Yannis Schumann
| Snapshot Date: 2026-01-01 13:45 -0500 (Thu, 01 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 Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-05 11:57 -0500 (Mon, 05 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" | 4883 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /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: 2026-01-01 21:20:26 -0500 (Thu, 01 Jan 2026) |
| EndedAt: 2026-01-01 21:21:56 -0500 (Thu, 01 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 25.131 1.307 17.921
* 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")
2026-01-01 21:21:18.209161 INFO::Formatting Data.
2026-01-01 21:21:18.210359 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:18.221065 INFO::Removing potential empty rows and columns
2026-01-01 21:21:18.491685 INFO::Found 0 missing values.
2026-01-01 21:21:18.495287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:18.495946 INFO::Done
2026-01-01 21:21:18.496529 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:18.50756 INFO::Starting hierarchical adjustment
2026-01-01 21:21:18.508336 INFO::Found 3 batches.
2026-01-01 21:21:18.508894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:18.510021 INFO::Using default BPPARAM
2026-01-01 21:21:18.510582 INFO::Processing subtree level 1
2026-01-01 21:21:18.611624 INFO::Adjusting the last 1 batches sequentially
2026-01-01 21:21:18.613359 INFO::Done
2026-01-01 21:21:18.614036 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:18.61668 INFO::ASW Batch was -0.000256888718976889 prior to batch effect correction and is now -0.000256888718976889 .
2026-01-01 21:21:18.617792 INFO::Total function execution time is 0.409176588058472 s and adjustment time is 0.10518217086792 s ( 25.71 )
2026-01-01 21:21:18.632109 INFO::Formatting Data.
2026-01-01 21:21:18.632895 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:18.633891 INFO::Removing potential empty rows and columns
2026-01-01 21:21:18.635109 INFO::Found 0 missing values.
2026-01-01 21:21:18.636089 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.
2026-01-01 21:21:18.647403 INFO::Formatting Data.
2026-01-01 21:21:18.64809 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:18.648976 INFO::Removing potential empty rows and columns
2026-01-01 21:21:18.650062 INFO::Found 0 missing values.
2026-01-01 21:21:18.651035 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.
2026-01-01 21:21:18.668397 INFO::Formatting Data.
2026-01-01 21:21:18.669175 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:18.670109 INFO::Removing potential empty rows and columns
2026-01-01 21:21:18.671198 INFO::Found 0 missing values.
2026-01-01 21:21:18.672165 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.
2026-01-01 21:21:18.676956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:18.677542 INFO::Done
2026-01-01 21:21:18.678096 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:18.680166 INFO::Starting hierarchical adjustment
2026-01-01 21:21:18.680915 INFO::Found 2 batches.
2026-01-01 21:21:18.681455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:18.682114 INFO::Using default BPPARAM
2026-01-01 21:21:18.682668 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:18.683633 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-01 21:21:18.705359 INFO::Done
2026-01-01 21:21:18.706118 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:18.708172 INFO::ASW Batch was 0.0507613554383244 prior to batch effect correction and is now -0.12150595357193 .
2026-01-01 21:21:18.708968 INFO::Total function execution time is 0.0406494140625 s and adjustment time is 0.0245707035064697 s ( 60.45 )
2026-01-01 21:21:18.71177 INFO::Formatting Data.
2026-01-01 21:21:18.712392 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:18.721265 INFO::Formatting Data.
2026-01-01 21:21:18.721969 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:18.72287 INFO::Removing potential empty rows and columns
2026-01-01 21:21:18.724192 INFO::Found 0 missing values.
2026-01-01 21:21:18.727196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:18.72775 INFO::Done
2026-01-01 21:21:18.728277 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:18.730287 INFO::Starting hierarchical adjustment
2026-01-01 21:21:18.731005 INFO::Found 2 batches.
2026-01-01 21:21:18.73156 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:18.755206 INFO::Using default BPPARAM
2026-01-01 21:21:18.757385 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:18.758315 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-01 21:21:18.77204 INFO::Done
2026-01-01 21:21:18.772619 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:18.774516 INFO::ASW Batch was -0.0249550772477162 prior to batch effect correction and is now -0.105913405219736 .
2026-01-01 21:21:18.775253 INFO::Total function execution time is 0.0540266036987305 s and adjustment time is 0.0411920547485352 s ( 76.24 )
2026-01-01 21:21:18.77624 INFO::Formatting Data.
2026-01-01 21:21:18.776814 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:18.7776 INFO::Removing potential empty rows and columns
2026-01-01 21:21:18.778537 INFO::Found 0 missing values.
2026-01-01 21:21:18.781155 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:18.78167 INFO::Done
2026-01-01 21:21:18.782165 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:18.784027 INFO::Starting hierarchical adjustment
2026-01-01 21:21:18.784713 INFO::Found 2 batches.
2026-01-01 21:21:18.785218 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:18.785814 INFO::Using default BPPARAM
2026-01-01 21:21:18.786315 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:18.787177 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-01 21:21:18.801424 INFO::Done
2026-01-01 21:21:18.802009 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:18.803894 INFO::ASW Batch was -0.0249550772477162 prior to batch effect correction and is now -0.105913405219736 .
2026-01-01 21:21:18.804631 INFO::Total function execution time is 0.0283823013305664 s and adjustment time is 0.0168642997741699 s ( 59.42 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-01 21:21:21.545827 INFO::Formatting Data.
2026-01-01 21:21:21.54649 INFO::Recognized SummarizedExperiment
2026-01-01 21:21:21.546967 INFO::Typecasting input to dataframe.
2026-01-01 21:21:21.575767 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:21.577021 INFO::Removing potential empty rows and columns
2026-01-01 21:21:21.580831 INFO::Found 0 missing values.
2026-01-01 21:21:21.588175 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:21.588797 INFO::Done
2026-01-01 21:21:21.589324 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:21.592904 INFO::Starting hierarchical adjustment
2026-01-01 21:21:21.59362 INFO::Found 2 batches.
2026-01-01 21:21:21.594141 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:21.595205 INFO::Using default BPPARAM
2026-01-01 21:21:21.595757 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:21.596728 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-01 21:21:21.652488 INFO::Done
2026-01-01 21:21:21.653182 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:21.656717 INFO::ASW Batch was -0.00778098559263848 prior to batch effect correction and is now -0.0965689866651569 .
2026-01-01 21:21:21.657551 INFO::Total function execution time is 0.11199688911438 s and adjustment time is 0.05899977684021 s ( 52.68 )
Warning: stack imbalance in '{', 73 then 75
2026-01-01 21:21:21.676081 INFO::Formatting Data.
2026-01-01 21:21:21.676809 INFO::Recognized SummarizedExperiment
2026-01-01 21:21:21.677339 INFO::Typecasting input to dataframe.
2026-01-01 21:21:21.686725 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:21.687826 INFO::Removing potential empty rows and columns
2026-01-01 21:21:21.691458 INFO::Found 0 missing values.
2026-01-01 21:21:21.698446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:21.699041 INFO::Done
2026-01-01 21:21:21.699561 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:21.703102 INFO::Starting hierarchical adjustment
2026-01-01 21:21:21.70385 INFO::Found 2 batches.
2026-01-01 21:21:21.704373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:21.704969 INFO::Using default BPPARAM
2026-01-01 21:21:21.70548 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:21.706439 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-01 21:21:21.731285 INFO::Done
2026-01-01 21:21:21.731974 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:21.735724 INFO::ASW Batch was 0.0127766918326231 prior to batch effect correction and is now 0.0127766918326231 .
2026-01-01 21:21:21.736561 INFO::Total function execution time is 0.0604531764984131 s and adjustment time is 0.0275437831878662 s ( 45.56 )
2026-01-01 21:21:21.754471 INFO::Formatting Data.
2026-01-01 21:21:21.755261 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:21.756166 INFO::Removing potential empty rows and columns
2026-01-01 21:21:21.757236 INFO::Found 0 missing values.
2026-01-01 21:21:21.760171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:21.76072 INFO::Done
2026-01-01 21:21:21.761226 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:21.763248 INFO::Starting hierarchical adjustment
2026-01-01 21:21:21.763952 INFO::Found 3 batches.
2026-01-01 21:21:21.76446 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:21.765103 INFO::Using default BPPARAM
2026-01-01 21:21:21.765643 INFO::Processing subtree level 1
2026-01-01 21:21:21.90217 INFO::Adjusting the last 1 batches sequentially
2026-01-01 21:21:21.903929 INFO::Done
2026-01-01 21:21:21.904562 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:21.907005 INFO::ASW Batch was -0.103659148229159 prior to batch effect correction and is now -0.181446131874486 .
2026-01-01 21:21:21.907936 INFO::Total function execution time is 0.153494119644165 s and adjustment time is 0.140102863311768 s ( 91.28 )
2026-01-01 21:21:21.922285 INFO::Skipping initial DF formatting
2026-01-01 21:21:21.922994 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:21.927131 INFO::Starting hierarchical adjustment
2026-01-01 21:21:21.927941 INFO::Found 5 batches.
2026-01-01 21:21:21.928476 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:21.929098 INFO::Using default BPPARAM
2026-01-01 21:21:21.929641 INFO::Processing subtree level 1
2026-01-01 21:21:22.154201 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:22.155852 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-01 21:21:22.175755 INFO::Done
2026-01-01 21:21:22.176517 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:22.180905 INFO::ASW Batch was 0.499294247102324 prior to batch effect correction and is now 0.499294247102324 .
2026-01-01 21:21:22.181682 INFO::ASW Label was 0.368917945148226 prior to batch effect correction and is now 0.368917945148227 .
2026-01-01 21:21:22.182576 INFO::Total function execution time is 0.260348081588745 s and adjustment time is 0.247952222824097 s ( 95.24 )
2026-01-01 21:21:22.24981 INFO::Formatting Data.
2026-01-01 21:21:22.250645 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:22.2516 INFO::Removing potential empty rows and columns
2026-01-01 21:21:22.252599 INFO::Found 0 missing values.
2026-01-01 21:21:22.256824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:22.257425 INFO::Done
2026-01-01 21:21:22.257972 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:22.261419 INFO::Starting hierarchical adjustment
2026-01-01 21:21:22.26219 INFO::Found 5 batches.
2026-01-01 21:21:22.262735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:22.263394 INFO::Using default BPPARAM
2026-01-01 21:21:22.263941 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.
2026-01-01 21:21:22.409992 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:22.411745 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-01 21:21:22.429255 INFO::Done
2026-01-01 21:21:22.430032 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:22.43349 INFO::ASW Batch was 0.453522653375055 prior to batch effect correction and is now 0.0250658658796157 .
2026-01-01 21:21:22.434117 INFO::ASW Label was 0.331070113221229 prior to batch effect correction and is now 0.723456370470571 .
2026-01-01 21:21:22.434925 INFO::Total function execution time is 0.185216426849365 s and adjustment time is 0.167188882827759 s ( 90.27 )
2026-01-01 21:21:22.435932 INFO::Formatting Data.
2026-01-01 21:21:22.43661 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:22.437611 INFO::Removing potential empty rows and columns
2026-01-01 21:21:22.438739 INFO::Found 0 missing values.
2026-01-01 21:21:22.443282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:22.443906 INFO::Done
2026-01-01 21:21:22.44444 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:22.447764 INFO::Starting hierarchical adjustment
2026-01-01 21:21:22.44853 INFO::Found 5 batches.
2026-01-01 21:21:22.449084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:22.449731 INFO::Using default BPPARAM
2026-01-01 21:21:22.450302 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.
2026-01-01 21:21:22.588857 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:22.590633 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-01 21:21:22.60854 INFO::Done
2026-01-01 21:21:22.60937 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:22.613156 INFO::ASW Batch was 0.453522653375055 prior to batch effect correction and is now 0.0250658658796157 .
2026-01-01 21:21:22.613829 INFO::ASW Label was 0.331070113221229 prior to batch effect correction and is now 0.723456370470571 .
2026-01-01 21:21:22.614704 INFO::Total function execution time is 0.178774118423462 s and adjustment time is 0.160116910934448 s ( 89.56 )
2026-01-01 21:21:22.629778 INFO::Formatting Data.
2026-01-01 21:21:22.630771 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:22.631819 INFO::Removing potential empty rows and columns
2026-01-01 21:21:22.632954 INFO::Found 0 missing values.
2026-01-01 21:21:22.63742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:22.638037 INFO::Done
2026-01-01 21:21:22.638597 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:22.641961 INFO::Starting hierarchical adjustment
2026-01-01 21:21:22.642727 INFO::Found 5 batches.
2026-01-01 21:21:22.643268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:22.643926 INFO::Using default BPPARAM
2026-01-01 21:21:22.64448 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.
2026-01-01 21:21:22.784441 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:22.786257 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-01 21:21:22.803871 INFO::Done
2026-01-01 21:21:22.804687 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:22.808401 INFO::ASW Batch was 0.241324360226344 prior to batch effect correction and is now -0.0597112163325552 .
2026-01-01 21:21:22.809081 INFO::ASW Label was 0.561331793601042 prior to batch effect correction and is now 0.870592050162673 .
2026-01-01 21:21:22.809978 INFO::Total function execution time is 0.180320262908936 s and adjustment time is 0.161276817321777 s ( 89.44 )
2026-01-01 21:21:22.810874 INFO::Formatting Data.
2026-01-01 21:21:22.811533 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:22.812502 INFO::Removing potential empty rows and columns
2026-01-01 21:21:22.8136 INFO::Found 0 missing values.
2026-01-01 21:21:22.817837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:22.818419 INFO::Done
2026-01-01 21:21:22.818976 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:22.822318 INFO::Starting hierarchical adjustment
2026-01-01 21:21:22.823104 INFO::Found 5 batches.
2026-01-01 21:21:22.823674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:22.824318 INFO::Using default BPPARAM
2026-01-01 21:21:22.824887 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.
2026-01-01 21:21:22.964189 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:22.965978 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-01 21:21:22.984597 INFO::Done
2026-01-01 21:21:23.002836 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.012097 INFO::ASW Batch was 0.241324360226344 prior to batch effect correction and is now -0.0597112163325552 .
2026-01-01 21:21:23.012882 INFO::ASW Label was 0.561331793601042 prior to batch effect correction and is now 0.870592050162673 .
2026-01-01 21:21:23.014455 INFO::Total function execution time is 0.203496217727661 s and adjustment time is 0.161575794219971 s ( 79.4 )
2026-01-01 21:21:23.036778 INFO::Formatting Data.
2026-01-01 21:21:23.037687 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:23.038835 INFO::Removing potential empty rows and columns
2026-01-01 21:21:23.04015 INFO::Found 0 missing values.
2026-01-01 21:21:23.04334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:23.043952 INFO::Done
2026-01-01 21:21:23.044546 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:23.047841 INFO::Starting hierarchical adjustment
2026-01-01 21:21:23.048655 INFO::Found 2 batches.
2026-01-01 21:21:23.049256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:23.05013 INFO::Using default BPPARAM
2026-01-01 21:21:23.050747 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:23.051762 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-01 21:21:23.074211 INFO::Done
2026-01-01 21:21:23.074972 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.078215 INFO::ASW Batch was 0.737803884660294 prior to batch effect correction and is now 0.0643304027942084 .
2026-01-01 21:21:23.078896 INFO::ASW Label was 0.308077922687129 prior to batch effect correction and is now 0.817220754924166 .
2026-01-01 21:21:23.079738 INFO::Total function execution time is 0.04306960105896 s and adjustment time is 0.0257329940795898 s ( 59.75 )
2026-01-01 21:21:23.08059 INFO::Formatting Data.
2026-01-01 21:21:23.081257 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:23.08221 INFO::Removing potential empty rows and columns
2026-01-01 21:21:23.083249 INFO::Found 0 missing values.
2026-01-01 21:21:23.086069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:23.086633 INFO::Done
2026-01-01 21:21:23.087198 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:23.090274 INFO::Starting hierarchical adjustment
2026-01-01 21:21:23.091024 INFO::Found 2 batches.
2026-01-01 21:21:23.09158 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:23.092221 INFO::Using default BPPARAM
2026-01-01 21:21:23.092796 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:23.093782 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-01 21:21:23.109488 INFO::Done
2026-01-01 21:21:23.110222 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.113384 INFO::ASW Batch was 0.737803884660294 prior to batch effect correction and is now 0.0643304027942084 .
2026-01-01 21:21:23.114064 INFO::ASW Label was 0.308077922687129 prior to batch effect correction and is now 0.817220754924166 .
2026-01-01 21:21:23.11494 INFO::Total function execution time is 0.034353494644165 s and adjustment time is 0.0185987949371338 s ( 54.14 )
2026-01-01 21:21:23.127362 INFO::Formatting Data.
2026-01-01 21:21:23.128219 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:23.129304 INFO::Removing potential empty rows and columns
2026-01-01 21:21:23.130316 INFO::Found 0 missing values.
2026-01-01 21:21:23.132682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:23.133258 INFO::Done
2026-01-01 21:21:23.13383 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:23.135984 INFO::Starting hierarchical adjustment
2026-01-01 21:21:23.136764 INFO::Found 2 batches.
2026-01-01 21:21:23.137341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:23.138016 INFO::Using default BPPARAM
2026-01-01 21:21:23.138583 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:23.139582 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-01 21:21:23.177496 INFO::Done
2026-01-01 21:21:23.178298 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.180457 INFO::ASW Batch was 0.247576311827152 prior to batch effect correction and is now -0.125201497151102 .
2026-01-01 21:21:23.181344 INFO::Total function execution time is 0.0540509223937988 s and adjustment time is 0.0408766269683838 s ( 75.63 )
2026-01-01 21:21:23.198003 INFO::Formatting Data.
2026-01-01 21:21:23.199381 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:23.200832 INFO::Removing potential empty rows and columns
2026-01-01 21:21:23.202479 INFO::Found 0 missing values.
2026-01-01 21:21:23.204296 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.
2026-01-01 21:21:23.212263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:23.213275 INFO::Done
2026-01-01 21:21:23.214199 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:23.219362 INFO::Starting hierarchical adjustment
2026-01-01 21:21:23.220563 INFO::Found 2 batches.
2026-01-01 21:21:23.221429 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:23.222445 INFO::Using default BPPARAM
2026-01-01 21:21:23.223324 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:23.224895 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-01 21:21:23.254402 INFO::Done
2026-01-01 21:21:23.255596 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.26043 INFO::ASW Batch was 0.514926213886439 prior to batch effect correction and is now 0.178961438975451 .
2026-01-01 21:21:23.261358 INFO::ASW Label was 0.635142965959595 prior to batch effect correction and is now 0.814431910960441 .
2026-01-01 21:21:23.262661 INFO::Total function execution time is 0.0648329257965088 s and adjustment time is 0.0340337753295898 s ( 52.49 )
2026-01-01 21:21:23.263991 INFO::Formatting Data.
2026-01-01 21:21:23.264985 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:23.266455 INFO::Removing potential empty rows and columns
2026-01-01 21:21:23.268074 INFO::Found 0 missing values.
2026-01-01 21:21:23.269476 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.
2026-01-01 21:21:23.277209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:23.278183 INFO::Done
2026-01-01 21:21:23.279092 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:23.284263 INFO::Starting hierarchical adjustment
2026-01-01 21:21:23.285481 INFO::Found 2 batches.
2026-01-01 21:21:23.286485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:23.287551 INFO::Using default BPPARAM
2026-01-01 21:21:23.288451 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:23.290111 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-01 21:21:23.313546 INFO::Done
2026-01-01 21:21:23.31434 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.317741 INFO::ASW Batch was 0.514926213886439 prior to batch effect correction and is now 0.178961438975451 .
2026-01-01 21:21:23.318391 INFO::ASW Label was 0.635142965959595 prior to batch effect correction and is now 0.814431910960441 .
2026-01-01 21:21:23.31924 INFO::Total function execution time is 0.0553696155548096 s and adjustment time is 0.0283069610595703 s ( 51.12 )
2026-01-01 21:21:23.525523 INFO::Formatting Data.
2026-01-01 21:21:23.526438 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:23.527387 INFO::Removing potential empty rows and columns
2026-01-01 21:21:23.528454 INFO::Found 0 missing values.
2026-01-01 21:21:23.531586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:23.532123 INFO::Done
2026-01-01 21:21:23.532658 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:23.534771 INFO::Starting hierarchical adjustment
2026-01-01 21:21:23.535478 INFO::Found 3 batches.
2026-01-01 21:21:23.536015 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:23.536633 INFO::Using default BPPARAM
2026-01-01 21:21:23.537159 INFO::Processing subtree level 1
2026-01-01 21:21:23.630145 INFO::Adjusting the last 1 batches sequentially
2026-01-01 21:21:23.631972 INFO::Done
2026-01-01 21:21:23.632621 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.635213 INFO::ASW Batch was -0.0430759110049634 prior to batch effect correction and is now -0.0430759110049634 .
2026-01-01 21:21:23.63618 INFO::Total function execution time is 0.110771656036377 s and adjustment time is 0.0966281890869141 s ( 87.23 )
2026-01-01 21:21:23.637269 INFO::Formatting Data.
2026-01-01 21:21:23.63793 INFO::Typecasting input to dataframe.
2026-01-01 21:21:23.638712 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:23.639678 INFO::Removing potential empty rows and columns
2026-01-01 21:21:23.6408 INFO::Found 0 missing values.
2026-01-01 21:21:23.643893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:23.644457 INFO::Done
2026-01-01 21:21:23.645018 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:23.64709 INFO::Starting hierarchical adjustment
2026-01-01 21:21:23.647827 INFO::Found 3 batches.
2026-01-01 21:21:23.648356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:23.649004 INFO::Using default BPPARAM
2026-01-01 21:21:23.649555 INFO::Processing subtree level 1
2026-01-01 21:21:23.739438 INFO::Adjusting the last 1 batches sequentially
2026-01-01 21:21:23.741235 INFO::Done
2026-01-01 21:21:23.741891 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.744373 INFO::ASW Batch was -0.0430759110049634 prior to batch effect correction and is now -0.0430759110049634 .
2026-01-01 21:21:23.745345 INFO::Total function execution time is 0.108038663864136 s and adjustment time is 0.0935549736022949 s ( 86.59 )
2026-01-01 21:21:23.758794 INFO::Formatting Data.
2026-01-01 21:21:23.759647 INFO::Typecasting input to dataframe.
2026-01-01 21:21:23.760528 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:23.76145 INFO::Removing potential empty rows and columns
2026-01-01 21:21:23.762556 INFO::Found 0 missing values.
2026-01-01 21:21:23.765528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:23.766088 INFO::Done
2026-01-01 21:21:23.76662 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:23.768666 INFO::Starting hierarchical adjustment
2026-01-01 21:21:23.769358 INFO::Found 3 batches.
2026-01-01 21:21:23.769905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:23.770522 INFO::Using default BPPARAM
2026-01-01 21:21:23.771071 INFO::Processing subtree level 1
2026-01-01 21:21:23.8621 INFO::Adjusting the last 1 batches sequentially
2026-01-01 21:21:23.863848 INFO::Done
2026-01-01 21:21:23.864519 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:23.867006 INFO::ASW Batch was -0.144409775486522 prior to batch effect correction and is now -0.144409775486522 .
2026-01-01 21:21:23.867945 INFO::Total function execution time is 0.109215259552002 s and adjustment time is 0.0946128368377686 s ( 86.63 )
2026-01-01 21:21:24.008997 INFO::Formatting Data.
2026-01-01 21:21:24.009855 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:24.011002 INFO::Removing potential empty rows and columns
2026-01-01 21:21:24.013853 INFO::Found 1000 missing values.
2026-01-01 21:21:24.045135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:24.046181 INFO::Done
2026-01-01 21:21:24.04682 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:24.053437 INFO::Starting hierarchical adjustment
2026-01-01 21:21:24.054317 INFO::Found 10 batches.
2026-01-01 21:21:24.054914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:24.055687 INFO::Using default BPPARAM
2026-01-01 21:21:24.056241 INFO::Processing subtree level 1
2026-01-01 21:21:24.215444 INFO::Processing subtree level 2
2026-01-01 21:21:24.357489 INFO::Adjusting the last 1 batches sequentially
2026-01-01 21:21:24.359502 INFO::Done
2026-01-01 21:21:24.360141 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:24.365936 INFO::ASW Batch was 0.530528896504385 prior to batch effect correction and is now 0.530528896504385 .
2026-01-01 21:21:24.366613 INFO::ASW Label was 0.27853507539893 prior to batch effect correction and is now 0.27853507539893 .
2026-01-01 21:21:24.367656 INFO::Total function execution time is 0.35866641998291 s and adjustment time is 0.30541729927063 s ( 85.15 )
2026-01-01 21:21:24.368675 INFO::Formatting Data.
2026-01-01 21:21:24.369346 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:24.370661 INFO::Removing potential empty rows and columns
2026-01-01 21:21:24.373651 INFO::Found 1000 missing values.
2026-01-01 21:21:24.393382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:24.394289 INFO::Done
2026-01-01 21:21:24.394916 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:24.400552 INFO::Starting hierarchical adjustment
2026-01-01 21:21:24.40135 INFO::Found 10 batches.
2026-01-01 21:21:25.964551 INFO::Set up parallel execution backend with 2 workers
2026-01-01 21:21:25.966797 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-01 21:21:27.352007 INFO::Adjusting the last 2 batches sequentially
2026-01-01 21:21:27.354117 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-01 21:21:27.371171 INFO::Done
2026-01-01 21:21:27.371903 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:27.37672 INFO::ASW Batch was 0.530528896504385 prior to batch effect correction and is now 0.530528896504385 .
2026-01-01 21:21:27.377322 INFO::ASW Label was 0.27853507539893 prior to batch effect correction and is now 0.27853507539893 .
2026-01-01 21:21:27.378096 INFO::Total function execution time is 3.00947642326355 s and adjustment time is 2.96993732452393 s ( 98.69 )
2026-01-01 21:21:27.572097 INFO::Formatting Data.
2026-01-01 21:21:27.572974 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:27.573973 INFO::Removing potential empty rows and columns
2026-01-01 21:21:27.575143 INFO::Found 0 missing values.
2026-01-01 21:21:27.578978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:27.57956 INFO::Done
2026-01-01 21:21:27.580091 INFO::Acquiring quality metrics before batch effect correction.
2026-01-01 21:21:27.582962 INFO::Starting hierarchical adjustment
2026-01-01 21:21:27.583702 INFO::Found 3 batches.
2026-01-01 21:21:27.584226 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-01 21:21:27.584875 INFO::Using default BPPARAM
2026-01-01 21:21:27.585402 INFO::Processing subtree level 1
2026-01-01 21:21:27.695445 INFO::Adjusting the last 1 batches sequentially
2026-01-01 21:21:27.697385 INFO::Done
2026-01-01 21:21:27.698118 INFO::Acquiring quality metrics after batch effect correction.
2026-01-01 21:21:27.701589 INFO::ASW Batch was 0.158046293289171 prior to batch effect correction and is now -0.146373925168524 .
2026-01-01 21:21:27.702272 INFO::ASW Label was -0.192648184830744 prior to batch effect correction and is now -0.123020163278578 .
2026-01-01 21:21:27.703214 INFO::Total function execution time is 0.131212949752808 s and adjustment time is 0.113823413848877 s ( 86.75 )
2026-01-01 21:21:27.827118 INFO::Formatting Data.
2026-01-01 21:21:27.828013 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:27.82893 INFO::Removing potential empty rows and columns
2026-01-01 21:21:27.829956 INFO::Found 2 missing values.
2026-01-01 21:21:27.832726 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:27.833234 INFO::Done
2026-01-01 21:21:27.860648 INFO::Found NA in Reference column
2026-01-01 21:21:27.870007 INFO::Require at least two references per batch.
2026-01-01 21:21:27.891037 INFO::Formatting Data.
2026-01-01 21:21:27.891865 INFO::Recognized SummarizedExperiment
2026-01-01 21:21:27.892389 INFO::Typecasting input to dataframe.
2026-01-01 21:21:27.902882 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:27.904104 INFO::Removing potential empty rows and columns
2026-01-01 21:21:27.907467 INFO::Found 0 missing values.
2026-01-01 21:21:27.913927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:27.914523 INFO::Done
2026-01-01 21:21:27.930007 INFO::Formatting Data.
2026-01-01 21:21:27.930754 INFO::Recognized SummarizedExperiment
2026-01-01 21:21:27.931261 INFO::Typecasting input to dataframe.
2026-01-01 21:21:27.948124 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:27.949554 INFO::Removing potential empty rows and columns
2026-01-01 21:21:27.953026 INFO::Found 0 missing values.
2026-01-01 21:21:27.963437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:27.964086 INFO::Done
2026-01-01 21:21:27.97958 INFO::Formatting Data.
2026-01-01 21:21:27.980304 INFO::Recognized SummarizedExperiment
2026-01-01 21:21:27.980822 INFO::Typecasting input to dataframe.
2026-01-01 21:21:27.996577 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:27.997612 INFO::Removing potential empty rows and columns
2026-01-01 21:21:27.998648 INFO::Found 0 missing values.
2026-01-01 21:21:27.999545 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.
2026-01-01 21:21:28.003696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:28.004198 INFO::Done
2026-01-01 21:21:28.014182 INFO::Formatting Data.
2026-01-01 21:21:28.014889 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:28.015722 INFO::Removing potential empty rows and columns
2026-01-01 21:21:28.016669 INFO::Found 0 missing values.
2026-01-01 21:21:28.019417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:28.019928 INFO::Done
2026-01-01 21:21:28.031368 INFO::Formatting Data.
2026-01-01 21:21:28.032321 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:28.033189 INFO::Removing potential empty rows and columns
2026-01-01 21:21:28.03419 INFO::Found 0 missing values.
2026-01-01 21:21:28.037024 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:28.037548 INFO::Done
2026-01-01 21:21:28.067149 INFO::Formatting Data.
2026-01-01 21:21:28.068021 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:28.069074 INFO::Removing potential empty rows and columns
2026-01-01 21:21:28.070212 INFO::Found 1 missing values.
2026-01-01 21:21:28.073031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:28.073553 INFO::Done
2026-01-01 21:21:28.092395 INFO::Formatting Data.
2026-01-01 21:21:28.093353 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:28.094301 INFO::Removing potential empty rows and columns
2026-01-01 21:21:28.095268 INFO::Found 2 missing values.
2026-01-01 21:21:28.096182 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.
2026-01-01 21:21:28.098439 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:28.098984 INFO::Done
2026-01-01 21:21:28.10932 INFO::Formatting Data.
2026-01-01 21:21:28.110141 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:28.11113 INFO::Removing potential empty rows and columns
2026-01-01 21:21:28.112104 INFO::Found 2 missing values.
2026-01-01 21:21:28.113765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:28.114312 INFO::Done
2026-01-01 21:21:28.124907 INFO::Formatting Data.
2026-01-01 21:21:28.125688 INFO::Typecasting input to dataframe.
2026-01-01 21:21:28.126475 INFO::Replacing NaNs with NAs.
2026-01-01 21:21:28.127331 INFO::Removing potential empty rows and columns
2026-01-01 21:21:28.128308 INFO::Found 0 missing values.
2026-01-01 21:21:28.131133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-01 21:21:28.131668 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.438 4.129 21.174
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.131 | 1.307 | 17.921 | |
| compute_asw | 0.024 | 0.001 | 0.025 | |
| count_existing | 0.011 | 0.003 | 0.015 | |
| generate_data_covariables | 0.011 | 0.002 | 0.013 | |
| generate_dataset | 0.009 | 0.003 | 0.013 | |