Yannis Schumann
| Snapshot Date: 2025-11-20 15:01 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-24 12:06 -0500 (Mon, 24 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4873 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4654 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4600 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-11-21 16:24:43 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 16:26:35 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 112.1 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* 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 29.739 1.17 30.606
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-11-21 16:26:07.941845 INFO::Formatting Data.
2025-11-21 16:26:07.947663 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:07.959898 INFO::Removing potential empty rows and columns
2025-11-21 16:26:08.385764 INFO::Found 0 missing values.
2025-11-21 16:26:08.389176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:08.389801 INFO::Done
2025-11-21 16:26:08.390369 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:08.406484 INFO::Starting hierarchical adjustment
2025-11-21 16:26:08.407597 INFO::Found 3 batches.
2025-11-21 16:26:08.408166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:08.40951 INFO::Using default BPPARAM
2025-11-21 16:26:08.410266 INFO::Processing subtree level 1
2025-11-21 16:26:08.564597 INFO::Adjusting the last 1 batches sequentially
2025-11-21 16:26:08.568541 INFO::Done
2025-11-21 16:26:08.569215 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:08.572829 INFO::ASW Batch was -0.0588343111492567 prior to batch effect correction and is now -0.0588343111492567 .
2025-11-21 16:26:08.579678 INFO::Total function execution time is 0.633606910705566 s and adjustment time is 0.161128997802734 s ( 25.43 )
2025-11-21 16:26:08.604402 INFO::Formatting Data.
2025-11-21 16:26:08.605485 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:08.606874 INFO::Removing potential empty rows and columns
2025-11-21 16:26:08.608888 INFO::Found 0 missing values.
2025-11-21 16:26:08.610166 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.
2025-11-21 16:26:08.623362 INFO::Formatting Data.
2025-11-21 16:26:08.624255 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:08.6253 INFO::Removing potential empty rows and columns
2025-11-21 16:26:08.626475 INFO::Found 0 missing values.
2025-11-21 16:26:08.627529 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.
2025-11-21 16:26:08.65055 INFO::Formatting Data.
2025-11-21 16:26:08.65162 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:08.652748 INFO::Removing potential empty rows and columns
2025-11-21 16:26:08.654111 INFO::Found 0 missing values.
2025-11-21 16:26:08.655244 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.
2025-11-21 16:26:08.660431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:08.661217 INFO::Done
2025-11-21 16:26:08.66182 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:08.6642 INFO::Starting hierarchical adjustment
2025-11-21 16:26:08.665 INFO::Found 2 batches.
2025-11-21 16:26:08.665557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:08.666261 INFO::Using default BPPARAM
2025-11-21 16:26:08.666776 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:08.66778 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 16:26:08.693559 INFO::Done
2025-11-21 16:26:08.694453 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:08.696875 INFO::ASW Batch was 0.0335802838431724 prior to batch effect correction and is now -0.0851219915643005 .
2025-11-21 16:26:08.698064 INFO::Total function execution time is 0.0476300716400146 s and adjustment time is 0.0286200046539307 s ( 60.09 )
2025-11-21 16:26:08.701523 INFO::Formatting Data.
2025-11-21 16:26:08.702203 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:08.713195 INFO::Formatting Data.
2025-11-21 16:26:08.71431 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:08.715581 INFO::Removing potential empty rows and columns
2025-11-21 16:26:08.716967 INFO::Found 0 missing values.
2025-11-21 16:26:08.720909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:08.721868 INFO::Done
2025-11-21 16:26:08.722484 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:08.725145 INFO::Starting hierarchical adjustment
2025-11-21 16:26:08.787245 INFO::Found 2 batches.
2025-11-21 16:26:08.788081 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:08.788678 INFO::Using default BPPARAM
2025-11-21 16:26:08.789133 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:08.790051 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 16:26:08.812428 INFO::Done
2025-11-21 16:26:08.813186 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:08.815216 INFO::ASW Batch was 0.0439187155290515 prior to batch effect correction and is now -0.127238004126698 .
2025-11-21 16:26:08.815995 INFO::Total function execution time is 0.102963924407959 s and adjustment time is 0.0863561630249023 s ( 83.87 )
2025-11-21 16:26:08.816885 INFO::Formatting Data.
2025-11-21 16:26:08.817399 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:08.818166 INFO::Removing potential empty rows and columns
2025-11-21 16:26:08.819066 INFO::Found 0 missing values.
2025-11-21 16:26:08.821592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:08.822164 INFO::Done
2025-11-21 16:26:08.822644 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:08.824608 INFO::Starting hierarchical adjustment
2025-11-21 16:26:08.825308 INFO::Found 2 batches.
2025-11-21 16:26:08.830436 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:08.831344 INFO::Using default BPPARAM
2025-11-21 16:26:08.831862 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:08.833148 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 16:26:08.852458 INFO::Done
2025-11-21 16:26:08.85326 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:08.855371 INFO::ASW Batch was 0.0439187155290515 prior to batch effect correction and is now -0.127238004126698 .
2025-11-21 16:26:08.856155 INFO::Total function execution time is 0.0392410755157471 s and adjustment time is 0.0272319316864014 s ( 69.4 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-21 16:26:13.52734 INFO::Formatting Data.
2025-11-21 16:26:13.528182 INFO::Recognized SummarizedExperiment
2025-11-21 16:26:13.528715 INFO::Typecasting input to dataframe.
2025-11-21 16:26:13.572605 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:13.57422 INFO::Removing potential empty rows and columns
2025-11-21 16:26:13.578091 INFO::Found 0 missing values.
2025-11-21 16:26:13.585036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:13.585683 INFO::Done
2025-11-21 16:26:13.586167 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:13.58985 INFO::Starting hierarchical adjustment
2025-11-21 16:26:13.590559 INFO::Found 2 batches.
2025-11-21 16:26:13.591044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:13.594512 INFO::Using default BPPARAM
2025-11-21 16:26:13.595426 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:13.59691 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 16:26:13.681336 INFO::Done
2025-11-21 16:26:13.682185 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:13.686136 INFO::ASW Batch was 0.0289551047476176 prior to batch effect correction and is now -0.090324538368487 .
2025-11-21 16:26:13.687363 INFO::Total function execution time is 0.160296201705933 s and adjustment time is 0.0908241271972656 s ( 56.66 )
Warning: stack imbalance in '{', 73 then 74
2025-11-21 16:26:13.715288 INFO::Formatting Data.
2025-11-21 16:26:13.716158 INFO::Recognized SummarizedExperiment
2025-11-21 16:26:13.716669 INFO::Typecasting input to dataframe.
2025-11-21 16:26:13.726641 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:13.72802 INFO::Removing potential empty rows and columns
2025-11-21 16:26:13.740127 INFO::Found 0 missing values.
2025-11-21 16:26:13.776616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:13.778535 INFO::Done
2025-11-21 16:26:13.780378 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:13.785572 INFO::Starting hierarchical adjustment
2025-11-21 16:26:13.786518 INFO::Found 2 batches.
2025-11-21 16:26:13.787075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:13.787681 INFO::Using default BPPARAM
2025-11-21 16:26:13.788164 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:13.789251 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 16:26:13.824216 INFO::Done
2025-11-21 16:26:13.82521 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:13.82909 INFO::ASW Batch was -0.00277717117827838 prior to batch effect correction and is now -0.00277717117827838 .
2025-11-21 16:26:13.830057 INFO::Total function execution time is 0.114829063415527 s and adjustment time is 0.037783145904541 s ( 32.9 )
2025-11-21 16:26:13.867664 INFO::Formatting Data.
2025-11-21 16:26:13.868509 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:13.869393 INFO::Removing potential empty rows and columns
2025-11-21 16:26:13.871374 INFO::Found 0 missing values.
2025-11-21 16:26:13.883563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:13.884487 INFO::Done
2025-11-21 16:26:13.885007 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:13.887192 INFO::Starting hierarchical adjustment
2025-11-21 16:26:13.891888 INFO::Found 3 batches.
2025-11-21 16:26:13.892538 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:13.895442 INFO::Using default BPPARAM
2025-11-21 16:26:13.896141 INFO::Processing subtree level 1
2025-11-21 16:26:14.119725 INFO::Adjusting the last 1 batches sequentially
2025-11-21 16:26:14.124043 INFO::Done
2025-11-21 16:26:14.125261 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:14.131009 INFO::ASW Batch was -0.0981987887020509 prior to batch effect correction and is now -0.168715328279051 .
2025-11-21 16:26:14.132169 INFO::Total function execution time is 0.264600038528442 s and adjustment time is 0.23250412940979 s ( 87.87 )
2025-11-21 16:26:14.15534 INFO::Skipping initial DF formatting
2025-11-21 16:26:14.156755 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:14.168563 INFO::Starting hierarchical adjustment
2025-11-21 16:26:14.170726 INFO::Found 5 batches.
2025-11-21 16:26:14.171406 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:14.172091 INFO::Using default BPPARAM
2025-11-21 16:26:14.172658 INFO::Processing subtree level 1
2025-11-21 16:26:14.482377 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:14.488761 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 16:26:14.513988 INFO::Done
2025-11-21 16:26:14.51535 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:14.52158 INFO::ASW Batch was 0.587211373011656 prior to batch effect correction and is now 0.587211373011656 .
2025-11-21 16:26:14.522322 INFO::ASW Label was 0.332745234196939 prior to batch effect correction and is now 0.332745234196939 .
2025-11-21 16:26:14.523868 INFO::Total function execution time is 0.368118047714233 s and adjustment time is 0.343513011932373 s ( 93.32 )
2025-11-21 16:26:14.625367 INFO::Formatting Data.
2025-11-21 16:26:14.626293 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:14.627275 INFO::Removing potential empty rows and columns
2025-11-21 16:26:14.628295 INFO::Found 0 missing values.
2025-11-21 16:26:14.632138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:14.632772 INFO::Done
2025-11-21 16:26:14.63326 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:14.636378 INFO::Starting hierarchical adjustment
2025-11-21 16:26:14.637146 INFO::Found 5 batches.
2025-11-21 16:26:14.637676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:14.6383 INFO::Using default BPPARAM
2025-11-21 16:26:14.638755 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.
2025-11-21 16:26:14.825129 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:14.83489 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 16:26:14.861619 INFO::Done
2025-11-21 16:26:14.862734 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:14.868002 INFO::ASW Batch was 0.56435983995277 prior to batch effect correction and is now -0.0620240414219951 .
2025-11-21 16:26:14.868793 INFO::ASW Label was 0.24796124235736 prior to batch effect correction and is now 0.746189587594786 .
2025-11-21 16:26:14.869891 INFO::Total function execution time is 0.244592905044556 s and adjustment time is 0.22452712059021 s ( 91.8 )
2025-11-21 16:26:14.870938 INFO::Formatting Data.
2025-11-21 16:26:14.871714 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:14.872828 INFO::Removing potential empty rows and columns
2025-11-21 16:26:14.87415 INFO::Found 0 missing values.
2025-11-21 16:26:14.880287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:14.881169 INFO::Done
2025-11-21 16:26:14.881811 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:14.885121 INFO::Starting hierarchical adjustment
2025-11-21 16:26:14.885958 INFO::Found 5 batches.
2025-11-21 16:26:14.886606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:14.887321 INFO::Using default BPPARAM
2025-11-21 16:26:14.887902 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.
2025-11-21 16:26:15.04152 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:15.052423 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 16:26:15.094906 INFO::Done
2025-11-21 16:26:15.095978 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:15.10565 INFO::ASW Batch was 0.56435983995277 prior to batch effect correction and is now -0.0620240414219951 .
2025-11-21 16:26:15.107244 INFO::ASW Label was 0.24796124235736 prior to batch effect correction and is now 0.746189587594786 .
2025-11-21 16:26:15.108722 INFO::Total function execution time is 0.237590074539185 s and adjustment time is 0.209031105041504 s ( 87.98 )
2025-11-21 16:26:15.136551 INFO::Formatting Data.
2025-11-21 16:26:15.137461 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:15.138785 INFO::Removing potential empty rows and columns
2025-11-21 16:26:15.139997 INFO::Found 0 missing values.
2025-11-21 16:26:15.144048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:15.144685 INFO::Done
2025-11-21 16:26:15.145239 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:15.148958 INFO::Starting hierarchical adjustment
2025-11-21 16:26:15.149781 INFO::Found 5 batches.
2025-11-21 16:26:15.150354 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:15.151023 INFO::Using default BPPARAM
2025-11-21 16:26:15.151546 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.
2025-11-21 16:26:15.360743 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:15.377467 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 16:26:15.414198 INFO::Done
2025-11-21 16:26:15.415501 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:15.423232 INFO::ASW Batch was 0.478686217742975 prior to batch effect correction and is now -0.0985998109478484 .
2025-11-21 16:26:15.424302 INFO::ASW Label was 0.271417027793862 prior to batch effect correction and is now 0.866990398180522 .
2025-11-21 16:26:15.425697 INFO::Total function execution time is 0.288838863372803 s and adjustment time is 0.264503002166748 s ( 91.57 )
2025-11-21 16:26:15.427002 INFO::Formatting Data.
2025-11-21 16:26:15.42769 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:15.429174 INFO::Removing potential empty rows and columns
2025-11-21 16:26:15.430369 INFO::Found 0 missing values.
2025-11-21 16:26:15.435149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:15.435817 INFO::Done
2025-11-21 16:26:15.436417 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:15.439973 INFO::Starting hierarchical adjustment
2025-11-21 16:26:15.440984 INFO::Found 5 batches.
2025-11-21 16:26:15.441557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:15.442279 INFO::Using default BPPARAM
2025-11-21 16:26:15.442871 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.
2025-11-21 16:26:15.616157 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:15.621748 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 16:26:15.650399 INFO::Done
2025-11-21 16:26:15.651454 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:15.657507 INFO::ASW Batch was 0.478686217742975 prior to batch effect correction and is now -0.0985998109478484 .
2025-11-21 16:26:15.658807 INFO::ASW Label was 0.271417027793862 prior to batch effect correction and is now 0.866990398180522 .
2025-11-21 16:26:15.659874 INFO::Total function execution time is 0.232810974121094 s and adjustment time is 0.209522008895874 s ( 90 )
2025-11-21 16:26:15.694096 INFO::Formatting Data.
2025-11-21 16:26:15.695046 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:15.696068 INFO::Removing potential empty rows and columns
2025-11-21 16:26:15.69724 INFO::Found 0 missing values.
2025-11-21 16:26:15.700496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:15.701206 INFO::Done
2025-11-21 16:26:15.701751 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:15.705204 INFO::Starting hierarchical adjustment
2025-11-21 16:26:15.706138 INFO::Found 2 batches.
2025-11-21 16:26:15.706703 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:15.707418 INFO::Using default BPPARAM
2025-11-21 16:26:15.707918 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:15.708823 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 16:26:15.72785 INFO::Done
2025-11-21 16:26:15.729661 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:15.734875 INFO::ASW Batch was 0.60811466195665 prior to batch effect correction and is now 0.043767513577116 .
2025-11-21 16:26:15.735771 INFO::ASW Label was 0.51471774271652 prior to batch effect correction and is now 0.911288329721684 .
2025-11-21 16:26:15.736647 INFO::Total function execution time is 0.0427098274230957 s and adjustment time is 0.0218350887298584 s ( 51.12 )
2025-11-21 16:26:15.737492 INFO::Formatting Data.
2025-11-21 16:26:15.738092 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:15.739083 INFO::Removing potential empty rows and columns
2025-11-21 16:26:15.740062 INFO::Found 0 missing values.
2025-11-21 16:26:15.745077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:15.745859 INFO::Done
2025-11-21 16:26:15.746416 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:15.749778 INFO::Starting hierarchical adjustment
2025-11-21 16:26:15.750666 INFO::Found 2 batches.
2025-11-21 16:26:15.751271 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:15.751906 INFO::Using default BPPARAM
2025-11-21 16:26:15.752395 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:15.753334 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 16:26:15.770058 INFO::Done
2025-11-21 16:26:15.770832 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:15.773916 INFO::ASW Batch was 0.60811466195665 prior to batch effect correction and is now 0.043767513577116 .
2025-11-21 16:26:15.774514 INFO::ASW Label was 0.51471774271652 prior to batch effect correction and is now 0.911288329721684 .
2025-11-21 16:26:15.775274 INFO::Total function execution time is 0.0377798080444336 s and adjustment time is 0.0195269584655762 s ( 51.69 )
2025-11-21 16:26:15.791185 INFO::Formatting Data.
2025-11-21 16:26:15.792041 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:15.800002 INFO::Removing potential empty rows and columns
2025-11-21 16:26:15.80217 INFO::Found 0 missing values.
2025-11-21 16:26:15.806217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:15.807007 INFO::Done
2025-11-21 16:26:15.80761 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:15.810016 INFO::Starting hierarchical adjustment
2025-11-21 16:26:15.81086 INFO::Found 2 batches.
2025-11-21 16:26:15.811408 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:15.812052 INFO::Using default BPPARAM
2025-11-21 16:26:15.812965 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:15.814903 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 16:26:15.869617 INFO::Done
2025-11-21 16:26:15.870493 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:15.872692 INFO::ASW Batch was -0.153778529157745 prior to batch effect correction and is now -0.161220921692817 .
2025-11-21 16:26:15.873619 INFO::Total function execution time is 0.0825638771057129 s and adjustment time is 0.0588719844818115 s ( 71.3 )
2025-11-21 16:26:15.890607 INFO::Formatting Data.
2025-11-21 16:26:15.893107 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:15.89489 INFO::Removing potential empty rows and columns
2025-11-21 16:26:15.896022 INFO::Found 0 missing values.
2025-11-21 16:26:15.897406 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.
2025-11-21 16:26:15.901894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:15.902518 INFO::Done
2025-11-21 16:26:15.911739 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:15.920278 INFO::Starting hierarchical adjustment
2025-11-21 16:26:15.921528 INFO::Found 2 batches.
2025-11-21 16:26:15.922237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:15.922941 INFO::Using default BPPARAM
2025-11-21 16:26:15.935556 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:15.937073 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 16:26:15.963716 INFO::Done
2025-11-21 16:26:15.964588 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:15.967637 INFO::ASW Batch was 0.7787022810445 prior to batch effect correction and is now -0.0231093543723994 .
2025-11-21 16:26:15.969697 INFO::ASW Label was 0.273448663452783 prior to batch effect correction and is now 0.887222222368697 .
2025-11-21 16:26:15.97143 INFO::Total function execution time is 0.0811378955841064 s and adjustment time is 0.0424098968505859 s ( 52.27 )
2025-11-21 16:26:15.972337 INFO::Formatting Data.
2025-11-21 16:26:15.972939 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:15.974274 INFO::Removing potential empty rows and columns
2025-11-21 16:26:15.975575 INFO::Found 0 missing values.
2025-11-21 16:26:15.976614 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.
2025-11-21 16:26:15.988126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:15.990179 INFO::Done
2025-11-21 16:26:15.993321 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:16.00231 INFO::Starting hierarchical adjustment
2025-11-21 16:26:16.003323 INFO::Found 2 batches.
2025-11-21 16:26:16.003869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:16.004466 INFO::Using default BPPARAM
2025-11-21 16:26:16.004934 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:16.005877 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 16:26:16.021859 INFO::Done
2025-11-21 16:26:16.022554 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:16.025431 INFO::ASW Batch was 0.7787022810445 prior to batch effect correction and is now -0.0231093543723994 .
2025-11-21 16:26:16.026072 INFO::ASW Label was 0.273448663452783 prior to batch effect correction and is now 0.887222222368697 .
2025-11-21 16:26:16.026833 INFO::Total function execution time is 0.0544970035552979 s and adjustment time is 0.018693208694458 s ( 34.3 )
2025-11-21 16:26:16.333456 INFO::Formatting Data.
2025-11-21 16:26:16.334312 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:16.335167 INFO::Removing potential empty rows and columns
2025-11-21 16:26:16.336184 INFO::Found 0 missing values.
2025-11-21 16:26:16.338796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:16.339314 INFO::Done
2025-11-21 16:26:16.339804 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:16.345489 INFO::Starting hierarchical adjustment
2025-11-21 16:26:16.347074 INFO::Found 3 batches.
2025-11-21 16:26:16.347662 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:16.348303 INFO::Using default BPPARAM
2025-11-21 16:26:16.348859 INFO::Processing subtree level 1
2025-11-21 16:26:16.485834 INFO::Adjusting the last 1 batches sequentially
2025-11-21 16:26:16.491126 INFO::Done
2025-11-21 16:26:16.492156 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:16.501391 INFO::ASW Batch was -0.104475288888426 prior to batch effect correction and is now -0.104475288888426 .
2025-11-21 16:26:16.502846 INFO::Total function execution time is 0.16946291923523 s and adjustment time is 0.144301891326904 s ( 85.15 )
2025-11-21 16:26:16.503969 INFO::Formatting Data.
2025-11-21 16:26:16.504596 INFO::Typecasting input to dataframe.
2025-11-21 16:26:16.505343 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:16.506695 INFO::Removing potential empty rows and columns
2025-11-21 16:26:16.507884 INFO::Found 0 missing values.
2025-11-21 16:26:16.510855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:16.51147 INFO::Done
2025-11-21 16:26:16.513496 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:16.518674 INFO::Starting hierarchical adjustment
2025-11-21 16:26:16.520124 INFO::Found 3 batches.
2025-11-21 16:26:16.52074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:16.521429 INFO::Using default BPPARAM
2025-11-21 16:26:16.52201 INFO::Processing subtree level 1
2025-11-21 16:26:16.659286 INFO::Adjusting the last 1 batches sequentially
2025-11-21 16:26:16.664742 INFO::Done
2025-11-21 16:26:16.665797 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:16.670103 INFO::ASW Batch was -0.104475288888426 prior to batch effect correction and is now -0.104475288888426 .
2025-11-21 16:26:16.671208 INFO::Total function execution time is 0.167198896408081 s and adjustment time is 0.14480710029602 s ( 86.61 )
2025-11-21 16:26:16.692147 INFO::Formatting Data.
2025-11-21 16:26:16.694117 INFO::Typecasting input to dataframe.
2025-11-21 16:26:16.695391 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:16.696439 INFO::Removing potential empty rows and columns
2025-11-21 16:26:16.70095 INFO::Found 0 missing values.
2025-11-21 16:26:16.704413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:16.705097 INFO::Done
2025-11-21 16:26:16.705629 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:16.707861 INFO::Starting hierarchical adjustment
2025-11-21 16:26:16.708671 INFO::Found 3 batches.
2025-11-21 16:26:16.709171 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:16.70982 INFO::Using default BPPARAM
2025-11-21 16:26:16.710358 INFO::Processing subtree level 1
2025-11-21 16:26:16.82352 INFO::Adjusting the last 1 batches sequentially
2025-11-21 16:26:16.828707 INFO::Done
2025-11-21 16:26:16.829896 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:16.834119 INFO::ASW Batch was -0.0306909682919623 prior to batch effect correction and is now -0.0306909682919623 .
2025-11-21 16:26:16.835237 INFO::Total function execution time is 0.143406867980957 s and adjustment time is 0.120136976242065 s ( 83.77 )
2025-11-21 16:26:17.015885 INFO::Formatting Data.
2025-11-21 16:26:17.016821 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:17.017975 INFO::Removing potential empty rows and columns
2025-11-21 16:26:17.020745 INFO::Found 1000 missing values.
2025-11-21 16:26:17.0379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:17.03884 INFO::Done
2025-11-21 16:26:17.039441 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:17.045561 INFO::Starting hierarchical adjustment
2025-11-21 16:26:17.046447 INFO::Found 10 batches.
2025-11-21 16:26:17.046966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:17.047594 INFO::Using default BPPARAM
2025-11-21 16:26:17.048073 INFO::Processing subtree level 1
2025-11-21 16:26:17.212025 INFO::Processing subtree level 2
2025-11-21 16:26:17.439866 INFO::Adjusting the last 1 batches sequentially
2025-11-21 16:26:17.447655 INFO::Done
2025-11-21 16:26:17.449113 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:17.461369 INFO::ASW Batch was 0.52920352135998 prior to batch effect correction and is now 0.52920352135998 .
2025-11-21 16:26:17.462697 INFO::ASW Label was 0.329029970948748 prior to batch effect correction and is now 0.329029970948748 .
2025-11-21 16:26:17.464677 INFO::Total function execution time is 0.448812961578369 s and adjustment time is 0.401342868804932 s ( 89.42 )
2025-11-21 16:26:17.465675 INFO::Formatting Data.
2025-11-21 16:26:17.466299 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:17.471471 INFO::Removing potential empty rows and columns
2025-11-21 16:26:17.474375 INFO::Found 1000 missing values.
2025-11-21 16:26:17.509272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:17.510271 INFO::Done
2025-11-21 16:26:17.510835 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:17.516946 INFO::Starting hierarchical adjustment
2025-11-21 16:26:17.517775 INFO::Found 10 batches.
2025-11-21 16:26:19.32286 INFO::Set up parallel execution backend with 2 workers
2025-11-21 16:26:19.323818 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-21 16:26:21.197736 INFO::Adjusting the last 2 batches sequentially
2025-11-21 16:26:21.199347 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 16:26:21.216658 INFO::Done
2025-11-21 16:26:21.217481 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:21.223816 INFO::ASW Batch was 0.52920352135998 prior to batch effect correction and is now 0.52920352135998 .
2025-11-21 16:26:21.224546 INFO::ASW Label was 0.329029970948748 prior to batch effect correction and is now 0.329029970948748 .
2025-11-21 16:26:21.22533 INFO::Total function execution time is 3.75967001914978 s and adjustment time is 3.69896602630615 s ( 98.39 )
2025-11-21 16:26:21.439343 INFO::Formatting Data.
2025-11-21 16:26:21.440393 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:21.441453 INFO::Removing potential empty rows and columns
2025-11-21 16:26:21.444418 INFO::Found 0 missing values.
2025-11-21 16:26:21.451418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:21.452327 INFO::Done
2025-11-21 16:26:21.4544 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 16:26:21.460771 INFO::Starting hierarchical adjustment
2025-11-21 16:26:21.461722 INFO::Found 3 batches.
2025-11-21 16:26:21.462318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 16:26:21.462973 INFO::Using default BPPARAM
2025-11-21 16:26:21.466981 INFO::Processing subtree level 1
2025-11-21 16:26:21.626094 INFO::Adjusting the last 1 batches sequentially
2025-11-21 16:26:21.63187 INFO::Done
2025-11-21 16:26:21.632985 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 16:26:21.639644 INFO::ASW Batch was 0.289655069015488 prior to batch effect correction and is now -0.109821315955142 .
2025-11-21 16:26:21.640925 INFO::ASW Label was -0.228223693262704 prior to batch effect correction and is now -0.0828212685992089 .
2025-11-21 16:26:21.643268 INFO::Total function execution time is 0.20403790473938 s and adjustment time is 0.170159101486206 s ( 83.4 )
2025-11-21 16:26:21.822034 INFO::Formatting Data.
2025-11-21 16:26:21.824979 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:21.826176 INFO::Removing potential empty rows and columns
2025-11-21 16:26:21.827351 INFO::Found 2 missing values.
2025-11-21 16:26:21.831052 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:21.831775 INFO::Done
2025-11-21 16:26:21.884329 INFO::Found NA in Reference column
2025-11-21 16:26:21.895121 INFO::Require at least two references per batch.
2025-11-21 16:26:21.933019 INFO::Formatting Data.
2025-11-21 16:26:21.934268 INFO::Recognized SummarizedExperiment
2025-11-21 16:26:21.934882 INFO::Typecasting input to dataframe.
2025-11-21 16:26:21.951768 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:21.953962 INFO::Removing potential empty rows and columns
2025-11-21 16:26:21.959762 INFO::Found 0 missing values.
2025-11-21 16:26:21.980177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:21.981195 INFO::Done
2025-11-21 16:26:22.004363 INFO::Formatting Data.
2025-11-21 16:26:22.006514 INFO::Recognized SummarizedExperiment
2025-11-21 16:26:22.007174 INFO::Typecasting input to dataframe.
2025-11-21 16:26:22.028443 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:22.030023 INFO::Removing potential empty rows and columns
2025-11-21 16:26:22.033994 INFO::Found 0 missing values.
2025-11-21 16:26:22.046384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:22.047315 INFO::Done
2025-11-21 16:26:22.067736 INFO::Formatting Data.
2025-11-21 16:26:22.06873 INFO::Recognized SummarizedExperiment
2025-11-21 16:26:22.075035 INFO::Typecasting input to dataframe.
2025-11-21 16:26:22.11689 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:22.118126 INFO::Removing potential empty rows and columns
2025-11-21 16:26:22.119224 INFO::Found 0 missing values.
2025-11-21 16:26:22.120217 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.
2025-11-21 16:26:22.124404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:22.125027 INFO::Done
2025-11-21 16:26:22.163073 INFO::Formatting Data.
2025-11-21 16:26:22.165929 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:22.182659 INFO::Removing potential empty rows and columns
2025-11-21 16:26:22.192455 INFO::Found 0 missing values.
2025-11-21 16:26:22.197274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:22.198072 INFO::Done
2025-11-21 16:26:22.217852 INFO::Formatting Data.
2025-11-21 16:26:22.218986 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:22.219908 INFO::Removing potential empty rows and columns
2025-11-21 16:26:22.221098 INFO::Found 0 missing values.
2025-11-21 16:26:22.224764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:22.225443 INFO::Done
2025-11-21 16:26:22.264317 INFO::Formatting Data.
2025-11-21 16:26:22.265313 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:22.266551 INFO::Removing potential empty rows and columns
2025-11-21 16:26:22.267845 INFO::Found 1 missing values.
2025-11-21 16:26:22.270738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:22.271453 INFO::Done
2025-11-21 16:26:22.295976 INFO::Formatting Data.
2025-11-21 16:26:22.296932 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:22.297819 INFO::Removing potential empty rows and columns
2025-11-21 16:26:22.298821 INFO::Found 2 missing values.
2025-11-21 16:26:22.299756 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.
2025-11-21 16:26:22.326974 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:22.334049 INFO::Done
2025-11-21 16:26:22.369784 INFO::Formatting Data.
2025-11-21 16:26:22.370803 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:22.371758 INFO::Removing potential empty rows and columns
2025-11-21 16:26:22.372723 INFO::Found 2 missing values.
2025-11-21 16:26:22.374398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:22.37497 INFO::Done
2025-11-21 16:26:22.388153 INFO::Formatting Data.
2025-11-21 16:26:22.389086 INFO::Typecasting input to dataframe.
2025-11-21 16:26:22.389887 INFO::Replacing NaNs with NAs.
2025-11-21 16:26:22.390738 INFO::Removing potential empty rows and columns
2025-11-21 16:26:22.391729 INFO::Found 0 missing values.
2025-11-21 16:26:22.39583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 16:26:22.396541 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.401 3.974 33.966
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.739 | 1.170 | 30.606 | |
| compute_asw | 0.032 | 0.002 | 0.038 | |
| count_existing | 0.016 | 0.001 | 0.025 | |
| generate_data_covariables | 0.014 | 0.001 | 0.016 | |
| generate_dataset | 0.013 | 0.001 | 0.015 | |