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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-03-06 22:41:20 -0500 (Fri, 06 Mar 2026) |
| EndedAt: 2026-03-06 22:43:00 -0500 (Fri, 06 Mar 2026) |
| EllapsedTime: 100.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-07 03:41:20 UTC
* 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 loading without being on the library search path ... 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 29.889 1.912 21.741
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 22:42:22.209557 INFO::Formatting Data.
2026-03-06 22:42:22.211212 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:22.223955 INFO::Removing potential empty rows and columns
2026-03-06 22:42:22.472694 INFO::Found 0 missing values.
2026-03-06 22:42:22.47649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:22.477319 INFO::Done
2026-03-06 22:42:22.47795 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:22.491705 INFO::Starting hierarchical adjustment
2026-03-06 22:42:22.492724 INFO::Found 3 batches.
2026-03-06 22:42:22.493336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:22.494473 INFO::Using default BPPARAM
2026-03-06 22:42:22.495069 INFO::Processing subtree level 1
2026-03-06 22:42:22.603826 INFO::Adjusting the last 1 batches sequentially
2026-03-06 22:42:22.605952 INFO::Done
2026-03-06 22:42:22.606813 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:22.609778 INFO::ASW Batch was -0.135271455174949 prior to batch effect correction and is now -0.135271455174949 .
2026-03-06 22:42:22.611043 INFO::Total function execution time is 0.402255773544312 s and adjustment time is 0.113399028778076 s ( 28.19 )
2026-03-06 22:42:22.626058 INFO::Formatting Data.
2026-03-06 22:42:22.627039 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:22.628104 INFO::Removing potential empty rows and columns
2026-03-06 22:42:22.629347 INFO::Found 0 missing values.
2026-03-06 22:42:22.63042 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 22:42:22.642231 INFO::Formatting Data.
2026-03-06 22:42:22.643208 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:22.644276 INFO::Removing potential empty rows and columns
2026-03-06 22:42:22.645533 INFO::Found 0 missing values.
2026-03-06 22:42:22.646603 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 22:42:22.665093 INFO::Formatting Data.
2026-03-06 22:42:22.666191 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:22.667342 INFO::Removing potential empty rows and columns
2026-03-06 22:42:22.668617 INFO::Found 0 missing values.
2026-03-06 22:42:22.669743 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 22:42:22.674853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:22.675604 INFO::Done
2026-03-06 22:42:22.676219 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:22.678628 INFO::Starting hierarchical adjustment
2026-03-06 22:42:22.679462 INFO::Found 2 batches.
2026-03-06 22:42:22.680197 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:22.680923 INFO::Using default BPPARAM
2026-03-06 22:42:22.681521 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:22.682613 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 22:42:22.705784 INFO::Done
2026-03-06 22:42:22.706741 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:22.70928 INFO::ASW Batch was -0.0572194855190257 prior to batch effect correction and is now -0.125446005206238 .
2026-03-06 22:42:22.710249 INFO::Total function execution time is 0.0452985763549805 s and adjustment time is 0.0264163017272949 s ( 58.32 )
2026-03-06 22:42:22.713578 INFO::Formatting Data.
2026-03-06 22:42:22.71432 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:22.724286 INFO::Formatting Data.
2026-03-06 22:42:22.72516 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:22.726182 INFO::Removing potential empty rows and columns
2026-03-06 22:42:22.727342 INFO::Found 0 missing values.
2026-03-06 22:42:22.730561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:22.731178 INFO::Done
2026-03-06 22:42:22.731768 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:22.734186 INFO::Starting hierarchical adjustment
2026-03-06 22:42:22.734984 INFO::Found 2 batches.
2026-03-06 22:42:22.73558 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:22.736279 INFO::Using default BPPARAM
2026-03-06 22:42:22.736883 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:22.737927 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 22:42:22.786306 INFO::Done
2026-03-06 22:42:22.78723 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:22.789653 INFO::ASW Batch was 0.0713604847328997 prior to batch effect correction and is now -0.118126506023225 .
2026-03-06 22:42:22.790663 INFO::Total function execution time is 0.0664281845092773 s and adjustment time is 0.0514192581176758 s ( 77.41 )
2026-03-06 22:42:22.791884 INFO::Formatting Data.
2026-03-06 22:42:22.792578 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:22.793554 INFO::Removing potential empty rows and columns
2026-03-06 22:42:22.794635 INFO::Found 0 missing values.
2026-03-06 22:42:22.79747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:22.798079 INFO::Done
2026-03-06 22:42:22.798644 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:22.80076 INFO::Starting hierarchical adjustment
2026-03-06 22:42:22.80149 INFO::Found 2 batches.
2026-03-06 22:42:22.802044 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:22.802683 INFO::Using default BPPARAM
2026-03-06 22:42:22.80322 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:22.804206 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 22:42:22.819559 INFO::Done
2026-03-06 22:42:22.820361 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:22.822566 INFO::ASW Batch was 0.0713604847328997 prior to batch effect correction and is now -0.118126506023225 .
2026-03-06 22:42:22.823435 INFO::Total function execution time is 0.031566858291626 s and adjustment time is 0.0181698799133301 s ( 57.56 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-06 22:42:26.217887 INFO::Formatting Data.
2026-03-06 22:42:26.219083 INFO::Recognized SummarizedExperiment
2026-03-06 22:42:26.219751 INFO::Typecasting input to dataframe.
2026-03-06 22:42:26.257071 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:26.258763 INFO::Removing potential empty rows and columns
2026-03-06 22:42:26.262472 INFO::Found 0 missing values.
2026-03-06 22:42:26.26966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:26.270486 INFO::Done
2026-03-06 22:42:26.271106 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:26.27505 INFO::Starting hierarchical adjustment
2026-03-06 22:42:26.275909 INFO::Found 2 batches.
2026-03-06 22:42:26.276474 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:26.277845 INFO::Using default BPPARAM
2026-03-06 22:42:26.27837 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:26.279395 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 22:42:26.338702 INFO::Done
2026-03-06 22:42:26.339638 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:26.343567 INFO::ASW Batch was -0.0116704382930408 prior to batch effect correction and is now -0.0923159174530737 .
2026-03-06 22:42:26.344618 INFO::Total function execution time is 0.127193212509155 s and adjustment time is 0.0629000663757324 s ( 49.45 )
Warning: stack imbalance in '{', 73 then 75
2026-03-06 22:42:26.366145 INFO::Formatting Data.
2026-03-06 22:42:26.367153 INFO::Recognized SummarizedExperiment
2026-03-06 22:42:26.367808 INFO::Typecasting input to dataframe.
2026-03-06 22:42:26.378148 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:26.379629 INFO::Removing potential empty rows and columns
2026-03-06 22:42:26.383536 INFO::Found 0 missing values.
2026-03-06 22:42:26.391428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:26.392316 INFO::Done
2026-03-06 22:42:26.392948 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:26.397144 INFO::Starting hierarchical adjustment
2026-03-06 22:42:26.398023 INFO::Found 2 batches.
2026-03-06 22:42:26.398647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:26.399452 INFO::Using default BPPARAM
2026-03-06 22:42:26.40004 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:26.40119 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 22:42:26.42928 INFO::Done
2026-03-06 22:42:26.430314 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:26.434803 INFO::ASW Batch was -0.00944560320940062 prior to batch effect correction and is now -0.00944560320940062 .
2026-03-06 22:42:26.435891 INFO::Total function execution time is 0.0697636604309082 s and adjustment time is 0.0313386917114258 s ( 44.92 )
2026-03-06 22:42:26.458995 INFO::Formatting Data.
2026-03-06 22:42:26.460129 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:26.461298 INFO::Removing potential empty rows and columns
2026-03-06 22:42:26.462602 INFO::Found 0 missing values.
2026-03-06 22:42:26.466128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:26.466769 INFO::Done
2026-03-06 22:42:26.46736 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:26.469981 INFO::Starting hierarchical adjustment
2026-03-06 22:42:26.470793 INFO::Found 3 batches.
2026-03-06 22:42:26.471638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:26.472306 INFO::Using default BPPARAM
2026-03-06 22:42:26.472892 INFO::Processing subtree level 1
2026-03-06 22:42:26.634698 INFO::Adjusting the last 1 batches sequentially
2026-03-06 22:42:26.636885 INFO::Done
2026-03-06 22:42:26.637657 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:26.640563 INFO::ASW Batch was -0.0418131330911088 prior to batch effect correction and is now -0.161554352694153 .
2026-03-06 22:42:26.641628 INFO::Total function execution time is 0.182788372039795 s and adjustment time is 0.166271209716797 s ( 90.96 )
2026-03-06 22:42:26.657999 INFO::Skipping initial DF formatting
2026-03-06 22:42:26.658983 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:26.663746 INFO::Starting hierarchical adjustment
2026-03-06 22:42:26.664792 INFO::Found 5 batches.
2026-03-06 22:42:26.665449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:26.666165 INFO::Using default BPPARAM
2026-03-06 22:42:26.666806 INFO::Processing subtree level 1
2026-03-06 22:42:26.805013 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:26.80707 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 22:42:26.841463 INFO::Done
2026-03-06 22:42:26.842743 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:26.848378 INFO::ASW Batch was 0.576721959556898 prior to batch effect correction and is now 0.576721959556898 .
2026-03-06 22:42:26.849236 INFO::ASW Label was 0.38078046186477 prior to batch effect correction and is now 0.38078046186477 .
2026-03-06 22:42:26.850861 INFO::Total function execution time is 0.192819833755493 s and adjustment time is 0.176723480224609 s ( 91.65 )
2026-03-06 22:42:26.873635 INFO::Formatting Data.
2026-03-06 22:42:26.874793 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:26.876128 INFO::Removing potential empty rows and columns
2026-03-06 22:42:26.8775 INFO::Found 0 missing values.
2026-03-06 22:42:26.882276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:26.882972 INFO::Done
2026-03-06 22:42:26.883598 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:26.887173 INFO::Starting hierarchical adjustment
2026-03-06 22:42:26.888058 INFO::Found 5 batches.
2026-03-06 22:42:26.88868 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:26.88948 INFO::Using default BPPARAM
2026-03-06 22:42:26.890118 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 22:42:27.017431 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.019386 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 22:42:27.037507 INFO::Done
2026-03-06 22:42:27.038435 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.042214 INFO::ASW Batch was 0.293871960500594 prior to batch effect correction and is now -0.022203501677914 .
2026-03-06 22:42:27.042995 INFO::ASW Label was 0.555788807695355 prior to batch effect correction and is now 0.752708504463371 .
2026-03-06 22:42:27.04396 INFO::Total function execution time is 0.170532464981079 s and adjustment time is 0.149569988250732 s ( 87.71 )
2026-03-06 22:42:27.044943 INFO::Formatting Data.
2026-03-06 22:42:27.045651 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:27.04665 INFO::Removing potential empty rows and columns
2026-03-06 22:42:27.047794 INFO::Found 0 missing values.
2026-03-06 22:42:27.052212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:27.052906 INFO::Done
2026-03-06 22:42:27.053495 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:27.056896 INFO::Starting hierarchical adjustment
2026-03-06 22:42:27.057745 INFO::Found 5 batches.
2026-03-06 22:42:27.058336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:27.059096 INFO::Using default BPPARAM
2026-03-06 22:42:27.059726 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 22:42:27.188818 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.190761 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 22:42:27.208823 INFO::Done
2026-03-06 22:42:27.209802 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.213764 INFO::ASW Batch was 0.293871960500594 prior to batch effect correction and is now -0.022203501677914 .
2026-03-06 22:42:27.214487 INFO::ASW Label was 0.555788807695355 prior to batch effect correction and is now 0.752708504463371 .
2026-03-06 22:42:27.215532 INFO::Total function execution time is 0.170595645904541 s and adjustment time is 0.151201963424683 s ( 88.63 )
2026-03-06 22:42:27.231085 INFO::Formatting Data.
2026-03-06 22:42:27.232087 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:27.233218 INFO::Removing potential empty rows and columns
2026-03-06 22:42:27.234411 INFO::Found 0 missing values.
2026-03-06 22:42:27.239059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:27.23974 INFO::Done
2026-03-06 22:42:27.240366 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:27.243964 INFO::Starting hierarchical adjustment
2026-03-06 22:42:27.244836 INFO::Found 5 batches.
2026-03-06 22:42:27.245428 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:27.246176 INFO::Using default BPPARAM
2026-03-06 22:42:27.246819 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 22:42:27.376282 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.378387 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 22:42:27.396623 INFO::Done
2026-03-06 22:42:27.397585 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.401676 INFO::ASW Batch was 0.412823998924616 prior to batch effect correction and is now -0.0970260236746857 .
2026-03-06 22:42:27.402469 INFO::ASW Label was 0.330656810638048 prior to batch effect correction and is now 0.82221318060442 .
2026-03-06 22:42:27.403461 INFO::Total function execution time is 0.172498464584351 s and adjustment time is 0.151922702789307 s ( 88.07 )
2026-03-06 22:42:27.404498 INFO::Formatting Data.
2026-03-06 22:42:27.405278 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:27.406331 INFO::Removing potential empty rows and columns
2026-03-06 22:42:27.407444 INFO::Found 0 missing values.
2026-03-06 22:42:27.411993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:27.412642 INFO::Done
2026-03-06 22:42:27.413226 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:27.416665 INFO::Starting hierarchical adjustment
2026-03-06 22:42:27.417454 INFO::Found 5 batches.
2026-03-06 22:42:27.418125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:27.418851 INFO::Using default BPPARAM
2026-03-06 22:42:27.419466 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 22:42:27.555697 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.557787 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 22:42:27.576018 INFO::Done
2026-03-06 22:42:27.577009 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.580928 INFO::ASW Batch was 0.412823998924616 prior to batch effect correction and is now -0.0970260236746857 .
2026-03-06 22:42:27.581655 INFO::ASW Label was 0.330656810638048 prior to batch effect correction and is now 0.82221318060442 .
2026-03-06 22:42:27.582668 INFO::Total function execution time is 0.178154945373535 s and adjustment time is 0.158666372299194 s ( 89.06 )
2026-03-06 22:42:27.598329 INFO::Formatting Data.
2026-03-06 22:42:27.599311 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:27.600393 INFO::Removing potential empty rows and columns
2026-03-06 22:42:27.601516 INFO::Found 0 missing values.
2026-03-06 22:42:27.604661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:27.605293 INFO::Done
2026-03-06 22:42:27.605898 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:27.609392 INFO::Starting hierarchical adjustment
2026-03-06 22:42:27.610259 INFO::Found 2 batches.
2026-03-06 22:42:27.6109 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:27.611626 INFO::Using default BPPARAM
2026-03-06 22:42:27.612277 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.613308 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 22:42:27.629975 INFO::Done
2026-03-06 22:42:27.63079 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.634151 INFO::ASW Batch was 0.529097772674942 prior to batch effect correction and is now -0.0231586460833598 .
2026-03-06 22:42:27.634839 INFO::ASW Label was 0.570183047055521 prior to batch effect correction and is now 0.944190300402851 .
2026-03-06 22:42:27.63578 INFO::Total function execution time is 0.0375878810882568 s and adjustment time is 0.0198683738708496 s ( 52.86 )
2026-03-06 22:42:27.636698 INFO::Formatting Data.
2026-03-06 22:42:27.637411 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:27.638415 INFO::Removing potential empty rows and columns
2026-03-06 22:42:27.639492 INFO::Found 0 missing values.
2026-03-06 22:42:27.642493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:27.643143 INFO::Done
2026-03-06 22:42:27.643763 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:27.647175 INFO::Starting hierarchical adjustment
2026-03-06 22:42:27.648004 INFO::Found 2 batches.
2026-03-06 22:42:27.648634 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:27.649332 INFO::Using default BPPARAM
2026-03-06 22:42:27.649984 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.651039 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-06 22:42:27.669062 INFO::Done
2026-03-06 22:42:27.670005 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.673655 INFO::ASW Batch was 0.529097772674942 prior to batch effect correction and is now -0.0231586460833598 .
2026-03-06 22:42:27.674369 INFO::ASW Label was 0.570183047055521 prior to batch effect correction and is now 0.944190300402851 .
2026-03-06 22:42:27.675335 INFO::Total function execution time is 0.0386354923248291 s and adjustment time is 0.0211648941040039 s ( 54.78 )
2026-03-06 22:42:27.689731 INFO::Formatting Data.
2026-03-06 22:42:27.690728 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:27.691844 INFO::Removing potential empty rows and columns
2026-03-06 22:42:27.692945 INFO::Found 0 missing values.
2026-03-06 22:42:27.695518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:27.696152 INFO::Done
2026-03-06 22:42:27.696781 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:27.699211 INFO::Starting hierarchical adjustment
2026-03-06 22:42:27.700036 INFO::Found 2 batches.
2026-03-06 22:42:27.700657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:27.701371 INFO::Using default BPPARAM
2026-03-06 22:42:27.702022 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.703117 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 22:42:27.74092 INFO::Done
2026-03-06 22:42:27.741917 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.744455 INFO::ASW Batch was -0.0566230277329331 prior to batch effect correction and is now -0.13656781243103 .
2026-03-06 22:42:27.745431 INFO::Total function execution time is 0.0558905601501465 s and adjustment time is 0.0409941673278809 s ( 73.35 )
2026-03-06 22:42:27.76032 INFO::Formatting Data.
2026-03-06 22:42:27.761264 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:27.762358 INFO::Removing potential empty rows and columns
2026-03-06 22:42:27.763526 INFO::Found 0 missing values.
2026-03-06 22:42:27.765032 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 22:42:27.770435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:27.782249 INFO::Done
2026-03-06 22:42:27.782987 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:27.786638 INFO::Starting hierarchical adjustment
2026-03-06 22:42:27.787457 INFO::Found 2 batches.
2026-03-06 22:42:27.788089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:27.788839 INFO::Using default BPPARAM
2026-03-06 22:42:27.789442 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.79063 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 22:42:27.809854 INFO::Done
2026-03-06 22:42:27.81073 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.814168 INFO::ASW Batch was 0.526113174429757 prior to batch effect correction and is now 0.147708260551378 .
2026-03-06 22:42:27.814911 INFO::ASW Label was 0.601328511808261 prior to batch effect correction and is now 0.848311709663092 .
2026-03-06 22:42:27.815899 INFO::Total function execution time is 0.0556685924530029 s and adjustment time is 0.0225393772125244 s ( 40.49 )
2026-03-06 22:42:27.816844 INFO::Formatting Data.
2026-03-06 22:42:27.817564 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:27.818696 INFO::Removing potential empty rows and columns
2026-03-06 22:42:27.819853 INFO::Found 0 missing values.
2026-03-06 22:42:27.820903 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 22:42:27.82605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:27.826693 INFO::Done
2026-03-06 22:42:27.827288 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:27.830766 INFO::Starting hierarchical adjustment
2026-03-06 22:42:27.831536 INFO::Found 2 batches.
2026-03-06 22:42:27.832186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:27.832892 INFO::Using default BPPARAM
2026-03-06 22:42:27.833491 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:27.834588 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 22:42:27.854054 INFO::Done
2026-03-06 22:42:27.855042 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:27.85866 INFO::ASW Batch was 0.526113174429757 prior to batch effect correction and is now 0.147708260551378 .
2026-03-06 22:42:27.859469 INFO::ASW Label was 0.601328511808261 prior to batch effect correction and is now 0.848311709663092 .
2026-03-06 22:42:27.860483 INFO::Total function execution time is 0.0436279773712158 s and adjustment time is 0.0226027965545654 s ( 51.81 )
2026-03-06 22:42:28.103893 INFO::Formatting Data.
2026-03-06 22:42:28.104948 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:28.106097 INFO::Removing potential empty rows and columns
2026-03-06 22:42:28.107301 INFO::Found 0 missing values.
2026-03-06 22:42:28.110848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:28.111494 INFO::Done
2026-03-06 22:42:28.11213 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:28.114487 INFO::Starting hierarchical adjustment
2026-03-06 22:42:28.115306 INFO::Found 3 batches.
2026-03-06 22:42:28.115908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:28.116632 INFO::Using default BPPARAM
2026-03-06 22:42:28.117251 INFO::Processing subtree level 1
2026-03-06 22:42:28.224999 INFO::Adjusting the last 1 batches sequentially
2026-03-06 22:42:28.227196 INFO::Done
2026-03-06 22:42:28.228059 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:28.231102 INFO::ASW Batch was -0.0196394143649076 prior to batch effect correction and is now -0.0196394143649076 .
2026-03-06 22:42:28.232333 INFO::Total function execution time is 0.128587484359741 s and adjustment time is 0.112022161483765 s ( 87.12 )
2026-03-06 22:42:28.233768 INFO::Formatting Data.
2026-03-06 22:42:28.234504 INFO::Typecasting input to dataframe.
2026-03-06 22:42:28.235447 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:28.236603 INFO::Removing potential empty rows and columns
2026-03-06 22:42:28.237866 INFO::Found 0 missing values.
2026-03-06 22:42:28.241273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:28.242018 INFO::Done
2026-03-06 22:42:28.242656 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:28.245114 INFO::Starting hierarchical adjustment
2026-03-06 22:42:28.24597 INFO::Found 3 batches.
2026-03-06 22:42:28.246584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:28.247315 INFO::Using default BPPARAM
2026-03-06 22:42:28.247992 INFO::Processing subtree level 1
2026-03-06 22:42:28.349078 INFO::Adjusting the last 1 batches sequentially
2026-03-06 22:42:28.35125 INFO::Done
2026-03-06 22:42:28.352387 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:28.35588 INFO::ASW Batch was -0.0196394143649076 prior to batch effect correction and is now -0.0196394143649076 .
2026-03-06 22:42:28.357232 INFO::Total function execution time is 0.123440980911255 s and adjustment time is 0.105417013168335 s ( 85.4 )
2026-03-06 22:42:28.373053 INFO::Formatting Data.
2026-03-06 22:42:28.374097 INFO::Typecasting input to dataframe.
2026-03-06 22:42:28.375152 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:28.376264 INFO::Removing potential empty rows and columns
2026-03-06 22:42:28.377457 INFO::Found 0 missing values.
2026-03-06 22:42:28.380706 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:28.38133 INFO::Done
2026-03-06 22:42:28.381934 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:28.384363 INFO::Starting hierarchical adjustment
2026-03-06 22:42:28.385177 INFO::Found 3 batches.
2026-03-06 22:42:28.385772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:28.386466 INFO::Using default BPPARAM
2026-03-06 22:42:28.387083 INFO::Processing subtree level 1
2026-03-06 22:42:28.492248 INFO::Adjusting the last 1 batches sequentially
2026-03-06 22:42:28.49464 INFO::Done
2026-03-06 22:42:28.495426 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:28.498349 INFO::ASW Batch was 0.00628824908398701 prior to batch effect correction and is now 0.00628824908398701 .
2026-03-06 22:42:28.499476 INFO::Total function execution time is 0.126563310623169 s and adjustment time is 0.109589099884033 s ( 86.59 )
2026-03-06 22:42:28.659705 INFO::Formatting Data.
2026-03-06 22:42:28.660707 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:28.66201 INFO::Removing potential empty rows and columns
2026-03-06 22:42:28.665058 INFO::Found 1000 missing values.
2026-03-06 22:42:28.68511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:28.686056 INFO::Done
2026-03-06 22:42:28.68672 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:28.692626 INFO::Starting hierarchical adjustment
2026-03-06 22:42:28.693498 INFO::Found 10 batches.
2026-03-06 22:42:28.694122 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:28.694873 INFO::Using default BPPARAM
2026-03-06 22:42:28.69549 INFO::Processing subtree level 1
2026-03-06 22:42:28.863616 INFO::Processing subtree level 2
2026-03-06 22:42:29.217882 INFO::Adjusting the last 1 batches sequentially
2026-03-06 22:42:29.220185 INFO::Done
2026-03-06 22:42:29.220962 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:29.227047 INFO::ASW Batch was 0.541333181002722 prior to batch effect correction and is now 0.541333181002722 .
2026-03-06 22:42:29.227877 INFO::ASW Label was 0.302802463930127 prior to batch effect correction and is now 0.302802463930127 .
2026-03-06 22:42:29.228934 INFO::Total function execution time is 0.569352388381958 s and adjustment time is 0.526822090148926 s ( 92.53 )
2026-03-06 22:42:29.229893 INFO::Formatting Data.
2026-03-06 22:42:29.230598 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:29.231876 INFO::Removing potential empty rows and columns
2026-03-06 22:42:29.234899 INFO::Found 1000 missing values.
2026-03-06 22:42:29.30553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:29.306437 INFO::Done
2026-03-06 22:42:29.307087 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:29.312898 INFO::Starting hierarchical adjustment
2026-03-06 22:42:29.313769 INFO::Found 10 batches.
2026-03-06 22:42:30.786443 INFO::Set up parallel execution backend with 2 workers
2026-03-06 22:42:30.78775 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-06 22:42:32.149405 INFO::Adjusting the last 2 batches sequentially
2026-03-06 22:42:32.152678 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-06 22:42:32.169658 INFO::Done
2026-03-06 22:42:32.170426 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:32.175205 INFO::ASW Batch was 0.541333181002722 prior to batch effect correction and is now 0.541333181002722 .
2026-03-06 22:42:32.175874 INFO::ASW Label was 0.302802463930127 prior to batch effect correction and is now 0.302802463930127 .
2026-03-06 22:42:32.176687 INFO::Total function execution time is 2.94684553146362 s and adjustment time is 2.8560266494751 s ( 96.92 )
2026-03-06 22:42:32.340782 INFO::Formatting Data.
2026-03-06 22:42:32.341781 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.342892 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.344104 INFO::Found 0 missing values.
2026-03-06 22:42:32.348089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.348761 INFO::Done
2026-03-06 22:42:32.349354 INFO::Acquiring quality metrics before batch effect correction.
2026-03-06 22:42:32.352355 INFO::Starting hierarchical adjustment
2026-03-06 22:42:32.353154 INFO::Found 3 batches.
2026-03-06 22:42:32.353755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-06 22:42:32.35447 INFO::Using default BPPARAM
2026-03-06 22:42:32.355078 INFO::Processing subtree level 1
2026-03-06 22:42:32.472294 INFO::Adjusting the last 1 batches sequentially
2026-03-06 22:42:32.474564 INFO::Done
2026-03-06 22:42:32.475367 INFO::Acquiring quality metrics after batch effect correction.
2026-03-06 22:42:32.479167 INFO::ASW Batch was 0.138818216792133 prior to batch effect correction and is now -0.153129156968901 .
2026-03-06 22:42:32.479903 INFO::ASW Label was -0.191562649424703 prior to batch effect correction and is now 0.0159107485195532 .
2026-03-06 22:42:32.480997 INFO::Total function execution time is 0.140275239944458 s and adjustment time is 0.121507406234741 s ( 86.62 )
2026-03-06 22:42:32.614404 INFO::Formatting Data.
2026-03-06 22:42:32.615478 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.616581 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.617762 INFO::Found 2 missing values.
2026-03-06 22:42:32.620806 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.621433 INFO::Done
2026-03-06 22:42:32.65044 INFO::Found NA in Reference column
2026-03-06 22:42:32.660449 INFO::Require at least two references per batch.
2026-03-06 22:42:32.681323 INFO::Formatting Data.
2026-03-06 22:42:32.682227 INFO::Recognized SummarizedExperiment
2026-03-06 22:42:32.68285 INFO::Typecasting input to dataframe.
2026-03-06 22:42:32.69293 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.694304 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.698051 INFO::Found 0 missing values.
2026-03-06 22:42:32.70508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.705804 INFO::Done
2026-03-06 22:42:32.721895 INFO::Formatting Data.
2026-03-06 22:42:32.722831 INFO::Recognized SummarizedExperiment
2026-03-06 22:42:32.723457 INFO::Typecasting input to dataframe.
2026-03-06 22:42:32.741513 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.742945 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.746706 INFO::Found 0 missing values.
2026-03-06 22:42:32.75817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.759063 INFO::Done
2026-03-06 22:42:32.776071 INFO::Formatting Data.
2026-03-06 22:42:32.777091 INFO::Recognized SummarizedExperiment
2026-03-06 22:42:32.777769 INFO::Typecasting input to dataframe.
2026-03-06 22:42:32.796006 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.797357 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.798616 INFO::Found 0 missing values.
2026-03-06 22:42:32.799632 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 22:42:32.804309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.804962 INFO::Done
2026-03-06 22:42:32.815922 INFO::Formatting Data.
2026-03-06 22:42:32.816867 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.817835 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.818936 INFO::Found 0 missing values.
2026-03-06 22:42:32.821997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.822614 INFO::Done
2026-03-06 22:42:32.834903 INFO::Formatting Data.
2026-03-06 22:42:32.835869 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.836874 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.838009 INFO::Found 0 missing values.
2026-03-06 22:42:32.841041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.841654 INFO::Done
2026-03-06 22:42:32.872306 INFO::Formatting Data.
2026-03-06 22:42:32.873245 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.874387 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.875751 INFO::Found 1 missing values.
2026-03-06 22:42:32.878477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.879143 INFO::Done
2026-03-06 22:42:32.89952 INFO::Formatting Data.
2026-03-06 22:42:32.90064 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.901846 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.902948 INFO::Found 2 missing values.
2026-03-06 22:42:32.90405 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 22:42:32.906595 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.907169 INFO::Done
2026-03-06 22:42:32.917879 INFO::Formatting Data.
2026-03-06 22:42:32.918794 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.919762 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.920751 INFO::Found 2 missing values.
2026-03-06 22:42:32.922387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.922993 INFO::Done
2026-03-06 22:42:32.933863 INFO::Formatting Data.
2026-03-06 22:42:32.934782 INFO::Typecasting input to dataframe.
2026-03-06 22:42:32.935708 INFO::Replacing NaNs with NAs.
2026-03-06 22:42:32.936668 INFO::Removing potential empty rows and columns
2026-03-06 22:42:32.937734 INFO::Found 0 missing values.
2026-03-06 22:42:32.940632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-06 22:42:32.941196 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.816 4.411 24.049
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.889 | 1.912 | 21.741 | |
| compute_asw | 0.025 | 0.001 | 0.026 | |
| count_existing | 0.015 | 0.000 | 0.015 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.012 | 0.001 | 0.013 | |