BPPARAM
2026-02-12 21:38:43.688089 INFO::Processing subtree level 1
2026-02-12 21:38:43.93143 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:43.93304 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:38:43.953301 INFO::Done
2026-02-12 21:38:43.954094 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:43.958462 INFO::ASW Batch was 0.591047595206647 prior to batch effect correction and is now 0.591047595206647 .
2026-02-12 21:38:43.959123 INFO::ASW Label was 0.365110363125397 prior to batch effect correction and is now 0.365110363125397 .
2026-02-12 21:38:44.012623 INFO::Total function execution time is 0.331973075866699 s and adjustment time is 0.267179250717163 s ( 80.48 )
2026-02-12 21:38:44.031336 INFO::Formatting Data.
2026-02-12 21:38:44.032142 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.033004 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.033958 INFO::Found 0 missing values.
2026-02-12 21:38:44.038144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.038819 INFO::Done
2026-02-12 21:38:44.039373 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.04241 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.043133 INFO::Found 5 batches.
2026-02-12 21:38:44.043686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.044323 INFO::Using default BPPARAM
2026-02-12 21:38:44.044858 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.
2026-02-12 21:38:44.183652 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.185297 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:38:44.202312 INFO::Done
2026-02-12 21:38:44.203034 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:44.206556 INFO::ASW Batch was 0.509294197368696 prior to batch effect correction and is now -0.0994905813852201 .
2026-02-12 21:38:44.207218 INFO::ASW Label was 0.210191748369976 prior to batch effect correction and is now 0.861410158902367 .
2026-02-12 21:38:44.208076 INFO::Total function execution time is 0.176807165145874 s and adjustment time is 0.159297943115234 s ( 90.1 )
2026-02-12 21:38:44.208958 INFO::Formatting Data.
2026-02-12 21:38:44.20961 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.210536 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.211709 INFO::Found 0 missing values.
2026-02-12 21:38:44.216008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.216566 INFO::Done
2026-02-12 21:38:44.217113 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.220211 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.220917 INFO::Found 5 batches.
2026-02-12 21:38:44.221465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.222166 INFO::Using default BPPARAM
2026-02-12 21:38:44.222727 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.
2026-02-12 21:38:44.351093 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.352821 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:38:44.369943 INFO::Done
2026-02-12 21:38:44.370693 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:44.37419 INFO::ASW Batch was 0.509294197368696 prior to batch effect correction and is now -0.0994905813852201 .
2026-02-12 21:38:44.374866 INFO::ASW Label was 0.210191748369976 prior to batch effect correction and is now 0.861410158902367 .
2026-02-12 21:38:44.375775 INFO::Total function execution time is 0.166815280914307 s and adjustment time is 0.149128198623657 s ( 89.4 )
2026-02-12 21:38:44.390291 INFO::Formatting Data.
2026-02-12 21:38:44.391141 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.392087 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.393154 INFO::Found 0 missing values.
2026-02-12 21:38:44.397455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.398027 INFO::Done
2026-02-12 21:38:44.398549 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.401476 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.402164 INFO::Found 5 batches.
2026-02-12 21:38:44.402704 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.403298 INFO::Using default BPPARAM
2026-02-12 21:38:44.403835 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.
2026-02-12 21:38:44.542459 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.545338 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:38:44.5818 INFO::Done
2026-02-12 21:38:44.5829 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:44.586659 INFO::ASW Batch was 0.357724977326178 prior to batch effect correction and is now -0.107735495715905 .
2026-02-12 21:38:44.587309 INFO::ASW Label was 0.374179448557414 prior to batch effect correction and is now 0.856849635844109 .
2026-02-12 21:38:44.588193 INFO::Total function execution time is 0.197965621948242 s and adjustment time is 0.179659843444824 s ( 90.75 )
2026-02-12 21:38:44.589128 INFO::Formatting Data.
2026-02-12 21:38:44.58981 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.590779 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.591887 INFO::Found 0 missing values.
2026-02-12 21:38:44.596431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.597075 INFO::Done
2026-02-12 21:38:44.597683 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.60123 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.602041 INFO::Found 5 batches.
2026-02-12 21:38:44.602667 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.603455 INFO::Using default BPPARAM
2026-02-12 21:38:44.604041 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.
2026-02-12 21:38:44.745778 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.747627 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:38:44.765932 INFO::Done
2026-02-12 21:38:44.766827 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:44.770648 INFO::ASW Batch was 0.357724977326178 prior to batch effect correction and is now -0.107735495715905 .
2026-02-12 21:38:44.771466 INFO::ASW Label was 0.374179448557414 prior to batch effect correction and is now 0.856849635844109 .
2026-02-12 21:38:44.772748 INFO::Total function execution time is 0.183616399765015 s and adjustment time is 0.163999557495117 s ( 89.32 )
2026-02-12 21:38:44.788246 INFO::Formatting Data.
2026-02-12 21:38:44.789094 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.790107 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.791211 INFO::Found 0 missing values.
2026-02-12 21:38:44.794152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.794771 INFO::Done
2026-02-12 21:38:44.79534 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.79863 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.799434 INFO::Found 2 batches.
2026-02-12 21:38:44.800017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.800706 INFO::Using default BPPARAM
2026-02-12 21:38:44.801306 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.802307 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:38:44.818231 INFO::Done
2026-02-12 21:38:44.819014 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:44.822126 INFO::ASW Batch was 0.537063106805432 prior to batch effect correction and is now 0.0719598779950697 .
2026-02-12 21:38:44.822744 INFO::ASW Label was 0.583514313300632 prior to batch effect correction and is now 0.892178778361475 .
2026-02-12 21:38:44.823565 INFO::Total function execution time is 0.0354113578796387 s and adjustment time is 0.0189366340637207 s ( 53.48 )
2026-02-12 21:38:44.824349 INFO::Formatting Data.
2026-02-12 21:38:44.824987 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.82585 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.82688 INFO::Found 0 missing values.
2026-02-12 21:38:44.829575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.830142 INFO::Done
2026-02-12 21:38:44.830679 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.833498 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.8342 INFO::Found 2 batches.
2026-02-12 21:38:44.834728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.835316 INFO::Using default BPPARAM
2026-02-12 21:38:44.835873 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.836771 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-12 21:38:44.851164 INFO::Done
2026-02-12 21:38:44.85188 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:44.854786 INFO::ASW Batch was 0.537063106805432 prior to batch effect correction and is now 0.0719598779950697 .
2026-02-12 21:38:44.855431 INFO::ASW Label was 0.583514313300632 prior to batch effect correction and is now 0.892178778361475 .
2026-02-12 21:38:44.856217 INFO::Total function execution time is 0.031879186630249 s and adjustment time is 0.0170731544494629 s ( 53.56 )
2026-02-12 21:38:44.868174 INFO::Formatting Data.
2026-02-12 21:38:44.869015 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.869973 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.870936 INFO::Found 0 missing values.
2026-02-12 21:38:44.873184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.873754 INFO::Done
2026-02-12 21:38:44.874269 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.876196 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.876897 INFO::Found 2 batches.
2026-02-12 21:38:44.877434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.878032 INFO::Using default BPPARAM
2026-02-12 21:38:44.87859 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.87953 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:38:44.912212 INFO::Done
2026-02-12 21:38:44.912985 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:44.915137 INFO::ASW Batch was -0.0979807246503448 prior to batch effect correction and is now -0.156647358544644 .
2026-02-12 21:38:44.916027 INFO::Total function execution time is 0.0479559898376465 s and adjustment time is 0.0354099273681641 s ( 73.84 )
2026-02-12 21:38:44.928456 INFO::Formatting Data.
2026-02-12 21:38:44.929327 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.930313 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.931409 INFO::Found 0 missing values.
2026-02-12 21:38:44.932664 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.
2026-02-12 21:38:44.937638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.938326 INFO::Done
2026-02-12 21:38:44.938916 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.942303 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.94312 INFO::Found 2 batches.
2026-02-12 21:38:44.943714 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.9444 INFO::Using default BPPARAM
2026-02-12 21:38:44.944962 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.94598 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:38:44.9642 INFO::Done
2026-02-12 21:38:44.965 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:44.968047 INFO::ASW Batch was 0.406104648778526 prior to batch effect correction and is now 0.0394087214030205 .
2026-02-12 21:38:44.96871 INFO::ASW Label was 0.682391653465549 prior to batch effect correction and is now 0.899255500617344 .
2026-02-12 21:38:44.969536 INFO::Total function execution time is 0.041203498840332 s and adjustment time is 0.0212140083312988 s ( 51.49 )
2026-02-12 21:38:44.970332 INFO::Formatting Data.
2026-02-12 21:38:44.970939 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:44.971828 INFO::Removing potential empty rows and columns
2026-02-12 21:38:44.972795 INFO::Found 0 missing values.
2026-02-12 21:38:44.973711 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.
2026-02-12 21:38:44.978264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:44.978891 INFO::Done
2026-02-12 21:38:44.979427 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:44.982519 INFO::Starting hierarchical adjustment
2026-02-12 21:38:44.983283 INFO::Found 2 batches.
2026-02-12 21:38:44.983868 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:44.984515 INFO::Using default BPPARAM
2026-02-12 21:38:44.985059 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:44.986065 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:38:45.002697 INFO::Done
2026-02-12 21:38:45.003443 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:45.006524 INFO::ASW Batch was 0.406104648778526 prior to batch effect correction and is now 0.0394087214030205 .
2026-02-12 21:38:45.007177 INFO::ASW Label was 0.682391653465549 prior to batch effect correction and is now 0.899255500617344 .
2026-02-12 21:38:45.008012 INFO::Total function execution time is 0.0376970767974854 s and adjustment time is 0.0195369720458984 s ( 51.83 )
2026-02-12 21:38:45.225582 INFO::Formatting Data.
2026-02-12 21:38:45.226475 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:45.22741 INFO::Removing potential empty rows and columns
2026-02-12 21:38:45.228508 INFO::Found 0 missing values.
2026-02-12 21:38:45.231566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:45.232111 INFO::Done
2026-02-12 21:38:45.232648 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:45.234753 INFO::Starting hierarchical adjustment
2026-02-12 21:38:45.23548 INFO::Found 3 batches.
2026-02-12 21:38:45.236021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:45.236712 INFO::Using default BPPARAM
2026-02-12 21:38:45.237247 INFO::Processing subtree level 1
2026-02-12 21:38:45.329193 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:38:45.331221 INFO::Done
2026-02-12 21:38:45.331987 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:45.334749 INFO::ASW Batch was -0.00511508630046416 prior to batch effect correction and is now -0.00511508630046416 .
2026-02-12 21:38:45.335821 INFO::Total function execution time is 0.110286474227905 s and adjustment time is 0.095872163772583 s ( 86.93 )
2026-02-12 21:38:45.336957 INFO::Formatting Data.
2026-02-12 21:38:45.337668 INFO::Typecasting input to dataframe.
2026-02-12 21:38:45.338472 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:45.339434 INFO::Removing potential empty rows and columns
2026-02-12 21:38:45.340622 INFO::Found 0 missing values.
2026-02-12 21:38:45.344022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:45.344641 INFO::Done
2026-02-12 21:38:45.34519 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:45.347284 INFO::Starting hierarchical adjustment
2026-02-12 21:38:45.348019 INFO::Found 3 batches.
2026-02-12 21:38:45.348585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:45.34922 INFO::Using default BPPARAM
2026-02-12 21:38:45.349834 INFO::Processing subtree level 1
2026-02-12 21:38:45.444543 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:38:45.447963 INFO::Done
2026-02-12 21:38:45.448795 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:45.451664 INFO::ASW Batch was -0.00511508630046416 prior to batch effect correction and is now -0.00511508630046416 .
2026-02-12 21:38:45.452746 INFO::Total function execution time is 0.115751504898071 s and adjustment time is 0.0999596118927002 s ( 86.36 )
2026-02-12 21:38:45.467063 INFO::Formatting Data.
2026-02-12 21:38:45.468009 INFO::Typecasting input to dataframe.
2026-02-12 21:38:45.468948 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:45.469941 INFO::Removing potential empty rows and columns
2026-02-12 21:38:45.471135 INFO::Found 0 missing values.
2026-02-12 21:38:45.482971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:45.483818 INFO::Done
2026-02-12 21:38:45.484415 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:45.486875 INFO::Starting hierarchical adjustment
2026-02-12 21:38:45.487723 INFO::Found 3 batches.
2026-02-12 21:38:45.488269 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:45.488955 INFO::Using default BPPARAM
2026-02-12 21:38:45.489528 INFO::Processing subtree level 1
2026-02-12 21:38:45.589132 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:38:45.591206 INFO::Done
2026-02-12 21:38:45.591944 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:45.594621 INFO::ASW Batch was -0.0094072286546367 prior to batch effect correction and is now -0.0094072286546367 .
2026-02-12 21:38:45.595684 INFO::Total function execution time is 0.128753423690796 s and adjustment time is 0.103657484054565 s ( 80.51 )
2026-02-12 21:38:45.747405 INFO::Formatting Data.
2026-02-12 21:38:45.748748 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:45.750041 INFO::Removing potential empty rows and columns
2026-02-12 21:38:45.753222 INFO::Found 1000 missing values.
2026-02-12 21:38:45.774688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:45.775501 INFO::Done
2026-02-12 21:38:45.776106 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:45.781923 INFO::Starting hierarchical adjustment
2026-02-12 21:38:45.782773 INFO::Found 10 batches.
2026-02-12 21:38:45.78336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:45.78407 INFO::Using default BPPARAM
2026-02-12 21:38:45.784646 INFO::Processing subtree level 1
2026-02-12 21:38:45.932742 INFO::Processing subtree level 2
2026-02-12 21:38:46.087048 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:38:46.089118 INFO::Done
2026-02-12 21:38:46.089877 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:46.095654 INFO::ASW Batch was 0.508184029194059 prior to batch effect correction and is now 0.508184029194059 .
2026-02-12 21:38:46.096454 INFO::ASW Label was 0.31558887688551 prior to batch effect correction and is now 0.31558887688551 .
2026-02-12 21:38:46.097486 INFO::Total function execution time is 0.350173234939575 s and adjustment time is 0.306501865386963 s ( 87.53 )
2026-02-12 21:38:46.098348 INFO::Formatting Data.
2026-02-12 21:38:46.099016 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:46.100291 INFO::Removing potential empty rows and columns
2026-02-12 21:38:46.103193 INFO::Found 1000 missing values.
2026-02-12 21:38:46.123494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:46.124277 INFO::Done
2026-02-12 21:38:46.124879 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:46.130608 INFO::Starting hierarchical adjustment
2026-02-12 21:38:46.1315 INFO::Found 10 batches.
2026-02-12 21:38:47.2237 INFO::Set up parallel execution backend with 2 workers
2026-02-12 21:38:47.225688 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-12 21:38:48.485056 INFO::Adjusting the last 2 batches sequentially
2026-02-12 21:38:48.48696 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-12 21:38:48.504241 INFO::Done
2026-02-12 21:38:48.504913 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:48.509428 INFO::ASW Batch was 0.508184029194059 prior to batch effect correction and is now 0.508184029194059 .
2026-02-12 21:38:48.510018 INFO::ASW Label was 0.31558887688551 prior to batch effect correction and is now 0.31558887688551 .
2026-02-12 21:38:48.510781 INFO::Total function execution time is 2.41246581077576 s and adjustment time is 2.37292385101318 s ( 98.36 )
2026-02-12 21:38:48.65275 INFO::Formatting Data.
2026-02-12 21:38:48.65357 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:48.6545 INFO::Removing potential empty rows and columns
2026-02-12 21:38:48.655578 INFO::Found 0 missing values.
2026-02-12 21:38:48.659246 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:48.659796 INFO::Done
2026-02-12 21:38:48.6603 INFO::Acquiring quality metrics before batch effect correction.
2026-02-12 21:38:48.663091 INFO::Starting hierarchical adjustment
2026-02-12 21:38:48.663794 INFO::Found 3 batches.
2026-02-12 21:38:48.66431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-12 21:38:48.664989 INFO::Using default BPPARAM
2026-02-12 21:38:48.665536 INFO::Processing subtree level 1
2026-02-12 21:38:48.768631 INFO::Adjusting the last 1 batches sequentially
2026-02-12 21:38:48.770452 INFO::Done
2026-02-12 21:38:48.771102 INFO::Acquiring quality metrics after batch effect correction.
2026-02-12 21:38:48.774341 INFO::ASW Batch was 0.212656030866818 prior to batch effect correction and is now -0.158887153590857 .
2026-02-12 21:38:48.774976 INFO::ASW Label was -0.201078936101515 prior to batch effect correction and is now 0.0728941542915207 .
2026-02-12 21:38:48.775951 INFO::Total function execution time is 0.123277187347412 s and adjustment time is 0.106750011444092 s ( 86.59 )
2026-02-12 21:38:48.897005 INFO::Formatting Data.
2026-02-12 21:38:48.897957 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:48.898967 INFO::Removing potential empty rows and columns
2026-02-12 21:38:48.900069 INFO::Found 2 missing values.
2026-02-12 21:38:48.903045 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:48.903645 INFO::Done
2026-02-12 21:38:48.93161 INFO::Found NA in Reference column
2026-02-12 21:38:48.941026 INFO::Require at least two references per batch.
2026-02-12 21:38:48.96244 INFO::Formatting Data.
2026-02-12 21:38:48.963253 INFO::Recognized SummarizedExperiment
2026-02-12 21:38:48.963845 INFO::Typecasting input to dataframe.
2026-02-12 21:38:48.973745 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:48.974927 INFO::Removing potential empty rows and columns
2026-02-12 21:38:48.978639 INFO::Found 0 missing values.
2026-02-12 21:38:48.985704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:48.986304 INFO::Done
2026-02-12 21:38:49.003745 INFO::Formatting Data.
2026-02-12 21:38:49.004578 INFO::Recognized SummarizedExperiment
2026-02-12 21:38:49.005152 INFO::Typecasting input to dataframe.
2026-02-12 21:38:49.023264 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:49.024574 INFO::Removing potential empty rows and columns
2026-02-12 21:38:49.028238 INFO::Found 0 missing values.
2026-02-12 21:38:49.039097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:49.039694 INFO::Done
2026-02-12 21:38:49.054981 INFO::Formatting Data.
2026-02-12 21:38:49.055701 INFO::Recognized SummarizedExperiment
2026-02-12 21:38:49.056224 INFO::Typecasting input to dataframe.
2026-02-12 21:38:49.072383 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:49.073412 INFO::Removing potential empty rows and columns
2026-02-12 21:38:49.074548 INFO::Found 0 missing values.
2026-02-12 21:38:49.07546 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.
2026-02-12 21:38:49.079765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:49.08032 INFO::Done
2026-02-12 21:38:49.090432 INFO::Formatting Data.
2026-02-12 21:38:49.091203 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:49.092078 INFO::Removing potential empty rows and columns
2026-02-12 21:38:49.093077 INFO::Found 0 missing values.
2026-02-12 21:38:49.095969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:49.096509 INFO::Done
2026-02-12 21:38:49.108098 INFO::Formatting Data.
2026-02-12 21:38:49.108876 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:49.109762 INFO::Removing potential empty rows and columns
2026-02-12 21:38:49.110792 INFO::Found 0 missing values.
2026-02-12 21:38:49.113742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:49.114258 INFO::Done
2026-02-12 21:38:49.143852 INFO::Formatting Data.
2026-02-12 21:38:49.144709 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:49.14574 INFO::Removing potential empty rows and columns
2026-02-12 21:38:49.146891 INFO::Found 1 missing values.
2026-02-12 21:38:49.149438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:49.149979 INFO::Done
2026-02-12 21:38:49.167938 INFO::Formatting Data.
2026-02-12 21:38:49.168696 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:49.169568 INFO::Removing potential empty rows and columns
2026-02-12 21:38:49.170493 INFO::Found 2 missing values.
2026-02-12 21:38:49.171377 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.
2026-02-12 21:38:49.173739 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:49.17425 INFO::Done
2026-02-12 21:38:49.183466 INFO::Formatting Data.
2026-02-12 21:38:49.184103 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:49.184923 INFO::Removing potential empty rows and columns
2026-02-12 21:38:49.185802 INFO::Found 2 missing values.
2026-02-12 21:38:49.187274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:49.187821 INFO::Done
2026-02-12 21:38:49.19741 INFO::Formatting Data.
2026-02-12 21:38:49.198109 INFO::Typecasting input to dataframe.
2026-02-12 21:38:49.198871 INFO::Replacing NaNs with NAs.
2026-02-12 21:38:49.199689 INFO::Removing potential empty rows and columns
2026-02-12 21:38:49.200649 INFO::Found 0 missing values.
2026-02-12 21:38:49.203431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-12 21:38:49.203941 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.975 3.822 20.392
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.260 | 1.117 | 16.525 | |
| compute_asw | 0.025 | 0.000 | 0.024 | |
| count_existing | 0.014 | 0.000 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |