Yannis Schumann
| Snapshot Date: 2026-02-24 13:40 -0500 (Tue, 24 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 2026-02-25 11:32 -0500 (Wed, 25 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" | 4874 |
| 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: 2026-02-24 21:47:20 -0500 (Tue, 24 Feb 2026) |
| EndedAt: 2026-02-24 21:48:54 -0500 (Tue, 24 Feb 2026) |
| EllapsedTime: 94.1 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 23.778 1.184 17.063
* 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")
2026-02-24 21:48:12.536666 INFO::Formatting Data.
2026-02-24 21:48:12.538195 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:12.549875 INFO::Removing potential empty rows and columns
2026-02-24 21:48:12.797541 INFO::Found 0 missing values.
2026-02-24 21:48:12.800839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:12.801512 INFO::Done
2026-02-24 21:48:12.802064 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:12.813392 INFO::Starting hierarchical adjustment
2026-02-24 21:48:12.814276 INFO::Found 3 batches.
2026-02-24 21:48:12.814842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:12.815938 INFO::Using default BPPARAM
2026-02-24 21:48:12.816492 INFO::Processing subtree level 1
2026-02-24 21:48:12.92207 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:48:12.924164 INFO::Done
2026-02-24 21:48:12.924943 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:12.927952 INFO::ASW Batch was -0.135597804350729 prior to batch effect correction and is now -0.135597804350729 .
2026-02-24 21:48:12.929122 INFO::Total function execution time is 0.393139839172363 s and adjustment time is 0.110020637512207 s ( 27.99 )
2026-02-24 21:48:12.943473 INFO::Formatting Data.
2026-02-24 21:48:12.944332 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:12.945347 INFO::Removing potential empty rows and columns
2026-02-24 21:48:12.946569 INFO::Found 0 missing values.
2026-02-24 21:48:12.947582 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.
2026-02-24 21:48:12.958771 INFO::Formatting Data.
2026-02-24 21:48:12.959593 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:12.960547 INFO::Removing potential empty rows and columns
2026-02-24 21:48:12.961657 INFO::Found 0 missing values.
2026-02-24 21:48:12.962597 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.
2026-02-24 21:48:12.978851 INFO::Formatting Data.
2026-02-24 21:48:12.979748 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:12.980711 INFO::Removing potential empty rows and columns
2026-02-24 21:48:12.981805 INFO::Found 0 missing values.
2026-02-24 21:48:12.982781 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.
2026-02-24 21:48:12.987468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:12.988096 INFO::Done
2026-02-24 21:48:12.988664 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:12.990858 INFO::Starting hierarchical adjustment
2026-02-24 21:48:12.991632 INFO::Found 2 batches.
2026-02-24 21:48:12.992195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:12.992883 INFO::Using default BPPARAM
2026-02-24 21:48:12.993438 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:12.994386 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:48:13.015532 INFO::Done
2026-02-24 21:48:13.016297 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:13.018689 INFO::ASW Batch was -0.0584188761582744 prior to batch effect correction and is now -0.112909880379012 .
2026-02-24 21:48:13.019584 INFO::Total function execution time is 0.0408046245574951 s and adjustment time is 0.0240397453308105 s ( 58.91 )
2026-02-24 21:48:13.022569 INFO::Formatting Data.
2026-02-24 21:48:13.023243 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:13.032679 INFO::Formatting Data.
2026-02-24 21:48:13.033548 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:13.034503 INFO::Removing potential empty rows and columns
2026-02-24 21:48:13.035589 INFO::Found 0 missing values.
2026-02-24 21:48:13.038669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:13.039239 INFO::Done
2026-02-24 21:48:13.039799 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:13.041899 INFO::Starting hierarchical adjustment
2026-02-24 21:48:13.04265 INFO::Found 2 batches.
2026-02-24 21:48:13.043193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:13.043837 INFO::Using default BPPARAM
2026-02-24 21:48:13.044412 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:13.04544 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:48:13.085263 INFO::Done
2026-02-24 21:48:13.085994 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:13.087948 INFO::ASW Batch was 0.031676183267135 prior to batch effect correction and is now -0.117335470713581 .
2026-02-24 21:48:13.088758 INFO::Total function execution time is 0.0561494827270508 s and adjustment time is 0.0427405834197998 s ( 76.12 )
2026-02-24 21:48:13.08975 INFO::Formatting Data.
2026-02-24 21:48:13.090322 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:13.091152 INFO::Removing potential empty rows and columns
2026-02-24 21:48:13.092117 INFO::Found 0 missing values.
2026-02-24 21:48:13.094758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:13.095287 INFO::Done
2026-02-24 21:48:13.095804 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:13.09766 INFO::Starting hierarchical adjustment
2026-02-24 21:48:13.098336 INFO::Found 2 batches.
2026-02-24 21:48:13.098847 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:13.099423 INFO::Using default BPPARAM
2026-02-24 21:48:13.09991 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:13.100814 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:48:13.114933 INFO::Done
2026-02-24 21:48:13.115622 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:13.117522 INFO::ASW Batch was 0.031676183267135 prior to batch effect correction and is now -0.117335470713581 .
2026-02-24 21:48:13.118261 INFO::Total function execution time is 0.0285089015960693 s and adjustment time is 0.0167138576507568 s ( 58.63 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-24 21:48:16.098822 INFO::Formatting Data.
2026-02-24 21:48:16.099657 INFO::Recognized SummarizedExperiment
2026-02-24 21:48:16.100244 INFO::Typecasting input to dataframe.
2026-02-24 21:48:16.132118 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:16.133386 INFO::Removing potential empty rows and columns
2026-02-24 21:48:16.137619 INFO::Found 0 missing values.
2026-02-24 21:48:16.145285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:16.145993 INFO::Done
2026-02-24 21:48:16.14656 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:16.150263 INFO::Starting hierarchical adjustment
2026-02-24 21:48:16.151024 INFO::Found 2 batches.
2026-02-24 21:48:16.15157 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:16.152731 INFO::Using default BPPARAM
2026-02-24 21:48:16.15329 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:16.154314 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:48:16.212303 INFO::Done
2026-02-24 21:48:16.213167 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:16.217052 INFO::ASW Batch was -0.0169291042657947 prior to batch effect correction and is now -0.0861909287333337 .
2026-02-24 21:48:16.217993 INFO::Total function execution time is 0.119506359100342 s and adjustment time is 0.061378002166748 s ( 51.36 )
Warning: stack imbalance in '{', 73 then 75
2026-02-24 21:48:16.238018 INFO::Formatting Data.
2026-02-24 21:48:16.238868 INFO::Recognized SummarizedExperiment
2026-02-24 21:48:16.239457 INFO::Typecasting input to dataframe.
2026-02-24 21:48:16.249159 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:16.250476 INFO::Removing potential empty rows and columns
2026-02-24 21:48:16.254453 INFO::Found 0 missing values.
2026-02-24 21:48:16.262086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:16.262714 INFO::Done
2026-02-24 21:48:16.263271 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:16.266906 INFO::Starting hierarchical adjustment
2026-02-24 21:48:16.267811 INFO::Found 2 batches.
2026-02-24 21:48:16.268346 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:16.26899 INFO::Using default BPPARAM
2026-02-24 21:48:16.26953 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:16.270555 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:48:16.297509 INFO::Done
2026-02-24 21:48:16.298381 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:16.302244 INFO::ASW Batch was -0.00101377946276573 prior to batch effect correction and is now -0.00101377946276573 .
2026-02-24 21:48:16.303202 INFO::Total function execution time is 0.0651686191558838 s and adjustment time is 0.0297777652740479 s ( 45.69 )
2026-02-24 21:48:16.32275 INFO::Formatting Data.
2026-02-24 21:48:16.323856 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:16.324855 INFO::Removing potential empty rows and columns
2026-02-24 21:48:16.325952 INFO::Found 0 missing values.
2026-02-24 21:48:16.329119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:16.329712 INFO::Done
2026-02-24 21:48:16.330249 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:16.332397 INFO::Starting hierarchical adjustment
2026-02-24 21:48:16.333116 INFO::Found 3 batches.
2026-02-24 21:48:16.333663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:16.334257 INFO::Using default BPPARAM
2026-02-24 21:48:16.334799 INFO::Processing subtree level 1
2026-02-24 21:48:16.487398 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:48:16.489524 INFO::Done
2026-02-24 21:48:16.490302 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:16.493185 INFO::ASW Batch was -0.0273593522661823 prior to batch effect correction and is now -0.150435445138786 .
2026-02-24 21:48:16.494325 INFO::Total function execution time is 0.17160439491272 s and adjustment time is 0.156507253646851 s ( 91.2 )
2026-02-24 21:48:16.511839 INFO::Skipping initial DF formatting
2026-02-24 21:48:16.512755 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:16.517338 INFO::Starting hierarchical adjustment
2026-02-24 21:48:16.518347 INFO::Found 5 batches.
2026-02-24 21:48:16.518978 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:16.51969 INFO::Using default BPPARAM
2026-02-24 21:48:16.520252 INFO::Processing subtree level 1
2026-02-24 21:48:16.817884 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:16.819693 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:48:16.840105 INFO::Done
2026-02-24 21:48:16.84092 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:16.845465 INFO::ASW Batch was 0.498746852559573 prior to batch effect correction and is now 0.498746852559573 .
2026-02-24 21:48:16.846141 INFO::ASW Label was 0.376722955833603 prior to batch effect correction and is now 0.376722955833603 .
2026-02-24 21:48:16.847097 INFO::Total function execution time is 0.335450172424316 s and adjustment time is 0.321959495544434 s ( 95.98 )
2026-02-24 21:48:16.912986 INFO::Formatting Data.
2026-02-24 21:48:16.913891 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:16.914863 INFO::Removing potential empty rows and columns
2026-02-24 21:48:16.915857 INFO::Found 0 missing values.
2026-02-24 21:48:16.91993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:16.92051 INFO::Done
2026-02-24 21:48:16.921089 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:16.924281 INFO::Starting hierarchical adjustment
2026-02-24 21:48:16.925033 INFO::Found 5 batches.
2026-02-24 21:48:16.925584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:16.926191 INFO::Using default BPPARAM
2026-02-24 21:48:16.926764 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.
2026-02-24 21:48:17.072222 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.074048 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:48:17.091952 INFO::Done
2026-02-24 21:48:17.092833 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.096603 INFO::ASW Batch was 0.251191523285671 prior to batch effect correction and is now -0.0190693137704728 .
2026-02-24 21:48:17.097386 INFO::ASW Label was 0.481534602375052 prior to batch effect correction and is now 0.812265339613544 .
2026-02-24 21:48:17.098282 INFO::Total function execution time is 0.185377836227417 s and adjustment time is 0.167030572891235 s ( 90.1 )
2026-02-24 21:48:17.099195 INFO::Formatting Data.
2026-02-24 21:48:17.099848 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:17.100828 INFO::Removing potential empty rows and columns
2026-02-24 21:48:17.101964 INFO::Found 0 missing values.
2026-02-24 21:48:17.106408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:17.107072 INFO::Done
2026-02-24 21:48:17.107639 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:17.110987 INFO::Starting hierarchical adjustment
2026-02-24 21:48:17.111787 INFO::Found 5 batches.
2026-02-24 21:48:17.112352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:17.113017 INFO::Using default BPPARAM
2026-02-24 21:48:17.113637 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.
2026-02-24 21:48:17.255942 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.258047 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:48:17.279229 INFO::Done
2026-02-24 21:48:17.280177 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.284325 INFO::ASW Batch was 0.251191523285671 prior to batch effect correction and is now -0.0190693137704728 .
2026-02-24 21:48:17.28514 INFO::ASW Label was 0.481534602375052 prior to batch effect correction and is now 0.812265339613544 .
2026-02-24 21:48:17.286208 INFO::Total function execution time is 0.186973571777344 s and adjustment time is 0.167533159255981 s ( 89.6 )
2026-02-24 21:48:17.306053 INFO::Formatting Data.
2026-02-24 21:48:17.307457 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:17.309143 INFO::Removing potential empty rows and columns
2026-02-24 21:48:17.311153 INFO::Found 0 missing values.
2026-02-24 21:48:17.31967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:17.320887 INFO::Done
2026-02-24 21:48:17.321933 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:17.327518 INFO::Starting hierarchical adjustment
2026-02-24 21:48:17.328849 INFO::Found 5 batches.
2026-02-24 21:48:17.329814 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:17.330921 INFO::Using default BPPARAM
2026-02-24 21:48:17.331914 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.
2026-02-24 21:48:17.505462 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.507479 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:48:17.527765 INFO::Done
2026-02-24 21:48:17.528882 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.533508 INFO::ASW Batch was 0.410928999098974 prior to batch effect correction and is now -0.0491409555831302 .
2026-02-24 21:48:17.534395 INFO::ASW Label was 0.376064480847072 prior to batch effect correction and is now 0.814001446836044 .
2026-02-24 21:48:17.535507 INFO::Total function execution time is 0.22961688041687 s and adjustment time is 0.19916558265686 s ( 86.74 )
2026-02-24 21:48:17.53656 INFO::Formatting Data.
2026-02-24 21:48:17.537349 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:17.538502 INFO::Removing potential empty rows and columns
2026-02-24 21:48:17.539695 INFO::Found 0 missing values.
2026-02-24 21:48:17.544513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:17.54515 INFO::Done
2026-02-24 21:48:17.545768 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:17.549645 INFO::Starting hierarchical adjustment
2026-02-24 21:48:17.550546 INFO::Found 5 batches.
2026-02-24 21:48:17.551177 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:17.55193 INFO::Using default BPPARAM
2026-02-24 21:48:17.552559 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.
2026-02-24 21:48:17.712749 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.714908 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:48:17.736808 INFO::Done
2026-02-24 21:48:17.737883 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.742084 INFO::ASW Batch was 0.410928999098974 prior to batch effect correction and is now -0.0491409555831302 .
2026-02-24 21:48:17.742954 INFO::ASW Label was 0.376064480847072 prior to batch effect correction and is now 0.814001446836044 .
2026-02-24 21:48:17.744201 INFO::Total function execution time is 0.207628965377808 s and adjustment time is 0.186344623565674 s ( 89.75 )
2026-02-24 21:48:17.761232 INFO::Formatting Data.
2026-02-24 21:48:17.762308 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:17.763585 INFO::Removing potential empty rows and columns
2026-02-24 21:48:17.764939 INFO::Found 0 missing values.
2026-02-24 21:48:17.768564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:17.769443 INFO::Done
2026-02-24 21:48:17.770149 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:17.773887 INFO::Starting hierarchical adjustment
2026-02-24 21:48:17.774836 INFO::Found 2 batches.
2026-02-24 21:48:17.775494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:17.776245 INFO::Using default BPPARAM
2026-02-24 21:48:17.776899 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.778057 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:48:17.7963 INFO::Done
2026-02-24 21:48:17.797271 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.800972 INFO::ASW Batch was 0.680376920818295 prior to batch effect correction and is now 0.0834809322994825 .
2026-02-24 21:48:17.801773 INFO::ASW Label was 0.416527468004576 prior to batch effect correction and is now 0.852258421247944 .
2026-02-24 21:48:17.802779 INFO::Total function execution time is 0.0416629314422607 s and adjustment time is 0.0215859413146973 s ( 51.81 )
2026-02-24 21:48:17.803716 INFO::Formatting Data.
2026-02-24 21:48:17.804416 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:17.805423 INFO::Removing potential empty rows and columns
2026-02-24 21:48:17.806526 INFO::Found 0 missing values.
2026-02-24 21:48:17.809541 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:17.810198 INFO::Done
2026-02-24 21:48:17.810769 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:17.813924 INFO::Starting hierarchical adjustment
2026-02-24 21:48:17.814777 INFO::Found 2 batches.
2026-02-24 21:48:17.815359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:17.816 INFO::Using default BPPARAM
2026-02-24 21:48:17.816603 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.817693 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-24 21:48:17.834884 INFO::Done
2026-02-24 21:48:17.835695 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.838849 INFO::ASW Batch was 0.680376920818295 prior to batch effect correction and is now 0.0834809322994825 .
2026-02-24 21:48:17.839569 INFO::ASW Label was 0.416527468004576 prior to batch effect correction and is now 0.852258421247944 .
2026-02-24 21:48:17.840492 INFO::Total function execution time is 0.0367801189422607 s and adjustment time is 0.020249605178833 s ( 55.06 )
2026-02-24 21:48:17.854014 INFO::Formatting Data.
2026-02-24 21:48:17.854994 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:17.856036 INFO::Removing potential empty rows and columns
2026-02-24 21:48:17.85706 INFO::Found 0 missing values.
2026-02-24 21:48:17.859454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:17.860026 INFO::Done
2026-02-24 21:48:17.860562 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:17.862648 INFO::Starting hierarchical adjustment
2026-02-24 21:48:17.8634 INFO::Found 2 batches.
2026-02-24 21:48:17.863931 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:17.864579 INFO::Using default BPPARAM
2026-02-24 21:48:17.865144 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.866165 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:48:17.89835 INFO::Done
2026-02-24 21:48:17.899166 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.901322 INFO::ASW Batch was -0.0879555535347537 prior to batch effect correction and is now -0.127270451373002 .
2026-02-24 21:48:17.90223 INFO::Total function execution time is 0.0483553409576416 s and adjustment time is 0.03505539894104 s ( 72.5 )
2026-02-24 21:48:17.914386 INFO::Formatting Data.
2026-02-24 21:48:17.915202 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:17.916088 INFO::Removing potential empty rows and columns
2026-02-24 21:48:17.917091 INFO::Found 0 missing values.
2026-02-24 21:48:17.918259 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.
2026-02-24 21:48:17.92284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:17.923427 INFO::Done
2026-02-24 21:48:17.923948 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:17.926985 INFO::Starting hierarchical adjustment
2026-02-24 21:48:17.927719 INFO::Found 2 batches.
2026-02-24 21:48:17.928252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:17.928894 INFO::Using default BPPARAM
2026-02-24 21:48:17.929433 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.930348 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:48:17.946454 INFO::Done
2026-02-24 21:48:17.947189 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.950131 INFO::ASW Batch was 0.341285790451998 prior to batch effect correction and is now -0.0146202329551534 .
2026-02-24 21:48:17.950761 INFO::ASW Label was 0.698564201317446 prior to batch effect correction and is now 0.920038013983381 .
2026-02-24 21:48:17.951598 INFO::Total function execution time is 0.037306547164917 s and adjustment time is 0.0188398361206055 s ( 50.5 )
2026-02-24 21:48:17.952401 INFO::Formatting Data.
2026-02-24 21:48:17.953027 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:17.953973 INFO::Removing potential empty rows and columns
2026-02-24 21:48:17.954945 INFO::Found 0 missing values.
2026-02-24 21:48:17.955858 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.
2026-02-24 21:48:17.960308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:17.9609 INFO::Done
2026-02-24 21:48:17.96143 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:17.964321 INFO::Starting hierarchical adjustment
2026-02-24 21:48:17.965049 INFO::Found 2 batches.
2026-02-24 21:48:17.965621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:17.966227 INFO::Using default BPPARAM
2026-02-24 21:48:17.966759 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:17.967703 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:48:17.983658 INFO::Done
2026-02-24 21:48:17.98436 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:17.987344 INFO::ASW Batch was 0.341285790451998 prior to batch effect correction and is now -0.0146202329551534 .
2026-02-24 21:48:17.98799 INFO::ASW Label was 0.698564201317446 prior to batch effect correction and is now 0.920038013983381 .
2026-02-24 21:48:17.988809 INFO::Total function execution time is 0.0364334583282471 s and adjustment time is 0.0187427997589111 s ( 51.44 )
2026-02-24 21:48:18.215024 INFO::Formatting Data.
2026-02-24 21:48:18.216182 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:18.217244 INFO::Removing potential empty rows and columns
2026-02-24 21:48:18.218522 INFO::Found 0 missing values.
2026-02-24 21:48:18.221843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:18.222466 INFO::Done
2026-02-24 21:48:18.223019 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:18.225523 INFO::Starting hierarchical adjustment
2026-02-24 21:48:18.226279 INFO::Found 3 batches.
2026-02-24 21:48:18.226849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:18.227608 INFO::Using default BPPARAM
2026-02-24 21:48:18.228171 INFO::Processing subtree level 1
2026-02-24 21:48:18.329226 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:48:18.331259 INFO::Done
2026-02-24 21:48:18.332007 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:18.334778 INFO::ASW Batch was -0.111314951989728 prior to batch effect correction and is now -0.111314951989728 .
2026-02-24 21:48:18.335972 INFO::Total function execution time is 0.121370077133179 s and adjustment time is 0.10511302947998 s ( 86.61 )
2026-02-24 21:48:18.337186 INFO::Formatting Data.
2026-02-24 21:48:18.337906 INFO::Typecasting input to dataframe.
2026-02-24 21:48:18.338761 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:18.339825 INFO::Removing potential empty rows and columns
2026-02-24 21:48:18.34148 INFO::Found 0 missing values.
2026-02-24 21:48:18.347021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:18.348197 INFO::Done
2026-02-24 21:48:18.349133 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:18.35243 INFO::Starting hierarchical adjustment
2026-02-24 21:48:18.353626 INFO::Found 3 batches.
2026-02-24 21:48:18.354499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:18.355526 INFO::Using default BPPARAM
2026-02-24 21:48:18.356434 INFO::Processing subtree level 1
2026-02-24 21:48:18.465775 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:48:18.467833 INFO::Done
2026-02-24 21:48:18.468662 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:18.471445 INFO::ASW Batch was -0.111314951989728 prior to batch effect correction and is now -0.111314951989728 .
2026-02-24 21:48:18.472523 INFO::Total function execution time is 0.13529896736145 s and adjustment time is 0.114505529403687 s ( 84.63 )
2026-02-24 21:48:18.487771 INFO::Formatting Data.
2026-02-24 21:48:18.488707 INFO::Typecasting input to dataframe.
2026-02-24 21:48:18.489698 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:18.490758 INFO::Removing potential empty rows and columns
2026-02-24 21:48:18.491966 INFO::Found 0 missing values.
2026-02-24 21:48:18.495206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:18.495813 INFO::Done
2026-02-24 21:48:18.496402 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:18.498741 INFO::Starting hierarchical adjustment
2026-02-24 21:48:18.499517 INFO::Found 3 batches.
2026-02-24 21:48:18.500077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:18.500785 INFO::Using default BPPARAM
2026-02-24 21:48:18.501347 INFO::Processing subtree level 1
2026-02-24 21:48:18.625541 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:48:18.635443 INFO::Done
2026-02-24 21:48:18.636665 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:18.643685 INFO::ASW Batch was -0.0602120729745825 prior to batch effect correction and is now -0.0602120729745825 .
2026-02-24 21:48:18.649362 INFO::Total function execution time is 0.161558389663696 s and adjustment time is 0.136015176773071 s ( 84.19 )
2026-02-24 21:48:18.972752 INFO::Formatting Data.
2026-02-24 21:48:18.974032 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:18.975852 INFO::Removing potential empty rows and columns
2026-02-24 21:48:18.980856 INFO::Found 1000 missing values.
2026-02-24 21:48:19.014654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:19.015751 INFO::Done
2026-02-24 21:48:19.016669 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:19.025362 INFO::Starting hierarchical adjustment
2026-02-24 21:48:19.026695 INFO::Found 10 batches.
2026-02-24 21:48:19.027608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:19.028612 INFO::Using default BPPARAM
2026-02-24 21:48:19.029451 INFO::Processing subtree level 1
2026-02-24 21:48:19.245985 INFO::Processing subtree level 2
2026-02-24 21:48:19.743638 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:48:19.766467 INFO::Done
2026-02-24 21:48:19.770222 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:19.794861 INFO::ASW Batch was 0.515606014869699 prior to batch effect correction and is now 0.515606014869699 .
2026-02-24 21:48:19.800064 INFO::ASW Label was 0.335514375566556 prior to batch effect correction and is now 0.335514375566556 .
2026-02-24 21:48:19.808595 INFO::Total function execution time is 0.833516120910645 s and adjustment time is 0.739444971084595 s ( 88.71 )
2026-02-24 21:48:19.8162 INFO::Formatting Data.
2026-02-24 21:48:19.839175 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:19.893728 INFO::Removing potential empty rows and columns
2026-02-24 21:48:19.974363 INFO::Found 1000 missing values.
2026-02-24 21:48:20.174923 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:20.179626 INFO::Done
2026-02-24 21:48:20.184027 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:20.216648 INFO::Starting hierarchical adjustment
2026-02-24 21:48:20.22449 INFO::Found 10 batches.
2026-02-24 21:48:23.519189 INFO::Set up parallel execution backend with 2 workers
2026-02-24 21:48:23.521082 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-24 21:48:24.616639 INFO::Adjusting the last 2 batches sequentially
2026-02-24 21:48:24.618656 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-24 21:48:24.636714 INFO::Done
2026-02-24 21:48:24.637556 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:24.642407 INFO::ASW Batch was 0.515606014869699 prior to batch effect correction and is now 0.515606014869699 .
2026-02-24 21:48:24.643122 INFO::ASW Label was 0.335514375566556 prior to batch effect correction and is now 0.335514375566556 .
2026-02-24 21:48:24.643945 INFO::Total function execution time is 4.82924604415894 s and adjustment time is 4.4144823551178 s ( 91.41 )
2026-02-24 21:48:24.809968 INFO::Formatting Data.
2026-02-24 21:48:24.811107 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:24.812272 INFO::Removing potential empty rows and columns
2026-02-24 21:48:24.81356 INFO::Found 0 missing values.
2026-02-24 21:48:24.817921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:24.818561 INFO::Done
2026-02-24 21:48:24.819143 INFO::Acquiring quality metrics before batch effect correction.
2026-02-24 21:48:24.822557 INFO::Starting hierarchical adjustment
2026-02-24 21:48:24.82336 INFO::Found 3 batches.
2026-02-24 21:48:24.823959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-24 21:48:24.824702 INFO::Using default BPPARAM
2026-02-24 21:48:24.825314 INFO::Processing subtree level 1
2026-02-24 21:48:24.951971 INFO::Adjusting the last 1 batches sequentially
2026-02-24 21:48:24.954196 INFO::Done
2026-02-24 21:48:24.955013 INFO::Acquiring quality metrics after batch effect correction.
2026-02-24 21:48:24.958843 INFO::ASW Batch was 0.255894385462294 prior to batch effect correction and is now -0.152066601247991 .
2026-02-24 21:48:24.959586 INFO::ASW Label was -0.178546277925931 prior to batch effect correction and is now 0.147112910052734 .
2026-02-24 21:48:24.960694 INFO::Total function execution time is 0.150877475738525 s and adjustment time is 0.130963087081909 s ( 86.8 )
2026-02-24 21:48:25.092746 INFO::Formatting Data.
2026-02-24 21:48:25.093823 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.094937 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.096161 INFO::Found 2 missing values.
2026-02-24 21:48:25.099437 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.10007 INFO::Done
2026-02-24 21:48:25.130482 INFO::Found NA in Reference column
2026-02-24 21:48:25.1412 INFO::Require at least two references per batch.
2026-02-24 21:48:25.164052 INFO::Formatting Data.
2026-02-24 21:48:25.164974 INFO::Recognized SummarizedExperiment
2026-02-24 21:48:25.165592 INFO::Typecasting input to dataframe.
2026-02-24 21:48:25.176339 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.177736 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.18166 INFO::Found 0 missing values.
2026-02-24 21:48:25.189158 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.189888 INFO::Done
2026-02-24 21:48:25.207707 INFO::Formatting Data.
2026-02-24 21:48:25.208687 INFO::Recognized SummarizedExperiment
2026-02-24 21:48:25.209329 INFO::Typecasting input to dataframe.
2026-02-24 21:48:25.229161 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.230657 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.234585 INFO::Found 0 missing values.
2026-02-24 21:48:25.246544 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.247355 INFO::Done
2026-02-24 21:48:25.264815 INFO::Formatting Data.
2026-02-24 21:48:25.265659 INFO::Recognized SummarizedExperiment
2026-02-24 21:48:25.266231 INFO::Typecasting input to dataframe.
2026-02-24 21:48:25.283674 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.284891 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.286087 INFO::Found 0 missing values.
2026-02-24 21:48:25.287097 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.
2026-02-24 21:48:25.29191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.292542 INFO::Done
2026-02-24 21:48:25.303564 INFO::Formatting Data.
2026-02-24 21:48:25.30444 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.305384 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.306439 INFO::Found 0 missing values.
2026-02-24 21:48:25.309431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.309973 INFO::Done
2026-02-24 21:48:25.322212 INFO::Formatting Data.
2026-02-24 21:48:25.32305 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.324003 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.325076 INFO::Found 0 missing values.
2026-02-24 21:48:25.328116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.328671 INFO::Done
2026-02-24 21:48:25.360016 INFO::Formatting Data.
2026-02-24 21:48:25.360926 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.36202 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.363226 INFO::Found 1 missing values.
2026-02-24 21:48:25.365927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.366513 INFO::Done
2026-02-24 21:48:25.387127 INFO::Formatting Data.
2026-02-24 21:48:25.388051 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.388974 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.389964 INFO::Found 2 missing values.
2026-02-24 21:48:25.390867 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.
2026-02-24 21:48:25.393264 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.393785 INFO::Done
2026-02-24 21:48:25.403562 INFO::Formatting Data.
2026-02-24 21:48:25.404336 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.405206 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.40611 INFO::Found 2 missing values.
2026-02-24 21:48:25.407647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.408195 INFO::Done
2026-02-24 21:48:25.418352 INFO::Formatting Data.
2026-02-24 21:48:25.419178 INFO::Typecasting input to dataframe.
2026-02-24 21:48:25.419987 INFO::Replacing NaNs with NAs.
2026-02-24 21:48:25.42084 INFO::Removing potential empty rows and columns
2026-02-24 21:48:25.421818 INFO::Found 0 missing values.
2026-02-24 21:48:25.424664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-24 21:48:25.425189 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.704 4.409 24.113
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.778 | 1.184 | 17.063 | |
| compute_asw | 0.023 | 0.000 | 0.023 | |
| count_existing | 0.012 | 0.001 | 0.013 | |
| generate_data_covariables | 0.010 | 0.002 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |