Yannis Schumann
| Snapshot Date: 2026-04-13 13:40 -0400 (Mon, 13 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-14 11:35 -0400 (Tue, 14 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4924 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4655 |
| 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 170/2394 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: /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: 2026-04-13 18:31:36 -0400 (Mon, 13 Apr 2026) |
| EndedAt: 2026-04-13 18:32:09 -0400 (Mon, 13 Apr 2026) |
| EllapsedTime: 33.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-13 22:31:36 UTC
* 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 9.544 0.354 6.787
* 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/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 version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-04-13 18:32:01.458802 INFO::Formatting Data.
2026-04-13 18:32:01.460631 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:01.465242 INFO::Removing potential empty rows and columns
2026-04-13 18:32:01.564796 INFO::Found 0 missing values.
2026-04-13 18:32:01.566137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:01.566479 INFO::Done
2026-04-13 18:32:01.566775 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:01.572716 INFO::Starting hierarchical adjustment
2026-04-13 18:32:01.573184 INFO::Found 3 batches.
2026-04-13 18:32:01.573486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:01.574038 INFO::Using default BPPARAM
2026-04-13 18:32:01.574325 INFO::Processing subtree level 1
2026-04-13 18:32:01.653827 INFO::Adjusting the last 1 batches sequentially
2026-04-13 18:32:01.655496 INFO::Done
2026-04-13 18:32:01.655947 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:01.657615 INFO::ASW Batch was -0.0404816208331671 prior to batch effect correction and is now -0.0404816208331671 .
2026-04-13 18:32:01.658303 INFO::Total function execution time is 0.199958086013794 s and adjustment time is 0.0823638439178467 s ( 41.19 )
2026-04-13 18:32:01.667722 INFO::Formatting Data.
2026-04-13 18:32:01.668408 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:01.669041 INFO::Removing potential empty rows and columns
2026-04-13 18:32:01.669907 INFO::Found 0 missing values.
2026-04-13 18:32:01.670686 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-13 18:32:01.676505 INFO::Formatting Data.
2026-04-13 18:32:01.677034 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:01.677518 INFO::Removing potential empty rows and columns
2026-04-13 18:32:01.678115 INFO::Found 0 missing values.
2026-04-13 18:32:01.678609 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-13 18:32:01.686653 INFO::Formatting Data.
2026-04-13 18:32:01.6872 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:01.687792 INFO::Removing potential empty rows and columns
2026-04-13 18:32:01.688317 INFO::Found 0 missing values.
2026-04-13 18:32:01.688809 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-13 18:32:01.690559 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:01.691001 INFO::Done
2026-04-13 18:32:01.691345 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:01.692304 INFO::Starting hierarchical adjustment
2026-04-13 18:32:01.692726 INFO::Found 2 batches.
2026-04-13 18:32:01.693108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:01.693538 INFO::Using default BPPARAM
2026-04-13 18:32:01.693876 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:01.694457 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-13 18:32:01.70506 INFO::Done
2026-04-13 18:32:01.705517 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:01.706466 INFO::ASW Batch was 0.0576770328877923 prior to batch effect correction and is now -0.121981066837862 .
2026-04-13 18:32:01.706942 INFO::Total function execution time is 0.0203311443328857 s and adjustment time is 0.012382984161377 s ( 60.91 )
2026-04-13 18:32:01.708204 INFO::Formatting Data.
2026-04-13 18:32:01.708592 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:01.712325 INFO::Formatting Data.
2026-04-13 18:32:01.712815 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:01.713339 INFO::Removing potential empty rows and columns
2026-04-13 18:32:01.713913 INFO::Found 0 missing values.
2026-04-13 18:32:01.715025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:01.715427 INFO::Done
2026-04-13 18:32:01.715743 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:01.71662 INFO::Starting hierarchical adjustment
2026-04-13 18:32:01.71706 INFO::Found 2 batches.
2026-04-13 18:32:01.717381 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:01.717702 INFO::Using default BPPARAM
2026-04-13 18:32:01.718045 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:01.71848 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:01.726822 INFO::Done
2026-04-13 18:32:01.72744 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:01.729116 INFO::ASW Batch was 0.0925418641490015 prior to batch effect correction and is now -0.119570749991389 .
2026-04-13 18:32:01.729594 INFO::Total function execution time is 0.0172920227050781 s and adjustment time is 0.00980114936828613 s ( 56.68 )
2026-04-13 18:32:01.730356 INFO::Formatting Data.
2026-04-13 18:32:01.730914 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:01.731532 INFO::Removing potential empty rows and columns
2026-04-13 18:32:01.732249 INFO::Found 0 missing values.
2026-04-13 18:32:01.733793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:01.734304 INFO::Done
2026-04-13 18:32:01.734743 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:01.735844 INFO::Starting hierarchical adjustment
2026-04-13 18:32:01.736935 INFO::Found 2 batches.
2026-04-13 18:32:01.737376 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:01.737739 INFO::Using default BPPARAM
2026-04-13 18:32:01.738204 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:01.738646 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:01.745425 INFO::Done
2026-04-13 18:32:01.745855 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:01.746759 INFO::ASW Batch was 0.0925418641490015 prior to batch effect correction and is now -0.119570749991389 .
2026-04-13 18:32:01.747351 INFO::Total function execution time is 0.0170271396636963 s and adjustment time is 0.00863194465637207 s ( 50.7 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-13 18:32:03.015381 INFO::Formatting Data.
2026-04-13 18:32:03.015835 INFO::Recognized SummarizedExperiment
2026-04-13 18:32:03.016144 INFO::Typecasting input to dataframe.
2026-04-13 18:32:03.02625 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.026846 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.028086 INFO::Found 0 missing values.
2026-04-13 18:32:03.030262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.030571 INFO::Done
2026-04-13 18:32:03.03085 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.032127 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.032455 INFO::Found 2 batches.
2026-04-13 18:32:03.032718 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.033158 INFO::Using default BPPARAM
2026-04-13 18:32:03.033418 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.033801 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-13 18:32:03.050185 INFO::Done
2026-04-13 18:32:03.050616 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.051928 INFO::ASW Batch was 0.00992901092009593 prior to batch effect correction and is now -0.0923649354504542 .
2026-04-13 18:32:03.052316 INFO::Total function execution time is 0.0370299816131592 s and adjustment time is 0.0177550315856934 s ( 47.95 )
Warning: stack imbalance in '{', 73 then 75
2026-04-13 18:32:03.059424 INFO::Formatting Data.
2026-04-13 18:32:03.060101 INFO::Recognized SummarizedExperiment
2026-04-13 18:32:03.060577 INFO::Typecasting input to dataframe.
2026-04-13 18:32:03.064187 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.064775 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.066101 INFO::Found 0 missing values.
2026-04-13 18:32:03.068538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.06888 INFO::Done
2026-04-13 18:32:03.069153 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.070502 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.070876 INFO::Found 2 batches.
2026-04-13 18:32:03.071139 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.071447 INFO::Using default BPPARAM
2026-04-13 18:32:03.071705 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.072127 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-13 18:32:03.080582 INFO::Done
2026-04-13 18:32:03.080967 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.082313 INFO::ASW Batch was -0.0217650684601888 prior to batch effect correction and is now -0.0217650684601888 .
2026-04-13 18:32:03.082725 INFO::Total function execution time is 0.0233151912689209 s and adjustment time is 0.00974392890930176 s ( 41.79 )
2026-04-13 18:32:03.08973 INFO::Formatting Data.
2026-04-13 18:32:03.090132 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.090542 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.091019 INFO::Found 0 missing values.
2026-04-13 18:32:03.092062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.092353 INFO::Done
2026-04-13 18:32:03.092616 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.093426 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.093759 INFO::Found 3 batches.
2026-04-13 18:32:03.094034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.094352 INFO::Using default BPPARAM
2026-04-13 18:32:03.094651 INFO::Processing subtree level 1
2026-04-13 18:32:03.26884 INFO::Adjusting the last 1 batches sequentially
2026-04-13 18:32:03.270495 INFO::Done
2026-04-13 18:32:03.27124 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.272952 INFO::ASW Batch was -0.0157197711743832 prior to batch effect correction and is now -0.161119408715562 .
2026-04-13 18:32:03.273652 INFO::Total function execution time is 0.183902978897095 s and adjustment time is 0.176780939102173 s ( 96.13 )
2026-04-13 18:32:03.281005 INFO::Skipping initial DF formatting
2026-04-13 18:32:03.28142 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.283497 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.284094 INFO::Found 5 batches.
2026-04-13 18:32:03.284416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.284777 INFO::Using default BPPARAM
2026-04-13 18:32:03.285065 INFO::Processing subtree level 1
2026-04-13 18:32:03.362887 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.364077 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-13 18:32:03.373733 INFO::Done
2026-04-13 18:32:03.374198 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.376282 INFO::ASW Batch was 0.48705050227633 prior to batch effect correction and is now 0.48705050227633 .
2026-04-13 18:32:03.376673 INFO::ASW Label was 0.399377491723307 prior to batch effect correction and is now 0.399377491723307 .
2026-04-13 18:32:03.377252 INFO::Total function execution time is 0.0962889194488525 s and adjustment time is 0.0897049903869629 s ( 93.16 )
2026-04-13 18:32:03.386124 INFO::Formatting Data.
2026-04-13 18:32:03.386571 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.387028 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.387515 INFO::Found 0 missing values.
2026-04-13 18:32:03.388856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.389179 INFO::Done
2026-04-13 18:32:03.38948 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.390564 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.390917 INFO::Found 5 batches.
2026-04-13 18:32:03.391202 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.391552 INFO::Using default BPPARAM
2026-04-13 18:32:03.391837 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.457916 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.458985 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.464752 INFO::Done
2026-04-13 18:32:03.465184 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.466444 INFO::ASW Batch was 0.462452158703588 prior to batch effect correction and is now -0.0900206736401141 .
2026-04-13 18:32:03.466766 INFO::ASW Label was 0.257991706964313 prior to batch effect correction and is now 0.828353916799032 .
2026-04-13 18:32:03.467186 INFO::Total function execution time is 0.0810930728912354 s and adjustment time is 0.0738778114318848 s ( 91.1 )
2026-04-13 18:32:03.467584 INFO::Formatting Data.
2026-04-13 18:32:03.467867 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.468269 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.468725 INFO::Found 0 missing values.
2026-04-13 18:32:03.469983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.470277 INFO::Done
2026-04-13 18:32:03.470535 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.4715 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.471835 INFO::Found 5 batches.
2026-04-13 18:32:03.472096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.472406 INFO::Using default BPPARAM
2026-04-13 18:32:03.472674 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.527966 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.528881 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.534784 INFO::Done
2026-04-13 18:32:03.535212 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.536501 INFO::ASW Batch was 0.462452158703588 prior to batch effect correction and is now -0.0900206736401141 .
2026-04-13 18:32:03.536821 INFO::ASW Label was 0.257991706964313 prior to batch effect correction and is now 0.828353916799032 .
2026-04-13 18:32:03.53722 INFO::Total function execution time is 0.0696158409118652 s and adjustment time is 0.062978982925415 s ( 90.47 )
2026-04-13 18:32:03.542784 INFO::Formatting Data.
2026-04-13 18:32:03.543162 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.543567 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.543993 INFO::Found 0 missing values.
2026-04-13 18:32:03.545296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.545643 INFO::Done
2026-04-13 18:32:03.545941 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.546963 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.547314 INFO::Found 5 batches.
2026-04-13 18:32:03.547593 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.547933 INFO::Using default BPPARAM
2026-04-13 18:32:03.548196 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.599055 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.600466 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.607009 INFO::Done
2026-04-13 18:32:03.607456 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.608809 INFO::ASW Batch was 0.264076638397206 prior to batch effect correction and is now -0.10099858548701 .
2026-04-13 18:32:03.609137 INFO::ASW Label was 0.462889221927516 prior to batch effect correction and is now 0.925107587588323 .
2026-04-13 18:32:03.609563 INFO::Total function execution time is 0.0667741298675537 s and adjustment time is 0.0597310066223145 s ( 89.45 )
2026-04-13 18:32:03.609996 INFO::Formatting Data.
2026-04-13 18:32:03.610317 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.610756 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.61122 INFO::Found 0 missing values.
2026-04-13 18:32:03.61254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.612842 INFO::Done
2026-04-13 18:32:03.613129 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.614157 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.614514 INFO::Found 5 batches.
2026-04-13 18:32:03.61479 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.615113 INFO::Using default BPPARAM
2026-04-13 18:32:03.61538 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.677 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.678126 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.684475 INFO::Done
2026-04-13 18:32:03.684955 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.686377 INFO::ASW Batch was 0.264076638397206 prior to batch effect correction and is now -0.10099858548701 .
2026-04-13 18:32:03.686751 INFO::ASW Label was 0.462889221927516 prior to batch effect correction and is now 0.925107587588323 .
2026-04-13 18:32:03.687254 INFO::Total function execution time is 0.0772061347961426 s and adjustment time is 0.0700027942657471 s ( 90.67 )
2026-04-13 18:32:03.6953 INFO::Formatting Data.
2026-04-13 18:32:03.696257 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.697525 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.698577 INFO::Found 0 missing values.
2026-04-13 18:32:03.701183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.701593 INFO::Done
2026-04-13 18:32:03.701938 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.704029 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.704468 INFO::Found 2 batches.
2026-04-13 18:32:03.704793 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.705175 INFO::Using default BPPARAM
2026-04-13 18:32:03.705478 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.706165 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.712028 INFO::Done
2026-04-13 18:32:03.712423 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.714266 INFO::ASW Batch was 0.620393493199843 prior to batch effect correction and is now -0.0347625535947931 .
2026-04-13 18:32:03.71516 INFO::ASW Label was 0.495741672224375 prior to batch effect correction and is now 0.918313553857226 .
2026-04-13 18:32:03.715969 INFO::Total function execution time is 0.0206339359283447 s and adjustment time is 0.00760293006896973 s ( 36.85 )
2026-04-13 18:32:03.716974 INFO::Formatting Data.
2026-04-13 18:32:03.717757 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.718466 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.719334 INFO::Found 0 missing values.
2026-04-13 18:32:03.722217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.723218 INFO::Done
2026-04-13 18:32:03.723962 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.726227 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.726697 INFO::Found 2 batches.
2026-04-13 18:32:03.726994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.727499 INFO::Using default BPPARAM
2026-04-13 18:32:03.727825 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.728476 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-13 18:32:03.73581 INFO::Done
2026-04-13 18:32:03.73626 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.737437 INFO::ASW Batch was 0.620393493199843 prior to batch effect correction and is now -0.0347625535947931 .
2026-04-13 18:32:03.737778 INFO::ASW Label was 0.495741672224375 prior to batch effect correction and is now 0.918313553857226 .
2026-04-13 18:32:03.73821 INFO::Total function execution time is 0.0212979316711426 s and adjustment time is 0.00914788246154785 s ( 42.95 )
2026-04-13 18:32:03.744516 INFO::Formatting Data.
2026-04-13 18:32:03.745489 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.746415 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.747395 INFO::Found 0 missing values.
2026-04-13 18:32:03.748967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.74946 INFO::Done
2026-04-13 18:32:03.749812 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.750682 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.75108 INFO::Found 2 batches.
2026-04-13 18:32:03.751416 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.751741 INFO::Using default BPPARAM
2026-04-13 18:32:03.752049 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.752473 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-13 18:32:03.762909 INFO::Done
2026-04-13 18:32:03.763348 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.764121 INFO::ASW Batch was 0.296496663006109 prior to batch effect correction and is now -0.105325347833184 .
2026-04-13 18:32:03.764567 INFO::Total function execution time is 0.0201668739318848 s and adjustment time is 0.0118730068206787 s ( 58.87 )
2026-04-13 18:32:03.769698 INFO::Formatting Data.
2026-04-13 18:32:03.77007 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.770507 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.770963 INFO::Found 0 missing values.
2026-04-13 18:32:03.771495 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-13 18:32:03.77301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.77341 INFO::Done
2026-04-13 18:32:03.773715 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.774729 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.775092 INFO::Found 2 batches.
2026-04-13 18:32:03.775435 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.775814 INFO::Using default BPPARAM
2026-04-13 18:32:03.776132 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.776573 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-13 18:32:03.781632 INFO::Done
2026-04-13 18:32:03.781995 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.782987 INFO::ASW Batch was 0.679446365342393 prior to batch effect correction and is now 0.245689840152652 .
2026-04-13 18:32:03.783337 INFO::ASW Label was 0.393446538620567 prior to batch effect correction and is now 0.583202863194807 .
2026-04-13 18:32:03.783734 INFO::Total function execution time is 0.0140519142150879 s and adjustment time is 0.00658106803894043 s ( 46.83 )
2026-04-13 18:32:03.784128 INFO::Formatting Data.
2026-04-13 18:32:03.784487 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.784928 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.785395 INFO::Found 0 missing values.
2026-04-13 18:32:03.785822 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-13 18:32:03.787264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.787586 INFO::Done
2026-04-13 18:32:03.787897 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.788864 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.789267 INFO::Found 2 batches.
2026-04-13 18:32:03.789571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.789871 INFO::Using default BPPARAM
2026-04-13 18:32:03.790205 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:03.790619 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-13 18:32:03.795615 INFO::Done
2026-04-13 18:32:03.795992 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:03.797 INFO::ASW Batch was 0.679446365342393 prior to batch effect correction and is now 0.245689840152652 .
2026-04-13 18:32:03.797327 INFO::ASW Label was 0.393446538620567 prior to batch effect correction and is now 0.583202863194807 .
2026-04-13 18:32:03.797681 INFO::Total function execution time is 0.0135509967803955 s and adjustment time is 0.00638699531555176 s ( 47.13 )
2026-04-13 18:32:03.895078 INFO::Formatting Data.
2026-04-13 18:32:03.895548 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:03.895987 INFO::Removing potential empty rows and columns
2026-04-13 18:32:03.896473 INFO::Found 0 missing values.
2026-04-13 18:32:03.897553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:03.89787 INFO::Done
2026-04-13 18:32:03.898177 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:03.89896 INFO::Starting hierarchical adjustment
2026-04-13 18:32:03.899331 INFO::Found 3 batches.
2026-04-13 18:32:03.899596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:03.899881 INFO::Using default BPPARAM
2026-04-13 18:32:03.900164 INFO::Processing subtree level 1
2026-04-13 18:32:03.995878 INFO::Adjusting the last 1 batches sequentially
2026-04-13 18:32:03.997831 INFO::Done
2026-04-13 18:32:03.998342 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:04.000008 INFO::ASW Batch was -0.081748009401653 prior to batch effect correction and is now -0.081748009401653 .
2026-04-13 18:32:04.000809 INFO::Total function execution time is 0.105719089508057 s and adjustment time is 0.0985338687896729 s ( 93.2 )
2026-04-13 18:32:04.00164 INFO::Formatting Data.
2026-04-13 18:32:04.00209 INFO::Typecasting input to dataframe.
2026-04-13 18:32:04.002653 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:04.003384 INFO::Removing potential empty rows and columns
2026-04-13 18:32:04.004309 INFO::Found 0 missing values.
2026-04-13 18:32:04.00637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:04.006826 INFO::Done
2026-04-13 18:32:04.007272 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:04.008592 INFO::Starting hierarchical adjustment
2026-04-13 18:32:04.009057 INFO::Found 3 batches.
2026-04-13 18:32:04.009399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:04.009817 INFO::Using default BPPARAM
2026-04-13 18:32:04.010178 INFO::Processing subtree level 1
2026-04-13 18:32:04.071974 INFO::Adjusting the last 1 batches sequentially
2026-04-13 18:32:04.073527 INFO::Done
2026-04-13 18:32:04.074276 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:04.076079 INFO::ASW Batch was -0.081748009401653 prior to batch effect correction and is now -0.081748009401653 .
2026-04-13 18:32:04.07719 INFO::Total function execution time is 0.0754859447479248 s and adjustment time is 0.0645480155944824 s ( 85.51 )
2026-04-13 18:32:04.085772 INFO::Formatting Data.
2026-04-13 18:32:04.086231 INFO::Typecasting input to dataframe.
2026-04-13 18:32:04.086915 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:04.088124 INFO::Removing potential empty rows and columns
2026-04-13 18:32:04.089331 INFO::Found 0 missing values.
2026-04-13 18:32:04.091087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:04.091567 INFO::Done
2026-04-13 18:32:04.091874 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:04.092739 INFO::Starting hierarchical adjustment
2026-04-13 18:32:04.093101 INFO::Found 3 batches.
2026-04-13 18:32:04.0934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:04.093826 INFO::Using default BPPARAM
2026-04-13 18:32:04.094111 INFO::Processing subtree level 1
2026-04-13 18:32:04.149234 INFO::Adjusting the last 1 batches sequentially
2026-04-13 18:32:04.150622 INFO::Done
2026-04-13 18:32:04.151139 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:04.152342 INFO::ASW Batch was -0.119700939602741 prior to batch effect correction and is now -0.119700939602741 .
2026-04-13 18:32:04.152864 INFO::Total function execution time is 0.0671179294586182 s and adjustment time is 0.0575709342956543 s ( 85.78 )
2026-04-13 18:32:04.236905 INFO::Formatting Data.
2026-04-13 18:32:04.237405 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:04.23801 INFO::Removing potential empty rows and columns
2026-04-13 18:32:04.239347 INFO::Found 1000 missing values.
2026-04-13 18:32:04.247638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:04.248073 INFO::Done
2026-04-13 18:32:04.248429 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:04.25075 INFO::Starting hierarchical adjustment
2026-04-13 18:32:04.251192 INFO::Found 10 batches.
2026-04-13 18:32:04.251531 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:04.251925 INFO::Using default BPPARAM
2026-04-13 18:32:04.25231 INFO::Processing subtree level 1
2026-04-13 18:32:04.348952 INFO::Processing subtree level 2
2026-04-13 18:32:04.434076 INFO::Adjusting the last 1 batches sequentially
2026-04-13 18:32:04.435511 INFO::Done
2026-04-13 18:32:04.435881 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:04.43858 INFO::ASW Batch was 0.470362422190826 prior to batch effect correction and is now 0.470362422190826 .
2026-04-13 18:32:04.439051 INFO::ASW Label was 0.368076816735339 prior to batch effect correction and is now 0.368076816735339 .
2026-04-13 18:32:04.439685 INFO::Total function execution time is 0.202749013900757 s and adjustment time is 0.184396982192993 s ( 90.95 )
2026-04-13 18:32:04.440291 INFO::Formatting Data.
2026-04-13 18:32:04.440776 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:04.441537 INFO::Removing potential empty rows and columns
2026-04-13 18:32:04.443209 INFO::Found 1000 missing values.
2026-04-13 18:32:04.454213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:04.454715 INFO::Done
2026-04-13 18:32:04.455157 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:04.457877 INFO::Starting hierarchical adjustment
2026-04-13 18:32:04.458696 INFO::Found 10 batches.
2026-04-13 18:32:04.878624 INFO::Set up parallel execution backend with 2 workers
2026-04-13 18:32:04.879127 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-13 18:32:05.454774 INFO::Adjusting the last 2 batches sequentially
2026-04-13 18:32:05.45561 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-13 18:32:05.461253 INFO::Done
2026-04-13 18:32:05.461667 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:05.463684 INFO::ASW Batch was 0.470362422190826 prior to batch effect correction and is now 0.470362422190826 .
2026-04-13 18:32:05.464 INFO::ASW Label was 0.368076816735339 prior to batch effect correction and is now 0.368076816735339 .
2026-04-13 18:32:05.464332 INFO::Total function execution time is 1.02408313751221 s and adjustment time is 1.00266909599304 s ( 97.91 )
2026-04-13 18:32:05.605477 INFO::Formatting Data.
2026-04-13 18:32:05.605937 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.606441 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.607212 INFO::Found 0 missing values.
2026-04-13 18:32:05.608839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.60918 INFO::Done
2026-04-13 18:32:05.609545 INFO::Acquiring quality metrics before batch effect correction.
2026-04-13 18:32:05.610662 INFO::Starting hierarchical adjustment
2026-04-13 18:32:05.611149 INFO::Found 3 batches.
2026-04-13 18:32:05.611595 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-13 18:32:05.611994 INFO::Using default BPPARAM
2026-04-13 18:32:05.612376 INFO::Processing subtree level 1
2026-04-13 18:32:05.672352 INFO::Adjusting the last 1 batches sequentially
2026-04-13 18:32:05.673742 INFO::Done
2026-04-13 18:32:05.674199 INFO::Acquiring quality metrics after batch effect correction.
2026-04-13 18:32:05.676019 INFO::ASW Batch was 0.240090541858831 prior to batch effect correction and is now -0.155553588555851 .
2026-04-13 18:32:05.676415 INFO::ASW Label was -0.204467334792862 prior to batch effect correction and is now -0.0558877783874074 .
2026-04-13 18:32:05.677086 INFO::Total function execution time is 0.071599006652832 s and adjustment time is 0.0626561641693115 s ( 87.51 )
2026-04-13 18:32:05.733091 INFO::Formatting Data.
2026-04-13 18:32:05.733583 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.734082 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.734591 INFO::Found 2 missing values.
2026-04-13 18:32:05.735661 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.735962 INFO::Done
2026-04-13 18:32:05.747086 INFO::Found NA in Reference column
2026-04-13 18:32:05.751128 INFO::Require at least two references per batch.
2026-04-13 18:32:05.760354 INFO::Formatting Data.
2026-04-13 18:32:05.760785 INFO::Recognized SummarizedExperiment
2026-04-13 18:32:05.761085 INFO::Typecasting input to dataframe.
2026-04-13 18:32:05.765118 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.765657 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.767064 INFO::Found 0 missing values.
2026-04-13 18:32:05.769718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.770045 INFO::Done
2026-04-13 18:32:05.775492 INFO::Formatting Data.
2026-04-13 18:32:05.775921 INFO::Recognized SummarizedExperiment
2026-04-13 18:32:05.776204 INFO::Typecasting input to dataframe.
2026-04-13 18:32:05.781975 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.782579 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.784005 INFO::Found 0 missing values.
2026-04-13 18:32:05.788343 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.788758 INFO::Done
2026-04-13 18:32:05.794929 INFO::Formatting Data.
2026-04-13 18:32:05.795362 INFO::Recognized SummarizedExperiment
2026-04-13 18:32:05.795695 INFO::Typecasting input to dataframe.
2026-04-13 18:32:05.801846 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.802355 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.802926 INFO::Found 0 missing values.
2026-04-13 18:32:05.803551 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-13 18:32:05.805659 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.80604 INFO::Done
2026-04-13 18:32:05.810993 INFO::Formatting Data.
2026-04-13 18:32:05.811379 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.811798 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.812252 INFO::Found 0 missing values.
2026-04-13 18:32:05.814254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.814716 INFO::Done
2026-04-13 18:32:05.820863 INFO::Formatting Data.
2026-04-13 18:32:05.821355 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.821892 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.822492 INFO::Found 0 missing values.
2026-04-13 18:32:05.823921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.824371 INFO::Done
2026-04-13 18:32:05.839747 INFO::Formatting Data.
2026-04-13 18:32:05.840304 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.840835 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.841407 INFO::Found 1 missing values.
2026-04-13 18:32:05.84249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.842838 INFO::Done
2026-04-13 18:32:05.85195 INFO::Formatting Data.
2026-04-13 18:32:05.852429 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.852871 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.853311 INFO::Found 2 missing values.
2026-04-13 18:32:05.853784 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-04-13 18:32:05.854881 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.855186 INFO::Done
2026-04-13 18:32:05.860429 INFO::Formatting Data.
2026-04-13 18:32:05.860941 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.861449 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.862015 INFO::Found 2 missing values.
2026-04-13 18:32:05.862797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.863143 INFO::Done
2026-04-13 18:32:05.868035 INFO::Formatting Data.
2026-04-13 18:32:05.868552 INFO::Typecasting input to dataframe.
2026-04-13 18:32:05.869062 INFO::Replacing NaNs with NAs.
2026-04-13 18:32:05.86955 INFO::Removing potential empty rows and columns
2026-04-13 18:32:05.870035 INFO::Found 0 missing values.
2026-04-13 18:32:05.871157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-13 18:32:05.871501 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.155 1.998 9.496
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.544 | 0.354 | 6.787 | |
| compute_asw | 0.009 | 0.000 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.004 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |