Yannis Schumann
| Snapshot Date: 2026-01-26 13:45 -0500 (Mon, 26 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-29 11:58 -0500 (Thu, 29 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4886 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-01-26 21:34:26 -0500 (Mon, 26 Jan 2026) |
| EndedAt: 2026-01-26 21:35:56 -0500 (Mon, 26 Jan 2026) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 23.702 1.13 17
* 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-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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")
2026-01-26 21:35:18.421916 INFO::Formatting Data.
2026-01-26 21:35:18.42344 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:18.435251 INFO::Removing potential empty rows and columns
2026-01-26 21:35:18.689749 INFO::Found 0 missing values.
2026-01-26 21:35:18.693334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:18.694039 INFO::Done
2026-01-26 21:35:18.694615 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:18.705966 INFO::Starting hierarchical adjustment
2026-01-26 21:35:18.706866 INFO::Found 3 batches.
2026-01-26 21:35:18.707447 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:18.708651 INFO::Using default BPPARAM
2026-01-26 21:35:18.709229 INFO::Processing subtree level 1
2026-01-26 21:35:18.827718 INFO::Adjusting the last 1 batches sequentially
2026-01-26 21:35:18.829676 INFO::Done
2026-01-26 21:35:18.83037 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:18.833175 INFO::ASW Batch was -0.112030556108282 prior to batch effect correction and is now -0.112030556108282 .
2026-01-26 21:35:18.834281 INFO::Total function execution time is 0.413289546966553 s and adjustment time is 0.122971296310425 s ( 29.75 )
2026-01-26 21:35:18.848981 INFO::Formatting Data.
2026-01-26 21:35:18.849796 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:18.850788 INFO::Removing potential empty rows and columns
2026-01-26 21:35:18.852323 INFO::Found 0 missing values.
2026-01-26 21:35:18.853386 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.
2026-01-26 21:35:18.864989 INFO::Formatting Data.
2026-01-26 21:35:18.865759 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:18.866696 INFO::Removing potential empty rows and columns
2026-01-26 21:35:18.86776 INFO::Found 0 missing values.
2026-01-26 21:35:18.8687 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.
2026-01-26 21:35:18.885483 INFO::Formatting Data.
2026-01-26 21:35:18.886266 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:18.887362 INFO::Removing potential empty rows and columns
2026-01-26 21:35:18.888721 INFO::Found 0 missing values.
2026-01-26 21:35:18.88989 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.
2026-01-26 21:35:18.895713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:18.896387 INFO::Done
2026-01-26 21:35:18.897081 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:18.899679 INFO::Starting hierarchical adjustment
2026-01-26 21:35:18.90057 INFO::Found 2 batches.
2026-01-26 21:35:18.901203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:18.902018 INFO::Using default BPPARAM
2026-01-26 21:35:18.90269 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:18.90384 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-26 21:35:18.928503 INFO::Done
2026-01-26 21:35:18.9294 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:18.931732 INFO::ASW Batch was -0.0361261464608405 prior to batch effect correction and is now -0.115257631494041 .
2026-01-26 21:35:18.932672 INFO::Total function execution time is 0.0472397804260254 s and adjustment time is 0.0281310081481934 s ( 59.55 )
2026-01-26 21:35:18.93583 INFO::Formatting Data.
2026-01-26 21:35:18.936484 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:18.945917 INFO::Formatting Data.
2026-01-26 21:35:18.946631 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:18.947577 INFO::Removing potential empty rows and columns
2026-01-26 21:35:18.948673 INFO::Found 0 missing values.
2026-01-26 21:35:18.951747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:18.952311 INFO::Done
2026-01-26 21:35:18.952866 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:18.982298 INFO::Starting hierarchical adjustment
2026-01-26 21:35:18.985383 INFO::Found 2 batches.
2026-01-26 21:35:18.986064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:18.986685 INFO::Using default BPPARAM
2026-01-26 21:35:18.98722 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:18.988248 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-26 21:35:19.004077 INFO::Done
2026-01-26 21:35:19.004857 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:19.007063 INFO::ASW Batch was 0.0905453674498459 prior to batch effect correction and is now -0.0899417216858134 .
2026-01-26 21:35:19.007926 INFO::Total function execution time is 0.0620481967926025 s and adjustment time is 0.0189008712768555 s ( 30.46 )
2026-01-26 21:35:19.009055 INFO::Formatting Data.
2026-01-26 21:35:19.009696 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:19.010586 INFO::Removing potential empty rows and columns
2026-01-26 21:35:19.011611 INFO::Found 0 missing values.
2026-01-26 21:35:19.014416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:19.014955 INFO::Done
2026-01-26 21:35:19.015453 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:19.017536 INFO::Starting hierarchical adjustment
2026-01-26 21:35:19.018244 INFO::Found 2 batches.
2026-01-26 21:35:19.018754 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:19.019353 INFO::Using default BPPARAM
2026-01-26 21:35:19.01988 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:19.020804 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-26 21:35:19.036559 INFO::Done
2026-01-26 21:35:19.037313 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:19.039503 INFO::ASW Batch was 0.0905453674498459 prior to batch effect correction and is now -0.0899417216858134 .
2026-01-26 21:35:19.040353 INFO::Total function execution time is 0.0313131809234619 s and adjustment time is 0.0184090137481689 s ( 58.79 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-26 21:35:22.503503 INFO::Formatting Data.
2026-01-26 21:35:22.504231 INFO::Recognized SummarizedExperiment
2026-01-26 21:35:22.504719 INFO::Typecasting input to dataframe.
2026-01-26 21:35:22.544976 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:22.546396 INFO::Removing potential empty rows and columns
2026-01-26 21:35:22.5504 INFO::Found 0 missing values.
2026-01-26 21:35:22.557888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:22.558559 INFO::Done
2026-01-26 21:35:22.5591 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:22.563079 INFO::Starting hierarchical adjustment
2026-01-26 21:35:22.56385 INFO::Found 2 batches.
2026-01-26 21:35:22.564372 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:22.565555 INFO::Using default BPPARAM
2026-01-26 21:35:22.566102 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:22.567113 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-26 21:35:22.627173 INFO::Done
2026-01-26 21:35:22.627908 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:22.631585 INFO::ASW Batch was 0.0102962589912745 prior to batch effect correction and is now -0.0900301025820305 .
2026-01-26 21:35:22.63248 INFO::Total function execution time is 0.129232168197632 s and adjustment time is 0.0634753704071045 s ( 49.12 )
Warning: stack imbalance in '{', 73 then 75
2026-01-26 21:35:22.652477 INFO::Formatting Data.
2026-01-26 21:35:22.653253 INFO::Recognized SummarizedExperiment
2026-01-26 21:35:22.653819 INFO::Typecasting input to dataframe.
2026-01-26 21:35:22.663441 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:22.66467 INFO::Removing potential empty rows and columns
2026-01-26 21:35:22.668535 INFO::Found 0 missing values.
2026-01-26 21:35:22.675744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:22.6764 INFO::Done
2026-01-26 21:35:22.676966 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:22.680658 INFO::Starting hierarchical adjustment
2026-01-26 21:35:22.681402 INFO::Found 2 batches.
2026-01-26 21:35:22.681951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:22.682558 INFO::Using default BPPARAM
2026-01-26 21:35:22.683087 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:22.684116 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-26 21:35:22.709967 INFO::Done
2026-01-26 21:35:22.710704 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:22.714522 INFO::ASW Batch was -0.00771579079218332 prior to batch effect correction and is now -0.00771579079218332 .
2026-01-26 21:35:22.715411 INFO::Total function execution time is 0.0629301071166992 s and adjustment time is 0.0286698341369629 s ( 45.56 )
2026-01-26 21:35:22.734305 INFO::Formatting Data.
2026-01-26 21:35:22.73523 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:22.736165 INFO::Removing potential empty rows and columns
2026-01-26 21:35:22.73721 INFO::Found 0 missing values.
2026-01-26 21:35:22.740238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:22.740812 INFO::Done
2026-01-26 21:35:22.741317 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:22.743404 INFO::Starting hierarchical adjustment
2026-01-26 21:35:22.744117 INFO::Found 3 batches.
2026-01-26 21:35:22.744647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:22.745387 INFO::Using default BPPARAM
2026-01-26 21:35:22.745918 INFO::Processing subtree level 1
2026-01-26 21:35:22.888049 INFO::Adjusting the last 1 batches sequentially
2026-01-26 21:35:22.88992 INFO::Done
2026-01-26 21:35:22.890605 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:22.893196 INFO::ASW Batch was 0.000595318327977757 prior to batch effect correction and is now -0.175155745106317 .
2026-01-26 21:35:22.894165 INFO::Total function execution time is 0.159909009933472 s and adjustment time is 0.145907878875732 s ( 91.24 )
2026-01-26 21:35:22.90921 INFO::Skipping initial DF formatting
2026-01-26 21:35:22.909946 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:22.914116 INFO::Starting hierarchical adjustment
2026-01-26 21:35:22.914946 INFO::Found 5 batches.
2026-01-26 21:35:22.915485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:22.916115 INFO::Using default BPPARAM
2026-01-26 21:35:22.916651 INFO::Processing subtree level 1
2026-01-26 21:35:23.217773 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:23.219603 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-26 21:35:23.240268 INFO::Done
2026-01-26 21:35:23.241114 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:23.246001 INFO::ASW Batch was 0.525483096802742 prior to batch effect correction and is now 0.525483096802742 .
2026-01-26 21:35:23.246843 INFO::ASW Label was 0.363089218330367 prior to batch effect correction and is now 0.363089218330367 .
2026-01-26 21:35:23.248191 INFO::Total function execution time is 0.338986873626709 s and adjustment time is 0.325439453125 s ( 96 )
2026-01-26 21:35:23.323554 INFO::Formatting Data.
2026-01-26 21:35:23.32442 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:23.325378 INFO::Removing potential empty rows and columns
2026-01-26 21:35:23.326418 INFO::Found 0 missing values.
2026-01-26 21:35:23.3306 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:23.331155 INFO::Done
2026-01-26 21:35:23.331698 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:23.334933 INFO::Starting hierarchical adjustment
2026-01-26 21:35:23.335725 INFO::Found 5 batches.
2026-01-26 21:35:23.336287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:23.336957 INFO::Using default BPPARAM
2026-01-26 21:35:23.337492 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.
2026-01-26 21:35:23.512808 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:23.515164 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-26 21:35:23.535221 INFO::Done
2026-01-26 21:35:23.536104 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:23.54002 INFO::ASW Batch was 0.400279492544034 prior to batch effect correction and is now -0.0554897630058107 .
2026-01-26 21:35:23.540739 INFO::ASW Label was 0.285093028517437 prior to batch effect correction and is now 0.801508500092471 .
2026-01-26 21:35:23.541724 INFO::Total function execution time is 0.218194484710693 s and adjustment time is 0.199671745300293 s ( 91.51 )
2026-01-26 21:35:23.542708 INFO::Formatting Data.
2026-01-26 21:35:23.543432 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:23.544466 INFO::Removing potential empty rows and columns
2026-01-26 21:35:23.545618 INFO::Found 0 missing values.
2026-01-26 21:35:23.550461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:23.551081 INFO::Done
2026-01-26 21:35:23.557254 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:23.561172 INFO::Starting hierarchical adjustment
2026-01-26 21:35:23.562035 INFO::Found 5 batches.
2026-01-26 21:35:23.562631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:23.563353 INFO::Using default BPPARAM
2026-01-26 21:35:23.563977 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.
2026-01-26 21:35:23.725434 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:23.727225 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-26 21:35:23.74518 INFO::Done
2026-01-26 21:35:23.745971 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:23.749639 INFO::ASW Batch was 0.400279492544034 prior to batch effect correction and is now -0.0554897630058107 .
2026-01-26 21:35:23.750287 INFO::ASW Label was 0.285093028517437 prior to batch effect correction and is now 0.801508500092471 .
2026-01-26 21:35:23.751211 INFO::Total function execution time is 0.20849871635437 s and adjustment time is 0.183306932449341 s ( 87.92 )
2026-01-26 21:35:23.766081 INFO::Formatting Data.
2026-01-26 21:35:23.766906 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:23.767912 INFO::Removing potential empty rows and columns
2026-01-26 21:35:23.769113 INFO::Found 0 missing values.
2026-01-26 21:35:23.773448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:23.774016 INFO::Done
2026-01-26 21:35:23.774553 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:23.777862 INFO::Starting hierarchical adjustment
2026-01-26 21:35:23.778627 INFO::Found 5 batches.
2026-01-26 21:35:23.779165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:23.779824 INFO::Using default BPPARAM
2026-01-26 21:35:23.780365 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.
2026-01-26 21:35:23.94093 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:23.943072 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-26 21:35:23.96121 INFO::Done
2026-01-26 21:35:23.962061 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:23.965675 INFO::ASW Batch was 0.294700566487678 prior to batch effect correction and is now -0.0778378420128273 .
2026-01-26 21:35:23.966315 INFO::ASW Label was 0.444836502922576 prior to batch effect correction and is now 0.847151613252097 .
2026-01-26 21:35:23.967212 INFO::Total function execution time is 0.201209545135498 s and adjustment time is 0.182730674743652 s ( 90.82 )
2026-01-26 21:35:23.968098 INFO::Formatting Data.
2026-01-26 21:35:23.968781 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:23.969724 INFO::Removing potential empty rows and columns
2026-01-26 21:35:23.970818 INFO::Found 0 missing values.
2026-01-26 21:35:23.975111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:23.975714 INFO::Done
2026-01-26 21:35:23.976255 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:23.979538 INFO::Starting hierarchical adjustment
2026-01-26 21:35:23.980298 INFO::Found 5 batches.
2026-01-26 21:35:23.980891 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:23.981549 INFO::Using default BPPARAM
2026-01-26 21:35:23.982123 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.
2026-01-26 21:35:24.133743 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:24.135932 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-26 21:35:24.154876 INFO::Done
2026-01-26 21:35:24.155696 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.159647 INFO::ASW Batch was 0.294700566487678 prior to batch effect correction and is now -0.0778378420128273 .
2026-01-26 21:35:24.160461 INFO::ASW Label was 0.444836502922576 prior to batch effect correction and is now 0.847151613252097 .
2026-01-26 21:35:24.161603 INFO::Total function execution time is 0.1934974193573 s and adjustment time is 0.174683570861816 s ( 90.28 )
2026-01-26 21:35:24.176322 INFO::Formatting Data.
2026-01-26 21:35:24.177167 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:24.178179 INFO::Removing potential empty rows and columns
2026-01-26 21:35:24.179324 INFO::Found 0 missing values.
2026-01-26 21:35:24.182304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:24.182919 INFO::Done
2026-01-26 21:35:24.183473 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:24.186838 INFO::Starting hierarchical adjustment
2026-01-26 21:35:24.187623 INFO::Found 2 batches.
2026-01-26 21:35:24.188192 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:24.188845 INFO::Using default BPPARAM
2026-01-26 21:35:24.189417 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:24.190392 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-26 21:35:24.206201 INFO::Done
2026-01-26 21:35:24.206915 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.210137 INFO::ASW Batch was 0.566844297123371 prior to batch effect correction and is now 0.0474966763104045 .
2026-01-26 21:35:24.210795 INFO::ASW Label was 0.561956930861647 prior to batch effect correction and is now 0.905252327822972 .
2026-01-26 21:35:24.211637 INFO::Total function execution time is 0.0353994369506836 s and adjustment time is 0.0187408924102783 s ( 52.94 )
2026-01-26 21:35:24.212502 INFO::Formatting Data.
2026-01-26 21:35:24.213194 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:24.214125 INFO::Removing potential empty rows and columns
2026-01-26 21:35:24.215206 INFO::Found 0 missing values.
2026-01-26 21:35:24.218169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:24.218757 INFO::Done
2026-01-26 21:35:24.219298 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:24.222645 INFO::Starting hierarchical adjustment
2026-01-26 21:35:24.223472 INFO::Found 2 batches.
2026-01-26 21:35:24.224077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:24.224757 INFO::Using default BPPARAM
2026-01-26 21:35:24.225314 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:24.226295 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-26 21:35:24.242377 INFO::Done
2026-01-26 21:35:24.243124 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.24636 INFO::ASW Batch was 0.566844297123371 prior to batch effect correction and is now 0.0474966763104045 .
2026-01-26 21:35:24.247015 INFO::ASW Label was 0.561956930861647 prior to batch effect correction and is now 0.905252327822972 .
2026-01-26 21:35:24.247852 INFO::Total function execution time is 0.0353679656982422 s and adjustment time is 0.019057035446167 s ( 53.88 )
2026-01-26 21:35:24.260085 INFO::Formatting Data.
2026-01-26 21:35:24.260892 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:24.261892 INFO::Removing potential empty rows and columns
2026-01-26 21:35:24.262922 INFO::Found 0 missing values.
2026-01-26 21:35:24.265314 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:24.265915 INFO::Done
2026-01-26 21:35:24.26646 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:24.268596 INFO::Starting hierarchical adjustment
2026-01-26 21:35:24.269337 INFO::Found 2 batches.
2026-01-26 21:35:24.269912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:24.270569 INFO::Using default BPPARAM
2026-01-26 21:35:24.271105 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:24.272037 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-26 21:35:24.305309 INFO::Done
2026-01-26 21:35:24.306054 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.308094 INFO::ASW Batch was -0.162561274705831 prior to batch effect correction and is now -0.163914649307744 .
2026-01-26 21:35:24.308954 INFO::Total function execution time is 0.0489664077758789 s and adjustment time is 0.0361063480377197 s ( 73.74 )
2026-01-26 21:35:24.321397 INFO::Formatting Data.
2026-01-26 21:35:24.3222 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:24.323126 INFO::Removing potential empty rows and columns
2026-01-26 21:35:24.32417 INFO::Found 0 missing values.
2026-01-26 21:35:24.325384 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.
2026-01-26 21:35:24.33014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:24.330719 INFO::Done
2026-01-26 21:35:24.331241 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:24.334249 INFO::Starting hierarchical adjustment
2026-01-26 21:35:24.33497 INFO::Found 2 batches.
2026-01-26 21:35:24.3355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:24.336126 INFO::Using default BPPARAM
2026-01-26 21:35:24.33666 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:24.337602 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-26 21:35:24.355086 INFO::Done
2026-01-26 21:35:24.355817 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.358886 INFO::ASW Batch was 0.755001254136163 prior to batch effect correction and is now 0.159017317768697 .
2026-01-26 21:35:24.359494 INFO::ASW Label was 0.304467388894769 prior to batch effect correction and is now 0.764490348929887 .
2026-01-26 21:35:24.360286 INFO::Total function execution time is 0.0389630794525146 s and adjustment time is 0.0202341079711914 s ( 51.93 )
2026-01-26 21:35:24.361095 INFO::Formatting Data.
2026-01-26 21:35:24.361735 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:24.362838 INFO::Removing potential empty rows and columns
2026-01-26 21:35:24.36389 INFO::Found 0 missing values.
2026-01-26 21:35:24.3648 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.
2026-01-26 21:35:24.369433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:24.370014 INFO::Done
2026-01-26 21:35:24.37053 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:24.373537 INFO::Starting hierarchical adjustment
2026-01-26 21:35:24.374267 INFO::Found 2 batches.
2026-01-26 21:35:24.374815 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:24.375427 INFO::Using default BPPARAM
2026-01-26 21:35:24.375984 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:24.37695 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-26 21:35:24.3941 INFO::Done
2026-01-26 21:35:24.394793 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.397794 INFO::ASW Batch was 0.755001254136163 prior to batch effect correction and is now 0.159017317768697 .
2026-01-26 21:35:24.398405 INFO::ASW Label was 0.304467388894769 prior to batch effect correction and is now 0.764490348929887 .
2026-01-26 21:35:24.399245 INFO::Total function execution time is 0.0381512641906738 s and adjustment time is 0.0199527740478516 s ( 52.3 )
2026-01-26 21:35:24.620353 INFO::Formatting Data.
2026-01-26 21:35:24.621201 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:24.622132 INFO::Removing potential empty rows and columns
2026-01-26 21:35:24.623176 INFO::Found 0 missing values.
2026-01-26 21:35:24.626253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:24.626808 INFO::Done
2026-01-26 21:35:24.627331 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:24.629385 INFO::Starting hierarchical adjustment
2026-01-26 21:35:24.630109 INFO::Found 3 batches.
2026-01-26 21:35:24.630648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:24.63125 INFO::Using default BPPARAM
2026-01-26 21:35:24.631781 INFO::Processing subtree level 1
2026-01-26 21:35:24.720913 INFO::Adjusting the last 1 batches sequentially
2026-01-26 21:35:24.722703 INFO::Done
2026-01-26 21:35:24.723349 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.725844 INFO::ASW Batch was -0.13446706440587 prior to batch effect correction and is now -0.13446706440587 .
2026-01-26 21:35:24.726795 INFO::Total function execution time is 0.106525182723999 s and adjustment time is 0.0927190780639648 s ( 87.04 )
2026-01-26 21:35:24.727868 INFO::Formatting Data.
2026-01-26 21:35:24.728543 INFO::Typecasting input to dataframe.
2026-01-26 21:35:24.729312 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:24.730237 INFO::Removing potential empty rows and columns
2026-01-26 21:35:24.731315 INFO::Found 0 missing values.
2026-01-26 21:35:24.734442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:24.734995 INFO::Done
2026-01-26 21:35:24.735543 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:24.737602 INFO::Starting hierarchical adjustment
2026-01-26 21:35:24.738323 INFO::Found 3 batches.
2026-01-26 21:35:24.738882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:24.739538 INFO::Using default BPPARAM
2026-01-26 21:35:24.740086 INFO::Processing subtree level 1
2026-01-26 21:35:24.828575 INFO::Adjusting the last 1 batches sequentially
2026-01-26 21:35:24.8305 INFO::Done
2026-01-26 21:35:24.831203 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.833674 INFO::ASW Batch was -0.13446706440587 prior to batch effect correction and is now -0.13446706440587 .
2026-01-26 21:35:24.834611 INFO::Total function execution time is 0.106722354888916 s and adjustment time is 0.0922946929931641 s ( 86.48 )
2026-01-26 21:35:24.847934 INFO::Formatting Data.
2026-01-26 21:35:24.84878 INFO::Typecasting input to dataframe.
2026-01-26 21:35:24.849655 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:24.850596 INFO::Removing potential empty rows and columns
2026-01-26 21:35:24.851717 INFO::Found 0 missing values.
2026-01-26 21:35:24.85484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:24.855378 INFO::Done
2026-01-26 21:35:24.855915 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:24.858386 INFO::Starting hierarchical adjustment
2026-01-26 21:35:24.859125 INFO::Found 3 batches.
2026-01-26 21:35:24.85967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:24.860296 INFO::Using default BPPARAM
2026-01-26 21:35:24.860849 INFO::Processing subtree level 1
2026-01-26 21:35:24.947837 INFO::Adjusting the last 1 batches sequentially
2026-01-26 21:35:24.949632 INFO::Done
2026-01-26 21:35:24.950295 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:24.95279 INFO::ASW Batch was -0.0644150697075712 prior to batch effect correction and is now -0.0644150697075712 .
2026-01-26 21:35:24.953732 INFO::Total function execution time is 0.105852127075195 s and adjustment time is 0.0906245708465576 s ( 85.61 )
2026-01-26 21:35:25.100214 INFO::Formatting Data.
2026-01-26 21:35:25.101129 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:25.102298 INFO::Removing potential empty rows and columns
2026-01-26 21:35:25.105108 INFO::Found 1000 missing values.
2026-01-26 21:35:25.124347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:25.125129 INFO::Done
2026-01-26 21:35:25.125715 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:25.131441 INFO::Starting hierarchical adjustment
2026-01-26 21:35:25.132246 INFO::Found 10 batches.
2026-01-26 21:35:25.132792 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:25.133414 INFO::Using default BPPARAM
2026-01-26 21:35:25.133966 INFO::Processing subtree level 1
2026-01-26 21:35:25.271657 INFO::Processing subtree level 2
2026-01-26 21:35:25.412631 INFO::Adjusting the last 1 batches sequentially
2026-01-26 21:35:25.414613 INFO::Done
2026-01-26 21:35:25.415257 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:25.420802 INFO::ASW Batch was 0.483994552065493 prior to batch effect correction and is now 0.483994552065493 .
2026-01-26 21:35:25.421431 INFO::ASW Label was 0.362928598478237 prior to batch effect correction and is now 0.362928598478237 .
2026-01-26 21:35:25.422366 INFO::Total function execution time is 0.322277307510376 s and adjustment time is 0.282498121261597 s ( 87.66 )
2026-01-26 21:35:25.4232 INFO::Formatting Data.
2026-01-26 21:35:25.423838 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:25.425045 INFO::Removing potential empty rows and columns
2026-01-26 21:35:25.427822 INFO::Found 1000 missing values.
2026-01-26 21:35:25.446587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:25.44733 INFO::Done
2026-01-26 21:35:25.447887 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:25.453369 INFO::Starting hierarchical adjustment
2026-01-26 21:35:25.454164 INFO::Found 10 batches.
2026-01-26 21:35:26.63975 INFO::Set up parallel execution backend with 2 workers
2026-01-26 21:35:26.641611 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-26 21:35:27.779495 INFO::Adjusting the last 2 batches sequentially
2026-01-26 21:35:27.781367 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-26 21:35:27.797537 INFO::Done
2026-01-26 21:35:27.79825 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:27.802843 INFO::ASW Batch was 0.483994552065493 prior to batch effect correction and is now 0.483994552065493 .
2026-01-26 21:35:27.803413 INFO::ASW Label was 0.362928598478237 prior to batch effect correction and is now 0.362928598478237 .
2026-01-26 21:35:27.804142 INFO::Total function execution time is 2.38097858428955 s and adjustment time is 2.34348845481873 s ( 98.43 )
2026-01-26 21:35:27.944701 INFO::Formatting Data.
2026-01-26 21:35:27.945426 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:27.9463 INFO::Removing potential empty rows and columns
2026-01-26 21:35:27.94731 INFO::Found 0 missing values.
2026-01-26 21:35:27.950756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:27.951272 INFO::Done
2026-01-26 21:35:27.951769 INFO::Acquiring quality metrics before batch effect correction.
2026-01-26 21:35:27.954376 INFO::Starting hierarchical adjustment
2026-01-26 21:35:27.955054 INFO::Found 3 batches.
2026-01-26 21:35:27.955554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-26 21:35:27.956133 INFO::Using default BPPARAM
2026-01-26 21:35:27.956635 INFO::Processing subtree level 1
2026-01-26 21:35:28.058843 INFO::Adjusting the last 1 batches sequentially
2026-01-26 21:35:28.060582 INFO::Done
2026-01-26 21:35:28.061206 INFO::Acquiring quality metrics after batch effect correction.
2026-01-26 21:35:28.064299 INFO::ASW Batch was 0.210425949868673 prior to batch effect correction and is now -0.148991524860667 .
2026-01-26 21:35:28.064915 INFO::ASW Label was -0.197528343420659 prior to batch effect correction and is now -0.0888976534855105 .
2026-01-26 21:35:28.065797 INFO::Total function execution time is 0.121148347854614 s and adjustment time is 0.105624675750732 s ( 87.19 )
2026-01-26 21:35:28.1916 INFO::Formatting Data.
2026-01-26 21:35:28.19245 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.193341 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.194386 INFO::Found 2 missing values.
2026-01-26 21:35:28.197085 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.197625 INFO::Done
2026-01-26 21:35:28.223396 INFO::Found NA in Reference column
2026-01-26 21:35:28.232325 INFO::Require at least two references per batch.
2026-01-26 21:35:28.252071 INFO::Formatting Data.
2026-01-26 21:35:28.252796 INFO::Recognized SummarizedExperiment
2026-01-26 21:35:28.253289 INFO::Typecasting input to dataframe.
2026-01-26 21:35:28.262599 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.263653 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.266901 INFO::Found 0 missing values.
2026-01-26 21:35:28.273181 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.273732 INFO::Done
2026-01-26 21:35:28.288528 INFO::Formatting Data.
2026-01-26 21:35:28.289217 INFO::Recognized SummarizedExperiment
2026-01-26 21:35:28.28974 INFO::Typecasting input to dataframe.
2026-01-26 21:35:28.306094 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.307273 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.31057 INFO::Found 0 missing values.
2026-01-26 21:35:28.320626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.321215 INFO::Done
2026-01-26 21:35:28.335844 INFO::Formatting Data.
2026-01-26 21:35:28.336487 INFO::Recognized SummarizedExperiment
2026-01-26 21:35:28.336979 INFO::Typecasting input to dataframe.
2026-01-26 21:35:28.352452 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.353415 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.354411 INFO::Found 0 missing values.
2026-01-26 21:35:28.355279 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.
2026-01-26 21:35:28.35934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.359862 INFO::Done
2026-01-26 21:35:28.369192 INFO::Formatting Data.
2026-01-26 21:35:28.369949 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.370759 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.371693 INFO::Found 0 missing values.
2026-01-26 21:35:28.374342 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.374849 INFO::Done
2026-01-26 21:35:28.386016 INFO::Formatting Data.
2026-01-26 21:35:28.386907 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.387957 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.389011 INFO::Found 0 missing values.
2026-01-26 21:35:28.39197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.392536 INFO::Done
2026-01-26 21:35:28.423974 INFO::Formatting Data.
2026-01-26 21:35:28.424863 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.42595 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.427241 INFO::Found 1 missing values.
2026-01-26 21:35:28.430153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.430737 INFO::Done
2026-01-26 21:35:28.451852 INFO::Formatting Data.
2026-01-26 21:35:28.45273 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.45366 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.454719 INFO::Found 2 missing values.
2026-01-26 21:35:28.455682 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.
2026-01-26 21:35:28.458183 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.458747 INFO::Done
2026-01-26 21:35:28.469435 INFO::Formatting Data.
2026-01-26 21:35:28.470276 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.471193 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.472162 INFO::Found 2 missing values.
2026-01-26 21:35:28.473919 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.474467 INFO::Done
2026-01-26 21:35:28.484998 INFO::Formatting Data.
2026-01-26 21:35:28.485689 INFO::Typecasting input to dataframe.
2026-01-26 21:35:28.486451 INFO::Replacing NaNs with NAs.
2026-01-26 21:35:28.487284 INFO::Removing potential empty rows and columns
2026-01-26 21:35:28.488256 INFO::Found 0 missing values.
2026-01-26 21:35:28.491178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-26 21:35:28.491723 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.166 4.906 22.769
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.702 | 1.130 | 17.000 | |
| compute_asw | 0.024 | 0.001 | 0.025 | |
| count_existing | 0.014 | 0.001 | 0.014 | |
| generate_data_covariables | 0.011 | 0.003 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |