Yannis Schumann
| Snapshot Date: 2026-04-22 13:40 -0400 (Wed, 22 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 2026-04-23 11:40 -0400 (Thu, 23 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4783 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4701 |
| 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 170/2404 | 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: 2026-04-22 18:35:05 -0400 (Wed, 22 Apr 2026) |
| EndedAt: 2026-04-22 18:35:39 -0400 (Wed, 22 Apr 2026) |
| EllapsedTime: 33.4 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 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: 2026-04-22 22:35:05 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 9.909 0.489 7.212
* 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")
2026-04-22 18:35:31.214295 INFO::Formatting Data.
2026-04-22 18:35:31.216127 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:31.220474 INFO::Removing potential empty rows and columns
2026-04-22 18:35:31.328248 INFO::Found 0 missing values.
2026-04-22 18:35:31.329893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:31.3303 INFO::Done
2026-04-22 18:35:31.330659 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:31.336959 INFO::Starting hierarchical adjustment
2026-04-22 18:35:31.337405 INFO::Found 3 batches.
2026-04-22 18:35:31.337724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:31.338272 INFO::Using default BPPARAM
2026-04-22 18:35:31.338685 INFO::Processing subtree level 1
2026-04-22 18:35:31.401031 INFO::Adjusting the last 1 batches sequentially
2026-04-22 18:35:31.402357 INFO::Done
2026-04-22 18:35:31.402723 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:31.404321 INFO::ASW Batch was -0.0580412902901363 prior to batch effect correction and is now -0.0580412902901363 .
2026-04-22 18:35:31.40512 INFO::Total function execution time is 0.191320896148682 s and adjustment time is 0.0649979114532471 s ( 33.97 )
2026-04-22 18:35:31.412852 INFO::Formatting Data.
2026-04-22 18:35:31.413386 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:31.413901 INFO::Removing potential empty rows and columns
2026-04-22 18:35:31.41447 INFO::Found 0 missing values.
2026-04-22 18:35:31.41502 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.
2026-04-22 18:35:31.421135 INFO::Formatting Data.
2026-04-22 18:35:31.421662 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:31.42215 INFO::Removing potential empty rows and columns
2026-04-22 18:35:31.422701 INFO::Found 0 missing values.
2026-04-22 18:35:31.423203 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.
2026-04-22 18:35:31.430242 INFO::Formatting Data.
2026-04-22 18:35:31.430648 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:31.4311 INFO::Removing potential empty rows and columns
2026-04-22 18:35:31.431563 INFO::Found 0 missing values.
2026-04-22 18:35:31.431966 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.
2026-04-22 18:35:31.433599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:31.433946 INFO::Done
2026-04-22 18:35:31.434261 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:31.435185 INFO::Starting hierarchical adjustment
2026-04-22 18:35:31.435598 INFO::Found 2 batches.
2026-04-22 18:35:31.435947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:31.439041 INFO::Using default BPPARAM
2026-04-22 18:35:31.439449 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:31.440015 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-22 18:35:31.44917 INFO::Done
2026-04-22 18:35:31.449604 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:31.450451 INFO::ASW Batch was 0.13856817512441 prior to batch effect correction and is now -0.122340883020958 .
2026-04-22 18:35:31.450839 INFO::Total function execution time is 0.0206260681152344 s and adjustment time is 0.0136270523071289 s ( 66.07 )
2026-04-22 18:35:31.452162 INFO::Formatting Data.
2026-04-22 18:35:31.452555 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:31.455854 INFO::Formatting Data.
2026-04-22 18:35:31.456229 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:31.456684 INFO::Removing potential empty rows and columns
2026-04-22 18:35:31.457183 INFO::Found 0 missing values.
2026-04-22 18:35:31.458276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:31.458596 INFO::Done
2026-04-22 18:35:31.458886 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:31.459643 INFO::Starting hierarchical adjustment
2026-04-22 18:35:31.460032 INFO::Found 2 batches.
2026-04-22 18:35:31.460334 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:31.460665 INFO::Using default BPPARAM
2026-04-22 18:35:31.460949 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:31.461363 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-22 18:35:31.467342 INFO::Done
2026-04-22 18:35:31.467699 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:31.468455 INFO::ASW Batch was 0.091502738630668 prior to batch effect correction and is now -0.109464801985454 .
2026-04-22 18:35:31.468824 INFO::Total function execution time is 0.012962818145752 s and adjustment time is 0.0073549747467041 s ( 56.74 )
2026-04-22 18:35:31.469412 INFO::Formatting Data.
2026-04-22 18:35:31.469778 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:31.470166 INFO::Removing potential empty rows and columns
2026-04-22 18:35:31.470613 INFO::Found 0 missing values.
2026-04-22 18:35:31.471704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:31.472021 INFO::Done
2026-04-22 18:35:31.472338 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:31.473204 INFO::Starting hierarchical adjustment
2026-04-22 18:35:31.473567 INFO::Found 2 batches.
2026-04-22 18:35:31.473927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:31.474281 INFO::Using default BPPARAM
2026-04-22 18:35:31.474579 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:31.475015 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-22 18:35:31.479811 INFO::Done
2026-04-22 18:35:31.48019 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:31.480896 INFO::ASW Batch was 0.091502738630668 prior to batch effect correction and is now -0.109464801985454 .
2026-04-22 18:35:31.48124 INFO::Total function execution time is 0.0118279457092285 s and adjustment time is 0.00629782676696777 s ( 53.25 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-22 18:35:32.731224 INFO::Formatting Data.
2026-04-22 18:35:32.731669 INFO::Recognized SummarizedExperiment
2026-04-22 18:35:32.731987 INFO::Typecasting input to dataframe.
2026-04-22 18:35:32.741927 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:32.742476 INFO::Removing potential empty rows and columns
2026-04-22 18:35:32.743651 INFO::Found 0 missing values.
2026-04-22 18:35:32.745791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:32.746081 INFO::Done
2026-04-22 18:35:32.746346 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:32.747575 INFO::Starting hierarchical adjustment
2026-04-22 18:35:32.747894 INFO::Found 2 batches.
2026-04-22 18:35:32.748186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:32.748597 INFO::Using default BPPARAM
2026-04-22 18:35:32.748899 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:32.749306 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-22 18:35:32.76536 INFO::Done
2026-04-22 18:35:32.76582 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:32.767211 INFO::ASW Batch was -0.00400534317288536 prior to batch effect correction and is now -0.0854827633769974 .
2026-04-22 18:35:32.767617 INFO::Total function execution time is 0.0364959239959717 s and adjustment time is 0.0174949169158936 s ( 47.94 )
Warning: stack imbalance in '{', 73 then 75
2026-04-22 18:35:32.773882 INFO::Formatting Data.
2026-04-22 18:35:32.774253 INFO::Recognized SummarizedExperiment
2026-04-22 18:35:32.774551 INFO::Typecasting input to dataframe.
2026-04-22 18:35:32.777356 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:32.777834 INFO::Removing potential empty rows and columns
2026-04-22 18:35:32.778992 INFO::Found 0 missing values.
2026-04-22 18:35:32.781091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:32.781374 INFO::Done
2026-04-22 18:35:32.781637 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:32.782841 INFO::Starting hierarchical adjustment
2026-04-22 18:35:32.783157 INFO::Found 2 batches.
2026-04-22 18:35:32.78341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:32.783687 INFO::Using default BPPARAM
2026-04-22 18:35:32.783948 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:32.784319 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-22 18:35:32.792118 INFO::Done
2026-04-22 18:35:32.792474 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:32.793728 INFO::ASW Batch was -0.0121398042102556 prior to batch effect correction and is now -0.0121398042102556 .
2026-04-22 18:35:32.794122 INFO::Total function execution time is 0.0202288627624512 s and adjustment time is 0.00899291038513184 s ( 44.46 )
2026-04-22 18:35:32.800762 INFO::Formatting Data.
2026-04-22 18:35:32.801161 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:32.801556 INFO::Removing potential empty rows and columns
2026-04-22 18:35:32.801994 INFO::Found 0 missing values.
2026-04-22 18:35:32.802984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:32.803308 INFO::Done
2026-04-22 18:35:32.80359 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:32.804296 INFO::Starting hierarchical adjustment
2026-04-22 18:35:32.804625 INFO::Found 3 batches.
2026-04-22 18:35:32.80491 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:32.805194 INFO::Using default BPPARAM
2026-04-22 18:35:32.805481 INFO::Processing subtree level 1
2026-04-22 18:35:32.924792 INFO::Adjusting the last 1 batches sequentially
2026-04-22 18:35:32.926036 INFO::Done
2026-04-22 18:35:32.926424 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:32.927879 INFO::ASW Batch was -0.0578435964128004 prior to batch effect correction and is now -0.165498950470759 .
2026-04-22 18:35:32.928494 INFO::Total function execution time is 0.127721786499023 s and adjustment time is 0.121437072753906 s ( 95.08 )
2026-04-22 18:35:32.936185 INFO::Skipping initial DF formatting
2026-04-22 18:35:32.936654 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:32.938222 INFO::Starting hierarchical adjustment
2026-04-22 18:35:32.938638 INFO::Found 5 batches.
2026-04-22 18:35:32.938943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:32.939279 INFO::Using default BPPARAM
2026-04-22 18:35:32.939567 INFO::Processing subtree level 1
2026-04-22 18:35:33.004017 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.005039 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-22 18:35:33.012657 INFO::Done
2026-04-22 18:35:33.013073 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.014798 INFO::ASW Batch was 0.484606903502452 prior to batch effect correction and is now 0.484606903502452 .
2026-04-22 18:35:33.015131 INFO::ASW Label was 0.410944648773083 prior to batch effect correction and is now 0.410944648773083 .
2026-04-22 18:35:33.015646 INFO::Total function execution time is 0.0794708728790283 s and adjustment time is 0.0740640163421631 s ( 93.2 )
2026-04-22 18:35:33.022571 INFO::Formatting Data.
2026-04-22 18:35:33.022964 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.0234 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.023844 INFO::Found 0 missing values.
2026-04-22 18:35:33.025088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.025402 INFO::Done
2026-04-22 18:35:33.025665 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.026659 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.02699 INFO::Found 5 batches.
2026-04-22 18:35:33.027244 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.027549 INFO::Using default BPPARAM
2026-04-22 18:35:33.027817 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.
2026-04-22 18:35:33.092179 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.093333 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-22 18:35:33.100885 INFO::Done
2026-04-22 18:35:33.101351 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.102796 INFO::ASW Batch was 0.289405062743489 prior to batch effect correction and is now -0.0358383473965499 .
2026-04-22 18:35:33.103158 INFO::ASW Label was 0.516766535665718 prior to batch effect correction and is now 0.805620354595278 .
2026-04-22 18:35:33.103638 INFO::Total function execution time is 0.0810539722442627 s and adjustment time is 0.0739288330078125 s ( 91.21 )
2026-04-22 18:35:33.104094 INFO::Formatting Data.
2026-04-22 18:35:33.104413 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.104861 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.105337 INFO::Found 0 missing values.
2026-04-22 18:35:33.106647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.106947 INFO::Done
2026-04-22 18:35:33.107261 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.108361 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.10876 INFO::Found 5 batches.
2026-04-22 18:35:33.109096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.109479 INFO::Using default BPPARAM
2026-04-22 18:35:33.109815 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.
2026-04-22 18:35:33.171051 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.172202 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-22 18:35:33.178912 INFO::Done
2026-04-22 18:35:33.179402 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.180746 INFO::ASW Batch was 0.289405062743489 prior to batch effect correction and is now -0.0358383473965499 .
2026-04-22 18:35:33.181102 INFO::ASW Label was 0.516766535665718 prior to batch effect correction and is now 0.805620354595278 .
2026-04-22 18:35:33.181521 INFO::Total function execution time is 0.0774068832397461 s and adjustment time is 0.0701828002929688 s ( 90.67 )
2026-04-22 18:35:33.18754 INFO::Formatting Data.
2026-04-22 18:35:33.18799 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.188391 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.188863 INFO::Found 0 missing values.
2026-04-22 18:35:33.190169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.190496 INFO::Done
2026-04-22 18:35:33.190805 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.191926 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.192305 INFO::Found 5 batches.
2026-04-22 18:35:33.192616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.192954 INFO::Using default BPPARAM
2026-04-22 18:35:33.19326 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.
2026-04-22 18:35:33.246945 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.248464 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-22 18:35:33.255036 INFO::Done
2026-04-22 18:35:33.255543 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.256823 INFO::ASW Batch was 0.216858523889171 prior to batch effect correction and is now 0.014593829058872 .
2026-04-22 18:35:33.257157 INFO::ASW Label was 0.577414565502332 prior to batch effect correction and is now 0.785490377279503 .
2026-04-22 18:35:33.257546 INFO::Total function execution time is 0.0700290203094482 s and adjustment time is 0.0627598762512207 s ( 89.62 )
2026-04-22 18:35:33.25794 INFO::Formatting Data.
2026-04-22 18:35:33.258234 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.258632 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.259048 INFO::Found 0 missing values.
2026-04-22 18:35:33.260334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.260641 INFO::Done
2026-04-22 18:35:33.260904 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.261967 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.262358 INFO::Found 5 batches.
2026-04-22 18:35:33.262626 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.262923 INFO::Using default BPPARAM
2026-04-22 18:35:33.263176 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.
2026-04-22 18:35:33.320705 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.322165 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-22 18:35:33.327873 INFO::Done
2026-04-22 18:35:33.328262 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.330805 INFO::ASW Batch was 0.216858523889171 prior to batch effect correction and is now 0.014593829058872 .
2026-04-22 18:35:33.331774 INFO::ASW Label was 0.577414565502332 prior to batch effect correction and is now 0.785490377279503 .
2026-04-22 18:35:33.332719 INFO::Total function execution time is 0.0746870040893555 s and adjustment time is 0.0655529499053955 s ( 87.77 )
2026-04-22 18:35:33.339523 INFO::Formatting Data.
2026-04-22 18:35:33.33994 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.340371 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.34086 INFO::Found 0 missing values.
2026-04-22 18:35:33.341806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.342111 INFO::Done
2026-04-22 18:35:33.342379 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.343536 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.343947 INFO::Found 2 batches.
2026-04-22 18:35:33.34423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.344559 INFO::Using default BPPARAM
2026-04-22 18:35:33.34486 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.345255 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-22 18:35:33.350194 INFO::Done
2026-04-22 18:35:33.350624 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.351686 INFO::ASW Batch was 0.58796346406983 prior to batch effect correction and is now -0.0270155093171416 .
2026-04-22 18:35:33.352026 INFO::ASW Label was 0.478014084756851 prior to batch effect correction and is now 0.902655584889465 .
2026-04-22 18:35:33.352477 INFO::Total function execution time is 0.0129818916320801 s and adjustment time is 0.00629615783691406 s ( 48.5 )
2026-04-22 18:35:33.352919 INFO::Formatting Data.
2026-04-22 18:35:33.353265 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.353672 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.354092 INFO::Found 0 missing values.
2026-04-22 18:35:33.355045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.355343 INFO::Done
2026-04-22 18:35:33.355641 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.356667 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.357022 INFO::Found 2 batches.
2026-04-22 18:35:33.357316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.357622 INFO::Using default BPPARAM
2026-04-22 18:35:33.357882 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.358262 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-22 18:35:33.363102 INFO::Done
2026-04-22 18:35:33.363489 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.364511 INFO::ASW Batch was 0.58796346406983 prior to batch effect correction and is now -0.0270155093171416 .
2026-04-22 18:35:33.364812 INFO::ASW Label was 0.478014084756851 prior to batch effect correction and is now 0.902655584889465 .
2026-04-22 18:35:33.365176 INFO::Total function execution time is 0.0122470855712891 s and adjustment time is 0.00612497329711914 s ( 50.01 )
2026-04-22 18:35:33.369646 INFO::Formatting Data.
2026-04-22 18:35:33.370002 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.370382 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.370773 INFO::Found 0 missing values.
2026-04-22 18:35:33.37152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.371793 INFO::Done
2026-04-22 18:35:33.37207 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.372764 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.373082 INFO::Found 2 batches.
2026-04-22 18:35:33.373351 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.373643 INFO::Using default BPPARAM
2026-04-22 18:35:33.373928 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.374296 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-22 18:35:33.385138 INFO::Done
2026-04-22 18:35:33.385612 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.386409 INFO::ASW Batch was -0.0859114969876078 prior to batch effect correction and is now -0.082202562686421 .
2026-04-22 18:35:33.386818 INFO::Total function execution time is 0.0171780586242676 s and adjustment time is 0.0120790004730225 s ( 70.32 )
2026-04-22 18:35:33.391623 INFO::Formatting Data.
2026-04-22 18:35:33.391984 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.392371 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.392784 INFO::Found 0 missing values.
2026-04-22 18:35:33.393325 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.
2026-04-22 18:35:33.394824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.395115 INFO::Done
2026-04-22 18:35:33.395398 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.396437 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.396785 INFO::Found 2 batches.
2026-04-22 18:35:33.39707 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.397365 INFO::Using default BPPARAM
2026-04-22 18:35:33.39763 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.398068 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-22 18:35:33.40387 INFO::Done
2026-04-22 18:35:33.404365 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.405514 INFO::ASW Batch was 0.609383007579268 prior to batch effect correction and is now -0.035104108168667 .
2026-04-22 18:35:33.405906 INFO::ASW Label was 0.45547488463868 prior to batch effect correction and is now 0.911723696968361 .
2026-04-22 18:35:33.406383 INFO::Total function execution time is 0.0147781372070312 s and adjustment time is 0.00710916519165039 s ( 48.11 )
2026-04-22 18:35:33.406808 INFO::Formatting Data.
2026-04-22 18:35:33.407163 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.407598 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.408043 INFO::Found 0 missing values.
2026-04-22 18:35:33.408485 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.
2026-04-22 18:35:33.409979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.410315 INFO::Done
2026-04-22 18:35:33.410587 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.411661 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.412035 INFO::Found 2 batches.
2026-04-22 18:35:33.412316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.412666 INFO::Using default BPPARAM
2026-04-22 18:35:33.412947 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:33.413362 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-22 18:35:33.419579 INFO::Done
2026-04-22 18:35:33.420155 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.421321 INFO::ASW Batch was 0.609383007579268 prior to batch effect correction and is now -0.035104108168667 .
2026-04-22 18:35:33.421718 INFO::ASW Label was 0.45547488463868 prior to batch effect correction and is now 0.911723696968361 .
2026-04-22 18:35:33.422158 INFO::Total function execution time is 0.0153429508209229 s and adjustment time is 0.00754714012145996 s ( 49.19 )
2026-04-22 18:35:33.488162 INFO::Formatting Data.
2026-04-22 18:35:33.488657 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.489104 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.489598 INFO::Found 0 missing values.
2026-04-22 18:35:33.490673 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.491002 INFO::Done
2026-04-22 18:35:33.491319 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.492175 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.492559 INFO::Found 3 batches.
2026-04-22 18:35:33.492916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.493264 INFO::Using default BPPARAM
2026-04-22 18:35:33.493556 INFO::Processing subtree level 1
2026-04-22 18:35:33.551037 INFO::Adjusting the last 1 batches sequentially
2026-04-22 18:35:33.552074 INFO::Done
2026-04-22 18:35:33.552376 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.553388 INFO::ASW Batch was -0.107678408380824 prior to batch effect correction and is now -0.107678408380824 .
2026-04-22 18:35:33.553865 INFO::Total function execution time is 0.0657520294189453 s and adjustment time is 0.0595598220825195 s ( 90.58 )
2026-04-22 18:35:33.55434 INFO::Formatting Data.
2026-04-22 18:35:33.55464 INFO::Typecasting input to dataframe.
2026-04-22 18:35:33.554985 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.555389 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.555846 INFO::Found 0 missing values.
2026-04-22 18:35:33.556871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.557249 INFO::Done
2026-04-22 18:35:33.557542 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.558307 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.558669 INFO::Found 3 batches.
2026-04-22 18:35:33.558969 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.559303 INFO::Using default BPPARAM
2026-04-22 18:35:33.559608 INFO::Processing subtree level 1
2026-04-22 18:35:33.610088 INFO::Adjusting the last 1 batches sequentially
2026-04-22 18:35:33.612682 INFO::Done
2026-04-22 18:35:33.613562 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.615376 INFO::ASW Batch was -0.107678408380824 prior to batch effect correction and is now -0.107678408380824 .
2026-04-22 18:35:33.615998 INFO::Total function execution time is 0.0616168975830078 s and adjustment time is 0.0540480613708496 s ( 87.72 )
2026-04-22 18:35:33.624543 INFO::Formatting Data.
2026-04-22 18:35:33.624954 INFO::Typecasting input to dataframe.
2026-04-22 18:35:33.625377 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.625826 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.626321 INFO::Found 0 missing values.
2026-04-22 18:35:33.627617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.627955 INFO::Done
2026-04-22 18:35:33.628243 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.629382 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.630257 INFO::Found 3 batches.
2026-04-22 18:35:33.630706 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.631124 INFO::Using default BPPARAM
2026-04-22 18:35:33.631587 INFO::Processing subtree level 1
2026-04-22 18:35:33.682179 INFO::Adjusting the last 1 batches sequentially
2026-04-22 18:35:33.683592 INFO::Done
2026-04-22 18:35:33.683955 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.685326 INFO::ASW Batch was -0.0576296394313588 prior to batch effect correction and is now -0.0576296394313588 .
2026-04-22 18:35:33.685974 INFO::Total function execution time is 0.0614218711853027 s and adjustment time is 0.0535869598388672 s ( 87.24 )
2026-04-22 18:35:33.758868 INFO::Formatting Data.
2026-04-22 18:35:33.759307 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.75978 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.760787 INFO::Found 1000 missing values.
2026-04-22 18:35:33.766466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.766849 INFO::Done
2026-04-22 18:35:33.767141 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.769131 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.769526 INFO::Found 10 batches.
2026-04-22 18:35:33.76985 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:33.770208 INFO::Using default BPPARAM
2026-04-22 18:35:33.770514 INFO::Processing subtree level 1
2026-04-22 18:35:33.843074 INFO::Processing subtree level 2
2026-04-22 18:35:33.909288 INFO::Adjusting the last 1 batches sequentially
2026-04-22 18:35:33.910532 INFO::Done
2026-04-22 18:35:33.910916 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:33.913255 INFO::ASW Batch was 0.553927855348656 prior to batch effect correction and is now 0.553927855348656 .
2026-04-22 18:35:33.913608 INFO::ASW Label was 0.265545967638931 prior to batch effect correction and is now 0.265545967638931 .
2026-04-22 18:35:33.914059 INFO::Total function execution time is 0.155202150344849 s and adjustment time is 0.141041994094849 s ( 90.88 )
2026-04-22 18:35:33.914434 INFO::Formatting Data.
2026-04-22 18:35:33.914732 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:33.915203 INFO::Removing potential empty rows and columns
2026-04-22 18:35:33.916149 INFO::Found 1000 missing values.
2026-04-22 18:35:33.921841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:33.922181 INFO::Done
2026-04-22 18:35:33.922484 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:33.924391 INFO::Starting hierarchical adjustment
2026-04-22 18:35:33.924764 INFO::Found 10 batches.
2026-04-22 18:35:34.341264 INFO::Set up parallel execution backend with 2 workers
2026-04-22 18:35:34.341744 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-22 18:35:34.894506 INFO::Adjusting the last 2 batches sequentially
2026-04-22 18:35:34.895406 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-22 18:35:34.901944 INFO::Done
2026-04-22 18:35:34.902349 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:34.904617 INFO::ASW Batch was 0.553927855348656 prior to batch effect correction and is now 0.553927855348656 .
2026-04-22 18:35:34.904942 INFO::ASW Label was 0.265545967638931 prior to batch effect correction and is now 0.265545967638931 .
2026-04-22 18:35:34.905338 INFO::Total function execution time is 0.990903854370117 s and adjustment time is 0.977213859558105 s ( 98.62 )
2026-04-22 18:35:35.055109 INFO::Formatting Data.
2026-04-22 18:35:35.055529 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.055974 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.056509 INFO::Found 0 missing values.
2026-04-22 18:35:35.05788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.058184 INFO::Done
2026-04-22 18:35:35.058462 INFO::Acquiring quality metrics before batch effect correction.
2026-04-22 18:35:35.059517 INFO::Starting hierarchical adjustment
2026-04-22 18:35:35.059884 INFO::Found 3 batches.
2026-04-22 18:35:35.060167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-22 18:35:35.060499 INFO::Using default BPPARAM
2026-04-22 18:35:35.060784 INFO::Processing subtree level 1
2026-04-22 18:35:35.127535 INFO::Adjusting the last 1 batches sequentially
2026-04-22 18:35:35.128876 INFO::Done
2026-04-22 18:35:35.129394 INFO::Acquiring quality metrics after batch effect correction.
2026-04-22 18:35:35.131205 INFO::ASW Batch was 0.183125103789914 prior to batch effect correction and is now -0.134800970872983 .
2026-04-22 18:35:35.131662 INFO::ASW Label was -0.152101626333186 prior to batch effect correction and is now 0.081838942169394 .
2026-04-22 18:35:35.132295 INFO::Total function execution time is 0.0771570205688477 s and adjustment time is 0.0690319538116455 s ( 89.47 )
2026-04-22 18:35:35.186498 INFO::Formatting Data.
2026-04-22 18:35:35.186966 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.18756 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.188239 INFO::Found 2 missing values.
2026-04-22 18:35:35.189373 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.189767 INFO::Done
2026-04-22 18:35:35.200602 INFO::Found NA in Reference column
2026-04-22 18:35:35.204389 INFO::Require at least two references per batch.
2026-04-22 18:35:35.212023 INFO::Formatting Data.
2026-04-22 18:35:35.212437 INFO::Recognized SummarizedExperiment
2026-04-22 18:35:35.212736 INFO::Typecasting input to dataframe.
2026-04-22 18:35:35.216476 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.217025 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.218368 INFO::Found 0 missing values.
2026-04-22 18:35:35.220794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.221139 INFO::Done
2026-04-22 18:35:35.227943 INFO::Formatting Data.
2026-04-22 18:35:35.22839 INFO::Recognized SummarizedExperiment
2026-04-22 18:35:35.228738 INFO::Typecasting input to dataframe.
2026-04-22 18:35:35.235737 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.236332 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.238097 INFO::Found 0 missing values.
2026-04-22 18:35:35.242225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.24275 INFO::Done
2026-04-22 18:35:35.248556 INFO::Formatting Data.
2026-04-22 18:35:35.24898 INFO::Recognized SummarizedExperiment
2026-04-22 18:35:35.249266 INFO::Typecasting input to dataframe.
2026-04-22 18:35:35.254456 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.254973 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.255467 INFO::Found 0 missing values.
2026-04-22 18:35:35.255904 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.
2026-04-22 18:35:35.257488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.257818 INFO::Done
2026-04-22 18:35:35.262229 INFO::Formatting Data.
2026-04-22 18:35:35.262644 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.263062 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.263522 INFO::Found 0 missing values.
2026-04-22 18:35:35.264598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.264939 INFO::Done
2026-04-22 18:35:35.271488 INFO::Formatting Data.
2026-04-22 18:35:35.272023 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.272506 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.273009 INFO::Found 0 missing values.
2026-04-22 18:35:35.274148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.274505 INFO::Done
2026-04-22 18:35:35.287881 INFO::Formatting Data.
2026-04-22 18:35:35.288397 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.288912 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.289478 INFO::Found 1 missing values.
2026-04-22 18:35:35.290612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.290937 INFO::Done
2026-04-22 18:35:35.299075 INFO::Formatting Data.
2026-04-22 18:35:35.299503 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.299941 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.300401 INFO::Found 2 missing values.
2026-04-22 18:35:35.300874 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.
2026-04-22 18:35:35.301863 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.302205 INFO::Done
2026-04-22 18:35:35.307103 INFO::Formatting Data.
2026-04-22 18:35:35.30755 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.307973 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.308403 INFO::Found 2 missing values.
2026-04-22 18:35:35.309109 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.309412 INFO::Done
2026-04-22 18:35:35.3142 INFO::Formatting Data.
2026-04-22 18:35:35.314655 INFO::Typecasting input to dataframe.
2026-04-22 18:35:35.315064 INFO::Replacing NaNs with NAs.
2026-04-22 18:35:35.3155 INFO::Removing potential empty rows and columns
2026-04-22 18:35:35.316258 INFO::Found 0 missing values.
2026-04-22 18:35:35.317853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-22 18:35:35.318295 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.117 1.680 9.004
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.909 | 0.489 | 7.212 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.000 | 0.005 | |
| generate_data_covariables | 0.004 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |