Yannis Schumann
| Snapshot Date: 2026-01-20 13:40 -0500 (Tue, 20 Jan 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-21 11:34 -0500 (Wed, 21 Jan 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" | 4805 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4539 |
| 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 168/2343 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-01-20 18:34:31 -0500 (Tue, 20 Jan 2026) |
| EndedAt: 2026-01-20 18:35:08 -0500 (Tue, 20 Jan 2026) |
| EllapsedTime: 37.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 10.794 0.435 8.129
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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: aarch64-apple-darwin20
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")
2026-01-20 18:34:58.734254 INFO::Formatting Data.
2026-01-20 18:34:58.736074 INFO::Replacing NaNs with NAs.
2026-01-20 18:34:58.741082 INFO::Removing potential empty rows and columns
2026-01-20 18:34:58.864281 INFO::Found 0 missing values.
2026-01-20 18:34:58.865585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:34:58.86582 INFO::Done
2026-01-20 18:34:58.866012 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:34:58.874014 INFO::Starting hierarchical adjustment
2026-01-20 18:34:58.874361 INFO::Found 3 batches.
2026-01-20 18:34:58.874536 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:34:58.874981 INFO::Using default BPPARAM
2026-01-20 18:34:58.875183 INFO::Processing subtree level 1
2026-01-20 18:34:58.948745 INFO::Adjusting the last 1 batches sequentially
2026-01-20 18:34:58.950902 INFO::Done
2026-01-20 18:34:58.951176 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:34:58.954125 INFO::ASW Batch was -0.0136874778491451 prior to batch effect correction and is now -0.0136874778491451 .
2026-01-20 18:34:58.955096 INFO::Total function execution time is 0.220776081085205 s and adjustment time is 0.0766098499298096 s ( 34.7 )
2026-01-20 18:34:58.96445 INFO::Formatting Data.
2026-01-20 18:34:58.964747 INFO::Replacing NaNs with NAs.
2026-01-20 18:34:58.965105 INFO::Removing potential empty rows and columns
2026-01-20 18:34:58.965576 INFO::Found 0 missing values.
2026-01-20 18:34:58.965948 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.
2026-01-20 18:34:58.970743 INFO::Formatting Data.
2026-01-20 18:34:58.971039 INFO::Replacing NaNs with NAs.
2026-01-20 18:34:58.971628 INFO::Removing potential empty rows and columns
2026-01-20 18:34:58.972758 INFO::Found 0 missing values.
2026-01-20 18:34:58.973329 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.
2026-01-20 18:34:58.981063 INFO::Formatting Data.
2026-01-20 18:34:58.981359 INFO::Replacing NaNs with NAs.
2026-01-20 18:34:58.981681 INFO::Removing potential empty rows and columns
2026-01-20 18:34:58.982151 INFO::Found 0 missing values.
2026-01-20 18:34:58.982467 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.
2026-01-20 18:34:58.985734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:34:58.986014 INFO::Done
2026-01-20 18:34:58.986228 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:34:58.987114 INFO::Starting hierarchical adjustment
2026-01-20 18:34:58.987369 INFO::Found 2 batches.
2026-01-20 18:34:58.987547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:34:58.987797 INFO::Using default BPPARAM
2026-01-20 18:34:58.987978 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:34:58.988289 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-20 18:34:58.997428 INFO::Done
2026-01-20 18:34:58.997744 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:34:58.998896 INFO::ASW Batch was 0.0624587701066567 prior to batch effect correction and is now -0.118142082706586 .
2026-01-20 18:34:58.999221 INFO::Total function execution time is 0.0181899070739746 s and adjustment time is 0.0100748538970947 s ( 55.39 )
2026-01-20 18:34:59.000534 INFO::Formatting Data.
2026-01-20 18:34:59.000801 INFO::Replacing NaNs with NAs.
2026-01-20 18:34:59.004733 INFO::Formatting Data.
2026-01-20 18:34:59.005042 INFO::Replacing NaNs with NAs.
2026-01-20 18:34:59.005397 INFO::Removing potential empty rows and columns
2026-01-20 18:34:59.005848 INFO::Found 0 missing values.
2026-01-20 18:34:59.007057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:34:59.007299 INFO::Done
2026-01-20 18:34:59.007528 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:34:59.00834 INFO::Starting hierarchical adjustment
2026-01-20 18:34:59.008634 INFO::Found 2 batches.
2026-01-20 18:34:59.008863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:34:59.009117 INFO::Using default BPPARAM
2026-01-20 18:34:59.009327 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:34:59.024392 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-20 18:34:59.036661 INFO::Done
2026-01-20 18:34:59.036943 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:34:59.037719 INFO::ASW Batch was 0.0464254568201773 prior to batch effect correction and is now -0.126758083939956 .
2026-01-20 18:34:59.037985 INFO::Total function execution time is 0.0332670211791992 s and adjustment time is 0.0280718803405762 s ( 84.38 )
2026-01-20 18:34:59.03832 INFO::Formatting Data.
2026-01-20 18:34:59.038492 INFO::Replacing NaNs with NAs.
2026-01-20 18:34:59.038749 INFO::Removing potential empty rows and columns
2026-01-20 18:34:59.039059 INFO::Found 0 missing values.
2026-01-20 18:34:59.039949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:34:59.040122 INFO::Done
2026-01-20 18:34:59.040278 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:34:59.040894 INFO::Starting hierarchical adjustment
2026-01-20 18:34:59.04112 INFO::Found 2 batches.
2026-01-20 18:34:59.041294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:34:59.041499 INFO::Using default BPPARAM
2026-01-20 18:34:59.041663 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:34:59.041934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-20 18:34:59.047096 INFO::Done
2026-01-20 18:34:59.047309 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:34:59.047959 INFO::ASW Batch was 0.0464254568201773 prior to batch effect correction and is now -0.126758083939956 .
2026-01-20 18:34:59.048206 INFO::Total function execution time is 0.00988292694091797 s and adjustment time is 0.00601601600646973 s ( 60.87 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-20 18:35:00.317214 INFO::Formatting Data.
2026-01-20 18:35:00.317487 INFO::Recognized SummarizedExperiment
2026-01-20 18:35:00.317649 INFO::Typecasting input to dataframe.
2026-01-20 18:35:00.328236 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:00.328662 INFO::Removing potential empty rows and columns
2026-01-20 18:35:00.329871 INFO::Found 0 missing values.
2026-01-20 18:35:00.332127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:00.332302 INFO::Done
2026-01-20 18:35:00.332453 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:00.333682 INFO::Starting hierarchical adjustment
2026-01-20 18:35:00.333901 INFO::Found 2 batches.
2026-01-20 18:35:00.334051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:00.334381 INFO::Using default BPPARAM
2026-01-20 18:35:00.33455 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:00.334856 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-20 18:35:00.358638 INFO::Done
2026-01-20 18:35:00.358967 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:00.360377 INFO::ASW Batch was -0.00399284894350334 prior to batch effect correction and is now -0.0916253513667387 .
2026-01-20 18:35:00.360707 INFO::Total function execution time is 0.0435910224914551 s and adjustment time is 0.0247530937194824 s ( 56.78 )
Warning: stack imbalance in '{', 73 then 75
2026-01-20 18:35:00.369226 INFO::Formatting Data.
2026-01-20 18:35:00.369676 INFO::Recognized SummarizedExperiment
2026-01-20 18:35:00.369906 INFO::Typecasting input to dataframe.
2026-01-20 18:35:00.373605 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:00.373988 INFO::Removing potential empty rows and columns
2026-01-20 18:35:00.375143 INFO::Found 0 missing values.
2026-01-20 18:35:00.377351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:00.377523 INFO::Done
2026-01-20 18:35:00.377677 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:00.378889 INFO::Starting hierarchical adjustment
2026-01-20 18:35:00.37911 INFO::Found 2 batches.
2026-01-20 18:35:00.379266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:00.379445 INFO::Using default BPPARAM
2026-01-20 18:35:00.379591 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:00.379878 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-20 18:35:00.388019 INFO::Done
2026-01-20 18:35:00.388229 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:00.389391 INFO::ASW Batch was -0.0241701006191491 prior to batch effect correction and is now -0.0241701006191491 .
2026-01-20 18:35:00.389657 INFO::Total function execution time is 0.0204908847808838 s and adjustment time is 0.00894904136657715 s ( 43.67 )
2026-01-20 18:35:00.397368 INFO::Formatting Data.
2026-01-20 18:35:00.397594 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:00.397864 INFO::Removing potential empty rows and columns
2026-01-20 18:35:00.398171 INFO::Found 0 missing values.
2026-01-20 18:35:00.399022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:00.399183 INFO::Done
2026-01-20 18:35:00.39934 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:00.399952 INFO::Starting hierarchical adjustment
2026-01-20 18:35:00.400155 INFO::Found 3 batches.
2026-01-20 18:35:00.400309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:00.40049 INFO::Using default BPPARAM
2026-01-20 18:35:00.400639 INFO::Processing subtree level 1
2026-01-20 18:35:00.48464 INFO::Adjusting the last 1 batches sequentially
2026-01-20 18:35:00.48643 INFO::Done
2026-01-20 18:35:00.48668 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:00.489205 INFO::ASW Batch was -0.0639810335893587 prior to batch effect correction and is now -0.16317647089806 .
2026-01-20 18:35:00.49017 INFO::Total function execution time is 0.0925850868225098 s and adjustment time is 0.0862829685211182 s ( 93.19 )
2026-01-20 18:35:00.499213 INFO::Skipping initial DF formatting
2026-01-20 18:35:00.499529 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:00.501314 INFO::Starting hierarchical adjustment
2026-01-20 18:35:00.501613 INFO::Found 5 batches.
2026-01-20 18:35:00.501812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:00.502103 INFO::Using default BPPARAM
2026-01-20 18:35:00.502308 INFO::Processing subtree level 1
2026-01-20 18:35:00.647553 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:00.654211 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-20 18:35:00.66829 INFO::Done
2026-01-20 18:35:00.668787 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:00.673596 INFO::ASW Batch was 0.478559008740823 prior to batch effect correction and is now 0.478559008740823 .
2026-01-20 18:35:00.674771 INFO::ASW Label was 0.422440233232122 prior to batch effect correction and is now 0.422440233232122 .
2026-01-20 18:35:00.675758 INFO::Total function execution time is 0.176429033279419 s and adjustment time is 0.166723012924194 s ( 94.5 )
2026-01-20 18:35:00.721899 INFO::Formatting Data.
2026-01-20 18:35:00.722258 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:00.722749 INFO::Removing potential empty rows and columns
2026-01-20 18:35:00.723197 INFO::Found 0 missing values.
2026-01-20 18:35:00.72494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:00.725196 INFO::Done
2026-01-20 18:35:00.725439 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:00.726839 INFO::Starting hierarchical adjustment
2026-01-20 18:35:00.727179 INFO::Found 5 batches.
2026-01-20 18:35:00.727439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:00.727703 INFO::Using default BPPARAM
2026-01-20 18:35:00.727896 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.
2026-01-20 18:35:00.808354 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:00.81316 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-20 18:35:00.837212 INFO::Done
2026-01-20 18:35:00.83779 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:00.839798 INFO::ASW Batch was 0.257525361365006 prior to batch effect correction and is now -0.0594274204046176 .
2026-01-20 18:35:00.840078 INFO::ASW Label was 0.49562220027166 prior to batch effect correction and is now 0.866280552451554 .
2026-01-20 18:35:00.840707 INFO::Total function execution time is 0.118610143661499 s and adjustment time is 0.110063076019287 s ( 92.79 )
2026-01-20 18:35:00.84124 INFO::Formatting Data.
2026-01-20 18:35:00.841454 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:00.841816 INFO::Removing potential empty rows and columns
2026-01-20 18:35:00.842264 INFO::Found 0 missing values.
2026-01-20 18:35:00.84398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:00.844238 INFO::Done
2026-01-20 18:35:00.844427 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:00.845583 INFO::Starting hierarchical adjustment
2026-01-20 18:35:00.845891 INFO::Found 5 batches.
2026-01-20 18:35:00.846104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:00.846323 INFO::Using default BPPARAM
2026-01-20 18:35:00.846541 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.
2026-01-20 18:35:00.919608 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:00.92636 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-20 18:35:00.940443 INFO::Done
2026-01-20 18:35:00.941019 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:00.942478 INFO::ASW Batch was 0.257525361365006 prior to batch effect correction and is now -0.0594274204046176 .
2026-01-20 18:35:00.942715 INFO::ASW Label was 0.49562220027166 prior to batch effect correction and is now 0.866280552451554 .
2026-01-20 18:35:00.944283 INFO::Total function execution time is 0.10181999206543 s and adjustment time is 0.094588041305542 s ( 92.9 )
2026-01-20 18:35:00.951674 INFO::Formatting Data.
2026-01-20 18:35:00.951964 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:00.952297 INFO::Removing potential empty rows and columns
2026-01-20 18:35:00.952674 INFO::Found 0 missing values.
2026-01-20 18:35:00.954221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:00.954431 INFO::Done
2026-01-20 18:35:00.954615 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:00.955813 INFO::Starting hierarchical adjustment
2026-01-20 18:35:00.95609 INFO::Found 5 batches.
2026-01-20 18:35:00.95628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:00.956508 INFO::Using default BPPARAM
2026-01-20 18:35:00.956705 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.
2026-01-20 18:35:01.03626 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:01.03876 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-20 18:35:01.052532 INFO::Done
2026-01-20 18:35:01.053483 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.055881 INFO::ASW Batch was 0.430415532250676 prior to batch effect correction and is now -0.0486071529022078 .
2026-01-20 18:35:01.056128 INFO::ASW Label was 0.418438562927489 prior to batch effect correction and is now 0.815346422296902 .
2026-01-20 18:35:01.05649 INFO::Total function execution time is 0.104844808578491 s and adjustment time is 0.0964767932891846 s ( 92.02 )
2026-01-20 18:35:01.056807 INFO::Formatting Data.
2026-01-20 18:35:01.057041 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.057438 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.05783 INFO::Found 0 missing values.
2026-01-20 18:35:01.059703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.059946 INFO::Done
2026-01-20 18:35:01.060167 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.06154 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.061809 INFO::Found 5 batches.
2026-01-20 18:35:01.061987 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.062238 INFO::Using default BPPARAM
2026-01-20 18:35:01.062416 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.
2026-01-20 18:35:01.132123 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:01.134384 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-20 18:35:01.144987 INFO::Done
2026-01-20 18:35:01.145465 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.147416 INFO::ASW Batch was 0.430415532250676 prior to batch effect correction and is now -0.0486071529022078 .
2026-01-20 18:35:01.147834 INFO::ASW Label was 0.418438562927489 prior to batch effect correction and is now 0.815346422296902 .
2026-01-20 18:35:01.148224 INFO::Total function execution time is 0.0913839340209961 s and adjustment time is 0.0832200050354004 s ( 91.07 )
2026-01-20 18:35:01.156538 INFO::Formatting Data.
2026-01-20 18:35:01.156864 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.157241 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.157725 INFO::Found 0 missing values.
2026-01-20 18:35:01.15874 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.158946 INFO::Done
2026-01-20 18:35:01.159143 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.160264 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.160549 INFO::Found 2 batches.
2026-01-20 18:35:01.161484 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.161777 INFO::Using default BPPARAM
2026-01-20 18:35:01.161964 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:01.162392 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-20 18:35:01.168219 INFO::Done
2026-01-20 18:35:01.168473 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.16967 INFO::ASW Batch was 0.556652200030439 prior to batch effect correction and is now 0.102110294779096 .
2026-01-20 18:35:01.169878 INFO::ASW Label was 0.528008764662762 prior to batch effect correction and is now 0.895598576612255 .
2026-01-20 18:35:01.170158 INFO::Total function execution time is 0.0136559009552002 s and adjustment time is 0.00772213935852051 s ( 56.55 )
2026-01-20 18:35:01.170416 INFO::Formatting Data.
2026-01-20 18:35:01.170615 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.170913 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.171244 INFO::Found 0 missing values.
2026-01-20 18:35:01.172147 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.17233 INFO::Done
2026-01-20 18:35:01.172503 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.173513 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.173759 INFO::Found 2 batches.
2026-01-20 18:35:01.173941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.174143 INFO::Using default BPPARAM
2026-01-20 18:35:01.174307 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:01.174607 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-20 18:35:01.180171 INFO::Done
2026-01-20 18:35:01.180414 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.181431 INFO::ASW Batch was 0.556652200030439 prior to batch effect correction and is now 0.102110294779096 .
2026-01-20 18:35:01.181633 INFO::ASW Label was 0.528008764662762 prior to batch effect correction and is now 0.895598576612255 .
2026-01-20 18:35:01.181885 INFO::Total function execution time is 0.0114569664001465 s and adjustment time is 0.0064539909362793 s ( 56.33 )
2026-01-20 18:35:01.187694 INFO::Formatting Data.
2026-01-20 18:35:01.188084 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.188476 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.188872 INFO::Found 0 missing values.
2026-01-20 18:35:01.189714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.189954 INFO::Done
2026-01-20 18:35:01.190144 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.190951 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.191237 INFO::Found 2 batches.
2026-01-20 18:35:01.191422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.19166 INFO::Using default BPPARAM
2026-01-20 18:35:01.19183 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:01.192164 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-20 18:35:01.204677 INFO::Done
2026-01-20 18:35:01.204973 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.205706 INFO::ASW Batch was 0.137664911268187 prior to batch effect correction and is now -0.144763823369992 .
2026-01-20 18:35:01.206025 INFO::Total function execution time is 0.0184030532836914 s and adjustment time is 0.0134999752044678 s ( 73.36 )
2026-01-20 18:35:01.211446 INFO::Formatting Data.
2026-01-20 18:35:01.211707 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.212004 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.212381 INFO::Found 0 missing values.
2026-01-20 18:35:01.212824 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.
2026-01-20 18:35:01.214429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.214602 INFO::Done
2026-01-20 18:35:01.214769 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.215881 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.216114 INFO::Found 2 batches.
2026-01-20 18:35:01.216295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.216485 INFO::Using default BPPARAM
2026-01-20 18:35:01.216664 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:01.217102 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-20 18:35:01.223794 INFO::Done
2026-01-20 18:35:01.223997 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.225092 INFO::ASW Batch was 0.541534447102625 prior to batch effect correction and is now 0.0427201350902395 .
2026-01-20 18:35:01.225302 INFO::ASW Label was 0.566863720838391 prior to batch effect correction and is now 0.908099340841727 .
2026-01-20 18:35:01.22557 INFO::Total function execution time is 0.0141479969024658 s and adjustment time is 0.00771594047546387 s ( 54.54 )
2026-01-20 18:35:01.225898 INFO::Formatting Data.
2026-01-20 18:35:01.226082 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.226451 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.226774 INFO::Found 0 missing values.
2026-01-20 18:35:01.227067 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.
2026-01-20 18:35:01.230259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.230589 INFO::Done
2026-01-20 18:35:01.230819 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.231979 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.232239 INFO::Found 2 batches.
2026-01-20 18:35:01.232422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.232625 INFO::Using default BPPARAM
2026-01-20 18:35:01.232785 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:01.233106 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-20 18:35:01.239147 INFO::Done
2026-01-20 18:35:01.239368 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.240289 INFO::ASW Batch was 0.541534447102625 prior to batch effect correction and is now 0.0427201350902395 .
2026-01-20 18:35:01.240483 INFO::ASW Label was 0.566863720838391 prior to batch effect correction and is now 0.908099340841727 .
2026-01-20 18:35:01.240747 INFO::Total function execution time is 0.0148539543151855 s and adjustment time is 0.00695681571960449 s ( 46.83 )
2026-01-20 18:35:01.314686 INFO::Formatting Data.
2026-01-20 18:35:01.315019 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.315356 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.315719 INFO::Found 0 missing values.
2026-01-20 18:35:01.31668 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.316857 INFO::Done
2026-01-20 18:35:01.317023 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.317714 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.317926 INFO::Found 3 batches.
2026-01-20 18:35:01.31808 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.318266 INFO::Using default BPPARAM
2026-01-20 18:35:01.318415 INFO::Processing subtree level 1
2026-01-20 18:35:01.38662 INFO::Adjusting the last 1 batches sequentially
2026-01-20 18:35:01.388402 INFO::Done
2026-01-20 18:35:01.388694 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.390774 INFO::ASW Batch was -0.109907938931058 prior to batch effect correction and is now -0.109907938931058 .
2026-01-20 18:35:01.392119 INFO::Total function execution time is 0.0772979259490967 s and adjustment time is 0.0705039501190186 s ( 91.21 )
2026-01-20 18:35:01.392587 INFO::Formatting Data.
2026-01-20 18:35:01.392817 INFO::Typecasting input to dataframe.
2026-01-20 18:35:01.393065 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.393398 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.393924 INFO::Found 0 missing values.
2026-01-20 18:35:01.394913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.395096 INFO::Done
2026-01-20 18:35:01.395264 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.395918 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.396153 INFO::Found 3 batches.
2026-01-20 18:35:01.396328 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.396552 INFO::Using default BPPARAM
2026-01-20 18:35:01.396724 INFO::Processing subtree level 1
2026-01-20 18:35:01.442889 INFO::Adjusting the last 1 batches sequentially
2026-01-20 18:35:01.445556 INFO::Done
2026-01-20 18:35:01.445928 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.448793 INFO::ASW Batch was -0.109907938931058 prior to batch effect correction and is now -0.109907938931058 .
2026-01-20 18:35:01.449714 INFO::Total function execution time is 0.0570988655090332 s and adjustment time is 0.0494229793548584 s ( 86.56 )
2026-01-20 18:35:01.457376 INFO::Formatting Data.
2026-01-20 18:35:01.457705 INFO::Typecasting input to dataframe.
2026-01-20 18:35:01.458 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.458405 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.459018 INFO::Found 0 missing values.
2026-01-20 18:35:01.460131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.460351 INFO::Done
2026-01-20 18:35:01.460554 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.461428 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.461717 INFO::Found 3 batches.
2026-01-20 18:35:01.461914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.462319 INFO::Using default BPPARAM
2026-01-20 18:35:01.462508 INFO::Processing subtree level 1
2026-01-20 18:35:01.504892 INFO::Adjusting the last 1 batches sequentially
2026-01-20 18:35:01.509665 INFO::Done
2026-01-20 18:35:01.510206 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.515297 INFO::ASW Batch was 0.024664756153304 prior to batch effect correction and is now 0.024664756153304 .
2026-01-20 18:35:01.516379 INFO::Total function execution time is 0.0589179992675781 s and adjustment time is 0.0479669570922852 s ( 81.41 )
2026-01-20 18:35:01.61266 INFO::Formatting Data.
2026-01-20 18:35:01.612961 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.613601 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.614549 INFO::Found 1000 missing values.
2026-01-20 18:35:01.62075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.621001 INFO::Done
2026-01-20 18:35:01.621181 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.623601 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.62395 INFO::Found 10 batches.
2026-01-20 18:35:01.624174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:01.624457 INFO::Using default BPPARAM
2026-01-20 18:35:01.624882 INFO::Processing subtree level 1
2026-01-20 18:35:01.71094 INFO::Processing subtree level 2
2026-01-20 18:35:01.82668 INFO::Adjusting the last 1 batches sequentially
2026-01-20 18:35:01.829745 INFO::Done
2026-01-20 18:35:01.83025 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:01.837479 INFO::ASW Batch was 0.523513442773645 prior to batch effect correction and is now 0.523513442773645 .
2026-01-20 18:35:01.837822 INFO::ASW Label was 0.290780196089202 prior to batch effect correction and is now 0.290780196089202 .
2026-01-20 18:35:01.838736 INFO::Total function execution time is 0.225886106491089 s and adjustment time is 0.205842971801758 s ( 91.13 )
2026-01-20 18:35:01.83956 INFO::Formatting Data.
2026-01-20 18:35:01.839981 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:01.840642 INFO::Removing potential empty rows and columns
2026-01-20 18:35:01.841858 INFO::Found 1000 missing values.
2026-01-20 18:35:01.84802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:01.848273 INFO::Done
2026-01-20 18:35:01.848463 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:01.851015 INFO::Starting hierarchical adjustment
2026-01-20 18:35:01.851363 INFO::Found 10 batches.
2026-01-20 18:35:02.34831 INFO::Set up parallel execution backend with 2 workers
2026-01-20 18:35:02.348651 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-20 18:35:03.002829 INFO::Adjusting the last 2 batches sequentially
2026-01-20 18:35:03.003408 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-20 18:35:03.011469 INFO::Done
2026-01-20 18:35:03.011688 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:03.013565 INFO::ASW Batch was 0.523513442773645 prior to batch effect correction and is now 0.523513442773645 .
2026-01-20 18:35:03.013738 INFO::ASW Label was 0.290780196089202 prior to batch effect correction and is now 0.290780196089202 .
2026-01-20 18:35:03.013982 INFO::Total function execution time is 1.17450594902039 s and adjustment time is 1.16017889976501 s ( 98.78 )
2026-01-20 18:35:03.093463 INFO::Formatting Data.
2026-01-20 18:35:03.093836 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.094274 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.09483 INFO::Found 0 missing values.
2026-01-20 18:35:03.096692 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.09691 INFO::Done
2026-01-20 18:35:03.09713 INFO::Acquiring quality metrics before batch effect correction.
2026-01-20 18:35:03.098456 INFO::Starting hierarchical adjustment
2026-01-20 18:35:03.098791 INFO::Found 3 batches.
2026-01-20 18:35:03.099329 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-20 18:35:03.099661 INFO::Using default BPPARAM
2026-01-20 18:35:03.099883 INFO::Processing subtree level 1
2026-01-20 18:35:03.164511 INFO::Adjusting the last 1 batches sequentially
2026-01-20 18:35:03.169504 INFO::Done
2026-01-20 18:35:03.170282 INFO::Acquiring quality metrics after batch effect correction.
2026-01-20 18:35:03.174388 INFO::ASW Batch was 0.212253470281678 prior to batch effect correction and is now -0.148186966758777 .
2026-01-20 18:35:03.175202 INFO::ASW Label was -0.15282029884576 prior to batch effect correction and is now -0.039471420942147 .
2026-01-20 18:35:03.176887 INFO::Total function execution time is 0.0829930305480957 s and adjustment time is 0.0707488059997559 s ( 85.25 )
2026-01-20 18:35:03.241116 INFO::Formatting Data.
2026-01-20 18:35:03.241496 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.24188 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.242331 INFO::Found 2 missing values.
2026-01-20 18:35:03.243378 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.243572 INFO::Done
2026-01-20 18:35:03.255471 INFO::Found NA in Reference column
2026-01-20 18:35:03.259478 INFO::Require at least two references per batch.
2026-01-20 18:35:03.271338 INFO::Formatting Data.
2026-01-20 18:35:03.271676 INFO::Recognized SummarizedExperiment
2026-01-20 18:35:03.271874 INFO::Typecasting input to dataframe.
2026-01-20 18:35:03.276164 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.276598 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.278045 INFO::Found 0 missing values.
2026-01-20 18:35:03.281041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.283214 INFO::Done
2026-01-20 18:35:03.290452 INFO::Formatting Data.
2026-01-20 18:35:03.290782 INFO::Recognized SummarizedExperiment
2026-01-20 18:35:03.291015 INFO::Typecasting input to dataframe.
2026-01-20 18:35:03.297883 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.298363 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.299761 INFO::Found 0 missing values.
2026-01-20 18:35:03.305625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.305872 INFO::Done
2026-01-20 18:35:03.311973 INFO::Formatting Data.
2026-01-20 18:35:03.312244 INFO::Recognized SummarizedExperiment
2026-01-20 18:35:03.312426 INFO::Typecasting input to dataframe.
2026-01-20 18:35:03.317991 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.31836 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.318758 INFO::Found 0 missing values.
2026-01-20 18:35:03.319085 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.
2026-01-20 18:35:03.320721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.320916 INFO::Done
2026-01-20 18:35:03.327305 INFO::Formatting Data.
2026-01-20 18:35:03.3276 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.327916 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.328325 INFO::Found 0 missing values.
2026-01-20 18:35:03.329342 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.32953 INFO::Done
2026-01-20 18:35:03.33589 INFO::Formatting Data.
2026-01-20 18:35:03.336197 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.336547 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.336968 INFO::Found 0 missing values.
2026-01-20 18:35:03.337997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.338186 INFO::Done
2026-01-20 18:35:03.353106 INFO::Formatting Data.
2026-01-20 18:35:03.35347 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.354303 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.354987 INFO::Found 1 missing values.
2026-01-20 18:35:03.356141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.356403 INFO::Done
2026-01-20 18:35:03.365432 INFO::Formatting Data.
2026-01-20 18:35:03.365747 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.366071 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.366396 INFO::Found 2 missing values.
2026-01-20 18:35:03.366703 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.
2026-01-20 18:35:03.367543 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.36776 INFO::Done
2026-01-20 18:35:03.371946 INFO::Formatting Data.
2026-01-20 18:35:03.372236 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.37258 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.372887 INFO::Found 2 missing values.
2026-01-20 18:35:03.3734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.373569 INFO::Done
2026-01-20 18:35:03.37793 INFO::Formatting Data.
2026-01-20 18:35:03.378191 INFO::Typecasting input to dataframe.
2026-01-20 18:35:03.378444 INFO::Replacing NaNs with NAs.
2026-01-20 18:35:03.378722 INFO::Removing potential empty rows and columns
2026-01-20 18:35:03.379056 INFO::Found 0 missing values.
2026-01-20 18:35:03.379968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-20 18:35:03.380195 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.537 1.912 9.962
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.794 | 0.435 | 8.129 | |
| compute_asw | 0.012 | 0.001 | 0.013 | |
| count_existing | 0.006 | 0.001 | 0.006 | |
| generate_data_covariables | 0.004 | 0.000 | 0.006 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |