Yannis Schumann
| Snapshot Date: 2026-03-06 13:40 -0500 (Fri, 06 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-07 11:33 -0500 (Sat, 07 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4453 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences" | 3376 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 169/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| 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: 2026-03-06 16:53:43 -0500 (Fri, 06 Mar 2026) |
| EndedAt: 2026-03-06 16:54:16 -0500 (Fri, 06 Mar 2026) |
| EllapsedTime: 32.4 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 Under development (unstable) (2026-02-28 r89501)
* 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 Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-06 21:53:43 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 9.794 0.442 7.318
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-03-06 16:54:07.528217 INFO::Formatting Data.
2026-03-06 16:54:07.529773 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:07.53432 INFO::Removing potential empty rows and columns
2026-03-06 16:54:07.641511 INFO::Found 0 missing values.
2026-03-06 16:54:07.643214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:07.643605 INFO::Done
2026-03-06 16:54:07.643886 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:07.652083 INFO::Starting hierarchical adjustment
2026-03-06 16:54:07.652376 INFO::Found 3 batches.
2026-03-06 16:54:07.652563 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:07.652962 INFO::Using default BPPARAM
2026-03-06 16:54:07.653147 INFO::Processing subtree level 1
2026-03-06 16:54:07.7261 INFO::Adjusting the last 1 batches sequentially
2026-03-06 16:54:07.727386 INFO::Done
2026-03-06 16:54:07.727667 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:07.729138 INFO::ASW Batch was 0.0101549119658742 prior to batch effect correction and is now 0.0101549119658742 .
2026-03-06 16:54:07.729719 INFO::Total function execution time is 0.20182991027832 s and adjustment time is 0.0750610828399658 s ( 37.19 )
2026-03-06 16:54:07.737175 INFO::Formatting Data.
2026-03-06 16:54:07.737447 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:07.737778 INFO::Removing potential empty rows and columns
2026-03-06 16:54:07.738215 INFO::Found 0 missing values.
2026-03-06 16:54:07.738579 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.
2026-03-06 16:54:07.743125 INFO::Formatting Data.
2026-03-06 16:54:07.743391 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:07.74372 INFO::Removing potential empty rows and columns
2026-03-06 16:54:07.744183 INFO::Found 0 missing values.
2026-03-06 16:54:07.744532 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.
2026-03-06 16:54:07.752116 INFO::Formatting Data.
2026-03-06 16:54:07.752451 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:07.752854 INFO::Removing potential empty rows and columns
2026-03-06 16:54:07.753325 INFO::Found 0 missing values.
2026-03-06 16:54:07.753704 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.
2026-03-06 16:54:07.755509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:07.755735 INFO::Done
2026-03-06 16:54:07.755951 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:07.756811 INFO::Starting hierarchical adjustment
2026-03-06 16:54:07.757087 INFO::Found 2 batches.
2026-03-06 16:54:07.757295 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:07.757556 INFO::Using default BPPARAM
2026-03-06 16:54:07.75776 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:07.758121 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 16:54:07.769336 INFO::Done
2026-03-06 16:54:07.769645 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:07.770649 INFO::ASW Batch was -0.0516282892555214 prior to batch effect correction and is now -0.114698760875809 .
2026-03-06 16:54:07.770954 INFO::Total function execution time is 0.0188751220703125 s and adjustment time is 0.0122890472412109 s ( 65.11 )
2026-03-06 16:54:07.772284 INFO::Formatting Data.
2026-03-06 16:54:07.772572 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:07.776061 INFO::Formatting Data.
2026-03-06 16:54:07.776323 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:07.77664 INFO::Removing potential empty rows and columns
2026-03-06 16:54:07.77703 INFO::Found 0 missing values.
2026-03-06 16:54:07.778133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:07.778347 INFO::Done
2026-03-06 16:54:07.77855 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:07.779323 INFO::Starting hierarchical adjustment
2026-03-06 16:54:07.779571 INFO::Found 2 batches.
2026-03-06 16:54:07.779783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:07.780047 INFO::Using default BPPARAM
2026-03-06 16:54:07.780285 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:07.780621 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 16:54:07.786935 INFO::Done
2026-03-06 16:54:07.787143 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:07.787894 INFO::ASW Batch was -0.00453033132383692 prior to batch effect correction and is now -0.110139271319088 .
2026-03-06 16:54:07.788231 INFO::Total function execution time is 0.0121579170227051 s and adjustment time is 0.00741982460021973 s ( 61.03 )
2026-03-06 16:54:07.788656 INFO::Formatting Data.
2026-03-06 16:54:07.78888 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:07.789287 INFO::Removing potential empty rows and columns
2026-03-06 16:54:07.7898 INFO::Found 0 missing values.
2026-03-06 16:54:07.791086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:07.791297 INFO::Done
2026-03-06 16:54:07.791544 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:07.792424 INFO::Starting hierarchical adjustment
2026-03-06 16:54:07.792771 INFO::Found 2 batches.
2026-03-06 16:54:07.793022 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:07.793274 INFO::Using default BPPARAM
2026-03-06 16:54:07.793479 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:07.793806 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 16:54:07.799569 INFO::Done
2026-03-06 16:54:07.799797 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:07.800542 INFO::ASW Batch was -0.00453033132383692 prior to batch effect correction and is now -0.110139271319088 .
2026-03-06 16:54:07.800841 INFO::Total function execution time is 0.0121688842773438 s and adjustment time is 0.00686502456665039 s ( 56.41 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-06 16:54:08.98426 INFO::Formatting Data.
2026-03-06 16:54:08.984511 INFO::Recognized SummarizedExperiment
2026-03-06 16:54:08.984669 INFO::Typecasting input to dataframe.
2026-03-06 16:54:08.994674 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:08.995058 INFO::Removing potential empty rows and columns
2026-03-06 16:54:08.996146 INFO::Found 0 missing values.
2026-03-06 16:54:08.998198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:08.998364 INFO::Done
2026-03-06 16:54:08.998516 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:08.999632 INFO::Starting hierarchical adjustment
2026-03-06 16:54:08.999826 INFO::Found 2 batches.
2026-03-06 16:54:08.999964 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.000249 INFO::Using default BPPARAM
2026-03-06 16:54:09.000387 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.000652 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 16:54:09.018004 INFO::Done
2026-03-06 16:54:09.018246 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.019454 INFO::ASW Batch was -0.00441203421559747 prior to batch effect correction and is now -0.0924088182435436 .
2026-03-06 16:54:09.019721 INFO::Total function execution time is 0.0355570316314697 s and adjustment time is 0.0182070732116699 s ( 51.21 )
Warning: stack imbalance in '{', 73 then 75
2026-03-06 16:54:09.025932 INFO::Formatting Data.
2026-03-06 16:54:09.026132 INFO::Recognized SummarizedExperiment
2026-03-06 16:54:09.026288 INFO::Typecasting input to dataframe.
2026-03-06 16:54:09.029179 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.029525 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.030666 INFO::Found 0 missing values.
2026-03-06 16:54:09.032785 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.032953 INFO::Done
2026-03-06 16:54:09.033109 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.034229 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.034424 INFO::Found 2 batches.
2026-03-06 16:54:09.034575 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.034748 INFO::Using default BPPARAM
2026-03-06 16:54:09.034886 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.035153 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 16:54:09.042904 INFO::Done
2026-03-06 16:54:09.043112 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.044201 INFO::ASW Batch was -0.0197521713523832 prior to batch effect correction and is now -0.0197521713523832 .
2026-03-06 16:54:09.044443 INFO::Total function execution time is 0.0185019969940186 s and adjustment time is 0.00851607322692871 s ( 46.03 )
2026-03-06 16:54:09.063161 INFO::Formatting Data.
2026-03-06 16:54:09.063411 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.063669 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.063955 INFO::Found 0 missing values.
2026-03-06 16:54:09.064739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.064886 INFO::Done
2026-03-06 16:54:09.065018 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.065615 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.06579 INFO::Found 3 batches.
2026-03-06 16:54:09.065917 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.066072 INFO::Using default BPPARAM
2026-03-06 16:54:09.066196 INFO::Processing subtree level 1
2026-03-06 16:54:09.247262 INFO::Adjusting the last 1 batches sequentially
2026-03-06 16:54:09.248992 INFO::Done
2026-03-06 16:54:09.249404 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.251403 INFO::ASW Batch was -0.102757671735796 prior to batch effect correction and is now -0.194241352484766 .
2026-03-06 16:54:09.252006 INFO::Total function execution time is 0.188821077346802 s and adjustment time is 0.183223009109497 s ( 97.04 )
2026-03-06 16:54:09.260077 INFO::Skipping initial DF formatting
2026-03-06 16:54:09.26041 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.262294 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.262673 INFO::Found 5 batches.
2026-03-06 16:54:09.262914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.263239 INFO::Using default BPPARAM
2026-03-06 16:54:09.263479 INFO::Processing subtree level 1
2026-03-06 16:54:09.368759 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.369829 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 16:54:09.379901 INFO::Done
2026-03-06 16:54:09.380302 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.382401 INFO::ASW Batch was 0.528223920832224 prior to batch effect correction and is now 0.528223920832224 .
2026-03-06 16:54:09.382644 INFO::ASW Label was 0.363361028356422 prior to batch effect correction and is now 0.363361028356422 .
2026-03-06 16:54:09.383116 INFO::Total function execution time is 0.12302303314209 s and adjustment time is 0.117275953292847 s ( 95.33 )
2026-03-06 16:54:09.392479 INFO::Formatting Data.
2026-03-06 16:54:09.392783 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.393175 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.393655 INFO::Found 0 missing values.
2026-03-06 16:54:09.395588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.395804 INFO::Done
2026-03-06 16:54:09.396026 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.397177 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.39746 INFO::Found 5 batches.
2026-03-06 16:54:09.397663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.39794 INFO::Using default BPPARAM
2026-03-06 16:54:09.398135 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.
2026-03-06 16:54:09.484999 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.486605 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 16:54:09.495469 INFO::Done
2026-03-06 16:54:09.495872 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.497415 INFO::ASW Batch was 0.462336606403704 prior to batch effect correction and is now -0.102028573446466 .
2026-03-06 16:54:09.49766 INFO::ASW Label was 0.22056673444666 prior to batch effect correction and is now 0.809236044947549 .
2026-03-06 16:54:09.498008 INFO::Total function execution time is 0.105502843856812 s and adjustment time is 0.0980401039123535 s ( 92.93 )
2026-03-06 16:54:09.498332 INFO::Formatting Data.
2026-03-06 16:54:09.498559 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.49887 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.49945 INFO::Found 0 missing values.
2026-03-06 16:54:09.501498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.501735 INFO::Done
2026-03-06 16:54:09.501943 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.503192 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.503505 INFO::Found 5 batches.
2026-03-06 16:54:09.503712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.504006 INFO::Using default BPPARAM
2026-03-06 16:54:09.504268 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.
2026-03-06 16:54:09.583914 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.584788 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 16:54:09.593283 INFO::Done
2026-03-06 16:54:09.593542 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.594809 INFO::ASW Batch was 0.462336606403704 prior to batch effect correction and is now -0.102028573446466 .
2026-03-06 16:54:09.595022 INFO::ASW Label was 0.22056673444666 prior to batch effect correction and is now 0.809236044947549 .
2026-03-06 16:54:09.595328 INFO::Total function execution time is 0.0969738960266113 s and adjustment time is 0.0898549556732178 s ( 92.66 )
2026-03-06 16:54:09.60234 INFO::Formatting Data.
2026-03-06 16:54:09.605694 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.606071 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.606467 INFO::Found 0 missing values.
2026-03-06 16:54:09.607777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.607959 INFO::Done
2026-03-06 16:54:09.608127 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.609153 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.609392 INFO::Found 5 batches.
2026-03-06 16:54:09.609787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.610013 INFO::Using default BPPARAM
2026-03-06 16:54:09.610208 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.
2026-03-06 16:54:09.695702 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.696601 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 16:54:09.704327 INFO::Done
2026-03-06 16:54:09.704679 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.706096 INFO::ASW Batch was 0.175579678068001 prior to batch effect correction and is now -0.0771156637492903 .
2026-03-06 16:54:09.706313 INFO::ASW Label was 0.530948386191136 prior to batch effect correction and is now 0.849344173725847 .
2026-03-06 16:54:09.706636 INFO::Total function execution time is 0.104314088821411 s and adjustment time is 0.0949690341949463 s ( 91.04 )
2026-03-06 16:54:09.706951 INFO::Formatting Data.
2026-03-06 16:54:09.707157 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.707531 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.707976 INFO::Found 0 missing values.
2026-03-06 16:54:09.709547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.709747 INFO::Done
2026-03-06 16:54:09.710057 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.711482 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.711852 INFO::Found 5 batches.
2026-03-06 16:54:09.712091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.712345 INFO::Using default BPPARAM
2026-03-06 16:54:09.712559 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.
2026-03-06 16:54:09.797706 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.798676 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 16:54:09.805841 INFO::Done
2026-03-06 16:54:09.806108 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.807453 INFO::ASW Batch was 0.175579678068001 prior to batch effect correction and is now -0.0771156637492903 .
2026-03-06 16:54:09.807687 INFO::ASW Label was 0.530948386191136 prior to batch effect correction and is now 0.849344173725847 .
2026-03-06 16:54:09.808025 INFO::Total function execution time is 0.101055860519409 s and adjustment time is 0.0941109657287598 s ( 93.13 )
2026-03-06 16:54:09.81423 INFO::Formatting Data.
2026-03-06 16:54:09.814505 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.814821 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.8152 INFO::Found 0 missing values.
2026-03-06 16:54:09.816114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.816293 INFO::Done
2026-03-06 16:54:09.816461 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.817454 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.817701 INFO::Found 2 batches.
2026-03-06 16:54:09.817884 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.818159 INFO::Using default BPPARAM
2026-03-06 16:54:09.818334 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.818629 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 16:54:09.823845 INFO::Done
2026-03-06 16:54:09.824095 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.825126 INFO::ASW Batch was 0.313025626778067 prior to batch effect correction and is now 0.0248166673530359 .
2026-03-06 16:54:09.825353 INFO::ASW Label was 0.728130287310476 prior to batch effect correction and is now 0.890461392985876 .
2026-03-06 16:54:09.825621 INFO::Total function execution time is 0.0114181041717529 s and adjustment time is 0.0061948299407959 s ( 54.25 )
2026-03-06 16:54:09.825885 INFO::Formatting Data.
2026-03-06 16:54:09.826091 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.826404 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.826754 INFO::Found 0 missing values.
2026-03-06 16:54:09.8277 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.827901 INFO::Done
2026-03-06 16:54:09.828061 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.829042 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.829298 INFO::Found 2 batches.
2026-03-06 16:54:09.829483 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.829687 INFO::Using default BPPARAM
2026-03-06 16:54:09.829883 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.830165 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 16:54:09.835576 INFO::Done
2026-03-06 16:54:09.835828 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.836889 INFO::ASW Batch was 0.313025626778067 prior to batch effect correction and is now 0.0248166673530359 .
2026-03-06 16:54:09.837114 INFO::ASW Label was 0.728130287310476 prior to batch effect correction and is now 0.890461392985876 .
2026-03-06 16:54:09.837387 INFO::Total function execution time is 0.0114991664886475 s and adjustment time is 0.00630998611450195 s ( 54.87 )
2026-03-06 16:54:09.842402 INFO::Formatting Data.
2026-03-06 16:54:09.842677 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.843008 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.843368 INFO::Found 0 missing values.
2026-03-06 16:54:09.844045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.844211 INFO::Done
2026-03-06 16:54:09.84438 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.844959 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.845189 INFO::Found 2 batches.
2026-03-06 16:54:09.845347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.845586 INFO::Using default BPPARAM
2026-03-06 16:54:09.845758 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.846041 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 16:54:09.8576 INFO::Done
2026-03-06 16:54:09.857868 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.858592 INFO::ASW Batch was -0.151277615798732 prior to batch effect correction and is now -0.162468516558094 .
2026-03-06 16:54:09.858884 INFO::Total function execution time is 0.0164968967437744 s and adjustment time is 0.0124421119689941 s ( 75.42 )
2026-03-06 16:54:09.863875 INFO::Formatting Data.
2026-03-06 16:54:09.864098 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.864398 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.864722 INFO::Found 0 missing values.
2026-03-06 16:54:09.86513 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.
2026-03-06 16:54:09.866492 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.866667 INFO::Done
2026-03-06 16:54:09.866828 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.867688 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.867901 INFO::Found 2 batches.
2026-03-06 16:54:09.868052 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.868231 INFO::Using default BPPARAM
2026-03-06 16:54:09.868377 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.868631 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 16:54:09.873645 INFO::Done
2026-03-06 16:54:09.873832 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.874663 INFO::ASW Batch was 0.399499994746988 prior to batch effect correction and is now 0.0389586639512806 .
2026-03-06 16:54:09.874846 INFO::ASW Label was 0.673364426090722 prior to batch effect correction and is now 0.906618370119954 .
2026-03-06 16:54:09.875067 INFO::Total function execution time is 0.0112161636352539 s and adjustment time is 0.00577807426452637 s ( 51.52 )
2026-03-06 16:54:09.875289 INFO::Formatting Data.
2026-03-06 16:54:09.875456 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.875721 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.876011 INFO::Found 0 missing values.
2026-03-06 16:54:09.876262 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.
2026-03-06 16:54:09.877503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.877669 INFO::Done
2026-03-06 16:54:09.877835 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.878652 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.878855 INFO::Found 2 batches.
2026-03-06 16:54:09.879007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.87918 INFO::Using default BPPARAM
2026-03-06 16:54:09.879323 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:09.879575 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 16:54:09.884395 INFO::Done
2026-03-06 16:54:09.884586 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:09.885412 INFO::ASW Batch was 0.399499994746988 prior to batch effect correction and is now 0.0389586639512806 .
2026-03-06 16:54:09.885577 INFO::ASW Label was 0.673364426090722 prior to batch effect correction and is now 0.906618370119954 .
2026-03-06 16:54:09.885813 INFO::Total function execution time is 0.0105190277099609 s and adjustment time is 0.00557112693786621 s ( 52.96 )
2026-03-06 16:54:09.955796 INFO::Formatting Data.
2026-03-06 16:54:09.956104 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:09.956424 INFO::Removing potential empty rows and columns
2026-03-06 16:54:09.956764 INFO::Found 0 missing values.
2026-03-06 16:54:09.957687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:09.957856 INFO::Done
2026-03-06 16:54:09.958017 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:09.9587 INFO::Starting hierarchical adjustment
2026-03-06 16:54:09.959077 INFO::Found 3 batches.
2026-03-06 16:54:09.959334 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:09.959936 INFO::Using default BPPARAM
2026-03-06 16:54:09.96013 INFO::Processing subtree level 1
2026-03-06 16:54:10.05048 INFO::Adjusting the last 1 batches sequentially
2026-03-06 16:54:10.051773 INFO::Done
2026-03-06 16:54:10.052054 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:10.05357 INFO::ASW Batch was -0.0670446482791389 prior to batch effect correction and is now -0.0670446482791389 .
2026-03-06 16:54:10.054146 INFO::Total function execution time is 0.0983610153198242 s and adjustment time is 0.0928201675415039 s ( 94.37 )
2026-03-06 16:54:10.054641 INFO::Formatting Data.
2026-03-06 16:54:10.054917 INFO::Typecasting input to dataframe.
2026-03-06 16:54:10.055253 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:10.055677 INFO::Removing potential empty rows and columns
2026-03-06 16:54:10.056196 INFO::Found 0 missing values.
2026-03-06 16:54:10.057439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:10.057652 INFO::Done
2026-03-06 16:54:10.057863 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:10.058656 INFO::Starting hierarchical adjustment
2026-03-06 16:54:10.058948 INFO::Found 3 batches.
2026-03-06 16:54:10.059155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:10.059449 INFO::Using default BPPARAM
2026-03-06 16:54:10.059663 INFO::Processing subtree level 1
2026-03-06 16:54:10.128422 INFO::Adjusting the last 1 batches sequentially
2026-03-06 16:54:10.129439 INFO::Done
2026-03-06 16:54:10.129694 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:10.130864 INFO::ASW Batch was -0.0670446482791389 prior to batch effect correction and is now -0.0670446482791389 .
2026-03-06 16:54:10.131317 INFO::Total function execution time is 0.0766661167144775 s and adjustment time is 0.0705420970916748 s ( 92.01 )
2026-03-06 16:54:10.137866 INFO::Formatting Data.
2026-03-06 16:54:10.138181 INFO::Typecasting input to dataframe.
2026-03-06 16:54:10.138515 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:10.138873 INFO::Removing potential empty rows and columns
2026-03-06 16:54:10.139347 INFO::Found 0 missing values.
2026-03-06 16:54:10.140472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:10.140686 INFO::Done
2026-03-06 16:54:10.140886 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:10.141702 INFO::Starting hierarchical adjustment
2026-03-06 16:54:10.14198 INFO::Found 3 batches.
2026-03-06 16:54:10.142172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:10.14243 INFO::Using default BPPARAM
2026-03-06 16:54:10.142621 INFO::Processing subtree level 1
2026-03-06 16:54:10.204655 INFO::Adjusting the last 1 batches sequentially
2026-03-06 16:54:10.205774 INFO::Done
2026-03-06 16:54:10.206036 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:10.207453 INFO::ASW Batch was -0.0523724221420892 prior to batch effect correction and is now -0.0523724221420892 .
2026-03-06 16:54:10.207976 INFO::Total function execution time is 0.0701181888580322 s and adjustment time is 0.0638489723205566 s ( 91.06 )
2026-03-06 16:54:10.296052 INFO::Formatting Data.
2026-03-06 16:54:10.296364 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:10.296818 INFO::Removing potential empty rows and columns
2026-03-06 16:54:10.297929 INFO::Found 1000 missing values.
2026-03-06 16:54:10.305711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:10.306059 INFO::Done
2026-03-06 16:54:10.3063 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:10.308983 INFO::Starting hierarchical adjustment
2026-03-06 16:54:10.309311 INFO::Found 10 batches.
2026-03-06 16:54:10.309548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:10.309836 INFO::Using default BPPARAM
2026-03-06 16:54:10.31006 INFO::Processing subtree level 1
2026-03-06 16:54:10.396271 INFO::Processing subtree level 2
2026-03-06 16:54:10.468458 INFO::Adjusting the last 1 batches sequentially
2026-03-06 16:54:10.469546 INFO::Done
2026-03-06 16:54:10.469763 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:10.472026 INFO::ASW Batch was 0.534579182296413 prior to batch effect correction and is now 0.534579182296413 .
2026-03-06 16:54:10.472255 INFO::ASW Label was 0.341650266449176 prior to batch effect correction and is now 0.341650266449176 .
2026-03-06 16:54:10.472663 INFO::Total function execution time is 0.176614999771118 s and adjustment time is 0.160315990447998 s ( 90.77 )
2026-03-06 16:54:10.472961 INFO::Formatting Data.
2026-03-06 16:54:10.473152 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:10.473558 INFO::Removing potential empty rows and columns
2026-03-06 16:54:10.474457 INFO::Found 1000 missing values.
2026-03-06 16:54:10.480143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:10.480371 INFO::Done
2026-03-06 16:54:10.480551 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:10.48242 INFO::Starting hierarchical adjustment
2026-03-06 16:54:10.482667 INFO::Found 10 batches.
2026-03-06 16:54:10.939751 INFO::Set up parallel execution backend with 2 workers
2026-03-06 16:54:10.940083 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-06 16:54:11.55137 INFO::Adjusting the last 2 batches sequentially
2026-03-06 16:54:11.551939 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 16:54:11.557815 INFO::Done
2026-03-06 16:54:11.558037 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:11.559871 INFO::ASW Batch was 0.534579182296413 prior to batch effect correction and is now 0.534579182296413 .
2026-03-06 16:54:11.560061 INFO::ASW Label was 0.341650266449176 prior to batch effect correction and is now 0.341650266449176 .
2026-03-06 16:54:11.5603 INFO::Total function execution time is 1.08734607696533 s and adjustment time is 1.07519388198853 s ( 98.88 )
2026-03-06 16:54:11.735798 INFO::Formatting Data.
2026-03-06 16:54:11.736298 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.736776 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.737393 INFO::Found 0 missing values.
2026-03-06 16:54:11.739026 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.739246 INFO::Done
2026-03-06 16:54:11.739463 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 16:54:11.740811 INFO::Starting hierarchical adjustment
2026-03-06 16:54:11.74117 INFO::Found 3 batches.
2026-03-06 16:54:11.741427 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 16:54:11.741767 INFO::Using default BPPARAM
2026-03-06 16:54:11.74198 INFO::Processing subtree level 1
2026-03-06 16:54:11.817995 INFO::Adjusting the last 1 batches sequentially
2026-03-06 16:54:11.818861 INFO::Done
2026-03-06 16:54:11.819064 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 16:54:11.820239 INFO::ASW Batch was 0.191930426401845 prior to batch effect correction and is now -0.143839686886225 .
2026-03-06 16:54:11.820432 INFO::ASW Label was -0.163831942390007 prior to batch effect correction and is now -0.0776228598275227 .
2026-03-06 16:54:11.820788 INFO::Total function execution time is 0.0850791931152344 s and adjustment time is 0.0777719020843506 s ( 91.41 )
2026-03-06 16:54:11.868273 INFO::Formatting Data.
2026-03-06 16:54:11.868633 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.868974 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.869376 INFO::Found 2 missing values.
2026-03-06 16:54:11.870408 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.870604 INFO::Done
2026-03-06 16:54:11.881293 INFO::Found NA in Reference column
2026-03-06 16:54:11.885014 INFO::Require at least two references per batch.
2026-03-06 16:54:11.892919 INFO::Formatting Data.
2026-03-06 16:54:11.893137 INFO::Recognized SummarizedExperiment
2026-03-06 16:54:11.893311 INFO::Typecasting input to dataframe.
2026-03-06 16:54:11.897001 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.897391 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.898734 INFO::Found 0 missing values.
2026-03-06 16:54:11.90118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.901344 INFO::Done
2026-03-06 16:54:11.90638 INFO::Formatting Data.
2026-03-06 16:54:11.906597 INFO::Recognized SummarizedExperiment
2026-03-06 16:54:11.906752 INFO::Typecasting input to dataframe.
2026-03-06 16:54:11.91218 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.912559 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.913811 INFO::Found 0 missing values.
2026-03-06 16:54:11.917816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.918006 INFO::Done
2026-03-06 16:54:11.923079 INFO::Formatting Data.
2026-03-06 16:54:11.923276 INFO::Recognized SummarizedExperiment
2026-03-06 16:54:11.923438 INFO::Typecasting input to dataframe.
2026-03-06 16:54:11.928426 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.928719 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.929033 INFO::Found 0 missing values.
2026-03-06 16:54:11.929324 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.
2026-03-06 16:54:11.930674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.930845 INFO::Done
2026-03-06 16:54:11.93466 INFO::Formatting Data.
2026-03-06 16:54:11.934875 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.935133 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.935445 INFO::Found 0 missing values.
2026-03-06 16:54:11.936336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.936499 INFO::Done
2026-03-06 16:54:11.940781 INFO::Formatting Data.
2026-03-06 16:54:11.940996 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.941243 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.941551 INFO::Found 0 missing values.
2026-03-06 16:54:11.942395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.94259 INFO::Done
2026-03-06 16:54:11.953148 INFO::Formatting Data.
2026-03-06 16:54:11.953405 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.953711 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.95407 INFO::Found 1 missing values.
2026-03-06 16:54:11.954856 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.955019 INFO::Done
2026-03-06 16:54:11.961755 INFO::Formatting Data.
2026-03-06 16:54:11.961985 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.962235 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.962508 INFO::Found 2 missing values.
2026-03-06 16:54:11.962777 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.
2026-03-06 16:54:11.963518 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.963673 INFO::Done
2026-03-06 16:54:11.967192 INFO::Formatting Data.
2026-03-06 16:54:11.9674 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.967648 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.967907 INFO::Found 2 missing values.
2026-03-06 16:54:11.968385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.968538 INFO::Done
2026-03-06 16:54:11.972109 INFO::Formatting Data.
2026-03-06 16:54:11.972319 INFO::Typecasting input to dataframe.
2026-03-06 16:54:11.972559 INFO::Replacing NaNs with NAs.
2026-03-06 16:54:11.972805 INFO::Removing potential empty rows and columns
2026-03-06 16:54:11.973099 INFO::Found 0 missing values.
2026-03-06 16:54:11.973954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 16:54:11.974125 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.594 2.255 9.044
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.794 | 0.442 | 7.318 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.004 | 0.001 | 0.006 | |
| generate_data_covariables | 0.004 | 0.000 | 0.004 | |
| generate_dataset | 0.004 | 0.001 | 0.004 | |