Yannis Schumann
| Snapshot Date: 2026-03-26 13:45 -0400 (Thu, 26 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-27 11:57 -0400 (Fri, 27 Mar 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" | 4893 |
| 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 | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| 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: 2026-03-26 22:17:12 -0400 (Thu, 26 Mar 2026) |
| EndedAt: 2026-03-26 22:18:41 -0400 (Thu, 26 Mar 2026) |
| EllapsedTime: 89.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 24.04.4 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 23.811 1.676 17.78
* 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")
2026-03-26 22:18:03.550463 INFO::Formatting Data.
2026-03-26 22:18:03.551786 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:03.562875 INFO::Removing potential empty rows and columns
2026-03-26 22:18:03.811109 INFO::Found 0 missing values.
2026-03-26 22:18:03.814454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:03.815099 INFO::Done
2026-03-26 22:18:03.815644 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:03.826953 INFO::Starting hierarchical adjustment
2026-03-26 22:18:03.827818 INFO::Found 3 batches.
2026-03-26 22:18:03.828374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:03.829502 INFO::Using default BPPARAM
2026-03-26 22:18:03.830036 INFO::Processing subtree level 1
2026-03-26 22:18:03.923847 INFO::Adjusting the last 1 batches sequentially
2026-03-26 22:18:03.925654 INFO::Done
2026-03-26 22:18:03.926344 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:03.928749 INFO::ASW Batch was -0.0598850958697207 prior to batch effect correction and is now -0.0598850958697207 .
2026-03-26 22:18:03.929804 INFO::Total function execution time is 0.380019426345825 s and adjustment time is 0.0979983806610107 s ( 25.79 )
2026-03-26 22:18:03.942987 INFO::Formatting Data.
2026-03-26 22:18:03.943732 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:03.944647 INFO::Removing potential empty rows and columns
2026-03-26 22:18:03.945762 INFO::Found 0 missing values.
2026-03-26 22:18:03.946684 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-26 22:18:03.957256 INFO::Formatting Data.
2026-03-26 22:18:03.958013 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:03.958916 INFO::Removing potential empty rows and columns
2026-03-26 22:18:03.959979 INFO::Found 0 missing values.
2026-03-26 22:18:03.960887 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-26 22:18:03.9763 INFO::Formatting Data.
2026-03-26 22:18:03.977004 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:03.977865 INFO::Removing potential empty rows and columns
2026-03-26 22:18:03.978868 INFO::Found 0 missing values.
2026-03-26 22:18:03.979766 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-26 22:18:03.984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:03.98454 INFO::Done
2026-03-26 22:18:03.985042 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:03.986941 INFO::Starting hierarchical adjustment
2026-03-26 22:18:03.987623 INFO::Found 2 batches.
2026-03-26 22:18:03.988129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:03.988754 INFO::Using default BPPARAM
2026-03-26 22:18:03.98926 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:03.990134 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 22:18:04.010464 INFO::Done
2026-03-26 22:18:04.011116 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:04.0132 INFO::ASW Batch was 0.0904109128940945 prior to batch effect correction and is now -0.102457936730477 .
2026-03-26 22:18:04.014092 INFO::Total function execution time is 0.0378503799438477 s and adjustment time is 0.0229511260986328 s ( 60.64 )
2026-03-26 22:18:04.016883 INFO::Formatting Data.
2026-03-26 22:18:04.017531 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:04.026331 INFO::Formatting Data.
2026-03-26 22:18:04.027031 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:04.027916 INFO::Removing potential empty rows and columns
2026-03-26 22:18:04.028952 INFO::Found 0 missing values.
2026-03-26 22:18:04.031916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:04.032477 INFO::Done
2026-03-26 22:18:04.033005 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:04.056456 INFO::Starting hierarchical adjustment
2026-03-26 22:18:04.057704 INFO::Found 2 batches.
2026-03-26 22:18:04.058206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:04.058759 INFO::Using default BPPARAM
2026-03-26 22:18:04.059238 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:04.060098 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:04.073471 INFO::Done
2026-03-26 22:18:04.074037 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:04.07585 INFO::ASW Batch was 0.048819914926604 prior to batch effect correction and is now -0.103661597873975 .
2026-03-26 22:18:04.076556 INFO::Total function execution time is 0.0502943992614746 s and adjustment time is 0.0159358978271484 s ( 31.69 )
2026-03-26 22:18:04.077537 INFO::Formatting Data.
2026-03-26 22:18:04.07808 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:04.078874 INFO::Removing potential empty rows and columns
2026-03-26 22:18:04.085968 INFO::Found 0 missing values.
2026-03-26 22:18:04.08906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:04.089648 INFO::Done
2026-03-26 22:18:04.090177 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:04.092459 INFO::Starting hierarchical adjustment
2026-03-26 22:18:04.093185 INFO::Found 2 batches.
2026-03-26 22:18:04.09373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:04.094378 INFO::Using default BPPARAM
2026-03-26 22:18:04.094907 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:04.09584 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:04.111714 INFO::Done
2026-03-26 22:18:04.112361 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:04.114368 INFO::ASW Batch was 0.048819914926604 prior to batch effect correction and is now -0.103661597873975 .
2026-03-26 22:18:04.115147 INFO::Total function execution time is 0.0375831127166748 s and adjustment time is 0.0186784267425537 s ( 49.7 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-26 22:18:07.005334 INFO::Formatting Data.
2026-03-26 22:18:07.006006 INFO::Recognized SummarizedExperiment
2026-03-26 22:18:07.006526 INFO::Typecasting input to dataframe.
2026-03-26 22:18:07.036285 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:07.037523 INFO::Removing potential empty rows and columns
2026-03-26 22:18:07.041362 INFO::Found 0 missing values.
2026-03-26 22:18:07.048593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:07.049221 INFO::Done
2026-03-26 22:18:07.049777 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:07.053326 INFO::Starting hierarchical adjustment
2026-03-26 22:18:07.054038 INFO::Found 2 batches.
2026-03-26 22:18:07.054569 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:07.055622 INFO::Using default BPPARAM
2026-03-26 22:18:07.056154 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:07.057128 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 22:18:07.113258 INFO::Done
2026-03-26 22:18:07.114027 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:07.117819 INFO::ASW Batch was -0.000422756516504731 prior to batch effect correction and is now -0.0853320157539035 .
2026-03-26 22:18:07.118717 INFO::Total function execution time is 0.113653421401978 s and adjustment time is 0.0593173503875732 s ( 52.19 )
Warning: stack imbalance in '{', 73 then 75
2026-03-26 22:18:07.137421 INFO::Formatting Data.
2026-03-26 22:18:07.138162 INFO::Recognized SummarizedExperiment
2026-03-26 22:18:07.138723 INFO::Typecasting input to dataframe.
2026-03-26 22:18:07.148014 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:07.149181 INFO::Removing potential empty rows and columns
2026-03-26 22:18:07.152944 INFO::Found 0 missing values.
2026-03-26 22:18:07.160105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:07.160742 INFO::Done
2026-03-26 22:18:07.161269 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:07.164864 INFO::Starting hierarchical adjustment
2026-03-26 22:18:07.165611 INFO::Found 2 batches.
2026-03-26 22:18:07.166135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:07.166774 INFO::Using default BPPARAM
2026-03-26 22:18:07.167306 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:07.168302 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 22:18:07.193727 INFO::Done
2026-03-26 22:18:07.194515 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:07.198256 INFO::ASW Batch was 0.00508799402037511 prior to batch effect correction and is now 0.00508799402037511 .
2026-03-26 22:18:07.199173 INFO::Total function execution time is 0.061751127243042 s and adjustment time is 0.0282270908355713 s ( 45.71 )
2026-03-26 22:18:07.218433 INFO::Formatting Data.
2026-03-26 22:18:07.219255 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:07.220212 INFO::Removing potential empty rows and columns
2026-03-26 22:18:07.221306 INFO::Found 0 missing values.
2026-03-26 22:18:07.224348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:07.224891 INFO::Done
2026-03-26 22:18:07.225435 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:07.227513 INFO::Starting hierarchical adjustment
2026-03-26 22:18:07.228198 INFO::Found 3 batches.
2026-03-26 22:18:07.228743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:07.229352 INFO::Using default BPPARAM
2026-03-26 22:18:07.229876 INFO::Processing subtree level 1
2026-03-26 22:18:07.368345 INFO::Adjusting the last 1 batches sequentially
2026-03-26 22:18:07.370423 INFO::Done
2026-03-26 22:18:07.371168 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:07.37397 INFO::ASW Batch was -0.0774455502452426 prior to batch effect correction and is now -0.172067775970332 .
2026-03-26 22:18:07.374965 INFO::Total function execution time is 0.156625747680664 s and adjustment time is 0.14229679107666 s ( 90.85 )
2026-03-26 22:18:07.390722 INFO::Skipping initial DF formatting
2026-03-26 22:18:07.391485 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:07.395771 INFO::Starting hierarchical adjustment
2026-03-26 22:18:07.396591 INFO::Found 5 batches.
2026-03-26 22:18:07.397129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:07.397771 INFO::Using default BPPARAM
2026-03-26 22:18:07.398321 INFO::Processing subtree level 1
2026-03-26 22:18:07.657311 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:07.661188 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 22:18:07.681484 INFO::Done
2026-03-26 22:18:07.682189 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:07.686621 INFO::ASW Batch was 0.500571128227884 prior to batch effect correction and is now 0.500571128227884 .
2026-03-26 22:18:07.687222 INFO::ASW Label was 0.384314216901625 prior to batch effect correction and is now 0.384314216901625 .
2026-03-26 22:18:07.688079 INFO::Total function execution time is 0.297470331192017 s and adjustment time is 0.285032272338867 s ( 95.82 )
2026-03-26 22:18:07.762999 INFO::Formatting Data.
2026-03-26 22:18:07.763824 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:07.764764 INFO::Removing potential empty rows and columns
2026-03-26 22:18:07.765797 INFO::Found 0 missing values.
2026-03-26 22:18:07.769911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:07.770452 INFO::Done
2026-03-26 22:18:07.770943 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:07.773825 INFO::Starting hierarchical adjustment
2026-03-26 22:18:07.774517 INFO::Found 5 batches.
2026-03-26 22:18:07.775017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:07.775622 INFO::Using default BPPARAM
2026-03-26 22:18:07.776136 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:07.914147 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:07.915971 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:07.935227 INFO::Done
2026-03-26 22:18:07.936014 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:07.939838 INFO::ASW Batch was 0.36807761560116 prior to batch effect correction and is now -0.0661379453760013 .
2026-03-26 22:18:07.940523 INFO::ASW Label was 0.461501425014942 prior to batch effect correction and is now 0.868266825030615 .
2026-03-26 22:18:07.941418 INFO::Total function execution time is 0.178486347198486 s and adjustment time is 0.160833835601807 s ( 90.11 )
2026-03-26 22:18:07.942391 INFO::Formatting Data.
2026-03-26 22:18:07.943107 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:07.944145 INFO::Removing potential empty rows and columns
2026-03-26 22:18:07.945324 INFO::Found 0 missing values.
2026-03-26 22:18:07.950115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:07.95073 INFO::Done
2026-03-26 22:18:07.95137 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:07.954716 INFO::Starting hierarchical adjustment
2026-03-26 22:18:07.955498 INFO::Found 5 batches.
2026-03-26 22:18:07.956074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:07.956774 INFO::Using default BPPARAM
2026-03-26 22:18:07.957352 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:08.089127 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:08.090905 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:08.108732 INFO::Done
2026-03-26 22:18:08.10946 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:08.112935 INFO::ASW Batch was 0.36807761560116 prior to batch effect correction and is now -0.0661379453760013 .
2026-03-26 22:18:08.113644 INFO::ASW Label was 0.461501425014942 prior to batch effect correction and is now 0.868266825030615 .
2026-03-26 22:18:08.114538 INFO::Total function execution time is 0.17217755317688 s and adjustment time is 0.153391122817993 s ( 89.09 )
2026-03-26 22:18:08.128982 INFO::Formatting Data.
2026-03-26 22:18:08.129764 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:08.130697 INFO::Removing potential empty rows and columns
2026-03-26 22:18:08.131737 INFO::Found 0 missing values.
2026-03-26 22:18:08.136062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:08.13664 INFO::Done
2026-03-26 22:18:08.137197 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:08.140374 INFO::Starting hierarchical adjustment
2026-03-26 22:18:08.141116 INFO::Found 5 batches.
2026-03-26 22:18:08.141704 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:08.142362 INFO::Using default BPPARAM
2026-03-26 22:18:08.142945 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:08.272696 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:08.274647 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:08.301846 INFO::Done
2026-03-26 22:18:08.302982 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:08.306886 INFO::ASW Batch was 0.360632494687694 prior to batch effect correction and is now -0.0259523911197391 .
2026-03-26 22:18:08.307545 INFO::ASW Label was 0.537812837605928 prior to batch effect correction and is now 0.687267647583661 .
2026-03-26 22:18:08.308429 INFO::Total function execution time is 0.179471015930176 s and adjustment time is 0.160640478134155 s ( 89.51 )
2026-03-26 22:18:08.309349 INFO::Formatting Data.
2026-03-26 22:18:08.310031 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:08.310989 INFO::Removing potential empty rows and columns
2026-03-26 22:18:08.312064 INFO::Found 0 missing values.
2026-03-26 22:18:08.316253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:08.316846 INFO::Done
2026-03-26 22:18:08.317409 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:08.320516 INFO::Starting hierarchical adjustment
2026-03-26 22:18:08.321301 INFO::Found 5 batches.
2026-03-26 22:18:08.321856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:08.322571 INFO::Using default BPPARAM
2026-03-26 22:18:08.323126 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:08.448571 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:08.450393 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:08.469755 INFO::Done
2026-03-26 22:18:08.470577 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:08.47449 INFO::ASW Batch was 0.360632494687694 prior to batch effect correction and is now -0.0259523911197391 .
2026-03-26 22:18:08.475292 INFO::ASW Label was 0.537812837605928 prior to batch effect correction and is now 0.687267647583661 .
2026-03-26 22:18:08.476428 INFO::Total function execution time is 0.167016983032227 s and adjustment time is 0.148593187332153 s ( 88.97 )
2026-03-26 22:18:08.492911 INFO::Formatting Data.
2026-03-26 22:18:08.493733 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:08.494654 INFO::Removing potential empty rows and columns
2026-03-26 22:18:08.495703 INFO::Found 0 missing values.
2026-03-26 22:18:08.498457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:08.498998 INFO::Done
2026-03-26 22:18:08.499543 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:08.502521 INFO::Starting hierarchical adjustment
2026-03-26 22:18:08.503251 INFO::Found 2 batches.
2026-03-26 22:18:08.503812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:08.504466 INFO::Using default BPPARAM
2026-03-26 22:18:08.505022 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:08.505931 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:08.521074 INFO::Done
2026-03-26 22:18:08.521759 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:08.524765 INFO::ASW Batch was 0.462102785353698 prior to batch effect correction and is now -0.0237107633179902 .
2026-03-26 22:18:08.52536 INFO::ASW Label was 0.498351758533025 prior to batch effect correction and is now 0.939126093595186 .
2026-03-26 22:18:08.526137 INFO::Total function execution time is 0.0333051681518555 s and adjustment time is 0.0179550647735596 s ( 53.91 )
2026-03-26 22:18:08.52693 INFO::Formatting Data.
2026-03-26 22:18:08.52759 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:08.528482 INFO::Removing potential empty rows and columns
2026-03-26 22:18:08.52948 INFO::Found 0 missing values.
2026-03-26 22:18:08.532179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:08.532717 INFO::Done
2026-03-26 22:18:08.53323 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:08.536154 INFO::Starting hierarchical adjustment
2026-03-26 22:18:08.536875 INFO::Found 2 batches.
2026-03-26 22:18:08.537412 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:08.538012 INFO::Using default BPPARAM
2026-03-26 22:18:08.538563 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:08.539473 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-26 22:18:08.555239 INFO::Done
2026-03-26 22:18:08.555993 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:08.559361 INFO::ASW Batch was 0.462102785353698 prior to batch effect correction and is now -0.0237107633179902 .
2026-03-26 22:18:08.559993 INFO::ASW Label was 0.498351758533025 prior to batch effect correction and is now 0.939126093595186 .
2026-03-26 22:18:08.560857 INFO::Total function execution time is 0.0339322090148926 s and adjustment time is 0.0184838771820068 s ( 54.47 )
2026-03-26 22:18:08.573208 INFO::Formatting Data.
2026-03-26 22:18:08.574004 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:08.574914 INFO::Removing potential empty rows and columns
2026-03-26 22:18:08.575852 INFO::Found 0 missing values.
2026-03-26 22:18:08.578013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:08.578549 INFO::Done
2026-03-26 22:18:08.579069 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:08.581031 INFO::Starting hierarchical adjustment
2026-03-26 22:18:08.581792 INFO::Found 2 batches.
2026-03-26 22:18:08.582319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:08.582912 INFO::Using default BPPARAM
2026-03-26 22:18:08.58347 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:08.584393 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 22:18:08.616574 INFO::Done
2026-03-26 22:18:08.617379 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:08.619356 INFO::ASW Batch was 0.0866916850031098 prior to batch effect correction and is now -0.0837015490165761 .
2026-03-26 22:18:08.620163 INFO::Total function execution time is 0.0470364093780518 s and adjustment time is 0.0348882675170898 s ( 74.17 )
2026-03-26 22:18:08.632209 INFO::Formatting Data.
2026-03-26 22:18:08.633075 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:08.633991 INFO::Removing potential empty rows and columns
2026-03-26 22:18:08.635039 INFO::Found 0 missing values.
2026-03-26 22:18:08.636297 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-26 22:18:08.640953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:08.641506 INFO::Done
2026-03-26 22:18:08.642 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:08.644939 INFO::Starting hierarchical adjustment
2026-03-26 22:18:08.645656 INFO::Found 2 batches.
2026-03-26 22:18:08.646167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:08.646759 INFO::Using default BPPARAM
2026-03-26 22:18:08.647252 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:08.648143 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 22:18:08.664191 INFO::Done
2026-03-26 22:18:08.664871 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:08.667814 INFO::ASW Batch was 0.552299249588824 prior to batch effect correction and is now 0.124947150406397 .
2026-03-26 22:18:08.668416 INFO::ASW Label was 0.567115460948259 prior to batch effect correction and is now 0.820697865044762 .
2026-03-26 22:18:08.669206 INFO::Total function execution time is 0.0370676517486572 s and adjustment time is 0.0186572074890137 s ( 50.33 )
2026-03-26 22:18:08.669997 INFO::Formatting Data.
2026-03-26 22:18:08.670634 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:08.671541 INFO::Removing potential empty rows and columns
2026-03-26 22:18:08.672519 INFO::Found 0 missing values.
2026-03-26 22:18:08.673437 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-26 22:18:08.677773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:08.678304 INFO::Done
2026-03-26 22:18:08.678808 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:08.681524 INFO::Starting hierarchical adjustment
2026-03-26 22:18:08.682197 INFO::Found 2 batches.
2026-03-26 22:18:08.682716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:08.683317 INFO::Using default BPPARAM
2026-03-26 22:18:08.683807 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:08.684671 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 22:18:08.699924 INFO::Done
2026-03-26 22:18:08.700536 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:08.703238 INFO::ASW Batch was 0.552299249588824 prior to batch effect correction and is now 0.124947150406397 .
2026-03-26 22:18:08.703793 INFO::ASW Label was 0.567115460948259 prior to batch effect correction and is now 0.820697865044762 .
2026-03-26 22:18:08.704531 INFO::Total function execution time is 0.0345602035522461 s and adjustment time is 0.017852783203125 s ( 51.66 )
2026-03-26 22:18:08.910371 INFO::Formatting Data.
2026-03-26 22:18:08.911207 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:08.912152 INFO::Removing potential empty rows and columns
2026-03-26 22:18:08.913214 INFO::Found 0 missing values.
2026-03-26 22:18:08.916304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:08.916842 INFO::Done
2026-03-26 22:18:08.91736 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:08.91942 INFO::Starting hierarchical adjustment
2026-03-26 22:18:08.920135 INFO::Found 3 batches.
2026-03-26 22:18:08.920675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:08.921287 INFO::Using default BPPARAM
2026-03-26 22:18:08.921813 INFO::Processing subtree level 1
2026-03-26 22:18:09.005427 INFO::Adjusting the last 1 batches sequentially
2026-03-26 22:18:09.007166 INFO::Done
2026-03-26 22:18:09.007817 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:09.010494 INFO::ASW Batch was -0.149063211149714 prior to batch effect correction and is now -0.149063211149714 .
2026-03-26 22:18:09.011416 INFO::Total function execution time is 0.101145267486572 s and adjustment time is 0.0871543884277344 s ( 86.17 )
2026-03-26 22:18:09.012457 INFO::Formatting Data.
2026-03-26 22:18:09.013126 INFO::Typecasting input to dataframe.
2026-03-26 22:18:09.013921 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:09.014903 INFO::Removing potential empty rows and columns
2026-03-26 22:18:09.016065 INFO::Found 0 missing values.
2026-03-26 22:18:09.019371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:09.019925 INFO::Done
2026-03-26 22:18:09.020487 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:09.022667 INFO::Starting hierarchical adjustment
2026-03-26 22:18:09.023397 INFO::Found 3 batches.
2026-03-26 22:18:09.023935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:09.024597 INFO::Using default BPPARAM
2026-03-26 22:18:09.025146 INFO::Processing subtree level 1
2026-03-26 22:18:09.107745 INFO::Adjusting the last 1 batches sequentially
2026-03-26 22:18:09.109472 INFO::Done
2026-03-26 22:18:09.110114 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:09.112618 INFO::ASW Batch was -0.149063211149714 prior to batch effect correction and is now -0.149063211149714 .
2026-03-26 22:18:09.113537 INFO::Total function execution time is 0.101084470748901 s and adjustment time is 0.086228609085083 s ( 85.3 )
2026-03-26 22:18:09.12624 INFO::Formatting Data.
2026-03-26 22:18:09.127005 INFO::Typecasting input to dataframe.
2026-03-26 22:18:09.127836 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:09.128748 INFO::Removing potential empty rows and columns
2026-03-26 22:18:09.129812 INFO::Found 0 missing values.
2026-03-26 22:18:09.132756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:09.133303 INFO::Done
2026-03-26 22:18:09.133828 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:09.135787 INFO::Starting hierarchical adjustment
2026-03-26 22:18:09.136506 INFO::Found 3 batches.
2026-03-26 22:18:09.137032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:09.137664 INFO::Using default BPPARAM
2026-03-26 22:18:09.138176 INFO::Processing subtree level 1
2026-03-26 22:18:09.215931 INFO::Adjusting the last 1 batches sequentially
2026-03-26 22:18:09.217645 INFO::Done
2026-03-26 22:18:09.218306 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:09.220865 INFO::ASW Batch was 0.0944525319648465 prior to batch effect correction and is now 0.0944525319648465 .
2026-03-26 22:18:09.221814 INFO::Total function execution time is 0.0956013202667236 s and adjustment time is 0.0812849998474121 s ( 85.02 )
2026-03-26 22:18:09.352547 INFO::Formatting Data.
2026-03-26 22:18:09.353318 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:09.354387 INFO::Removing potential empty rows and columns
2026-03-26 22:18:09.357113 INFO::Found 1000 missing values.
2026-03-26 22:18:09.376034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:09.376745 INFO::Done
2026-03-26 22:18:09.377295 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:09.382632 INFO::Starting hierarchical adjustment
2026-03-26 22:18:09.383376 INFO::Found 10 batches.
2026-03-26 22:18:09.383921 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:09.384539 INFO::Using default BPPARAM
2026-03-26 22:18:09.385064 INFO::Processing subtree level 1
2026-03-26 22:18:09.510767 INFO::Processing subtree level 2
2026-03-26 22:18:09.645359 INFO::Adjusting the last 1 batches sequentially
2026-03-26 22:18:09.647596 INFO::Done
2026-03-26 22:18:09.648409 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:09.655199 INFO::ASW Batch was 0.494670946568561 prior to batch effect correction and is now 0.494670946568561 .
2026-03-26 22:18:09.656019 INFO::ASW Label was 0.339529542197811 prior to batch effect correction and is now 0.339529542197811 .
2026-03-26 22:18:09.657174 INFO::Total function execution time is 0.304640293121338 s and adjustment time is 0.264338731765747 s ( 86.77 )
2026-03-26 22:18:09.658228 INFO::Formatting Data.
2026-03-26 22:18:09.659059 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:09.660502 INFO::Removing potential empty rows and columns
2026-03-26 22:18:09.664037 INFO::Found 1000 missing values.
2026-03-26 22:18:09.688494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:09.689316 INFO::Done
2026-03-26 22:18:09.689978 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:09.696033 INFO::Starting hierarchical adjustment
2026-03-26 22:18:09.696833 INFO::Found 10 batches.
2026-03-26 22:18:10.680996 INFO::Set up parallel execution backend with 2 workers
2026-03-26 22:18:10.683778 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-26 22:18:11.902171 INFO::Adjusting the last 2 batches sequentially
2026-03-26 22:18:11.904086 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-26 22:18:11.920659 INFO::Done
2026-03-26 22:18:11.921364 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:11.925775 INFO::ASW Batch was 0.494670946568561 prior to batch effect correction and is now 0.494670946568561 .
2026-03-26 22:18:11.932312 INFO::ASW Label was 0.339529542197811 prior to batch effect correction and is now 0.339529542197811 .
2026-03-26 22:18:11.933297 INFO::Total function execution time is 2.27509379386902 s and adjustment time is 2.22395277023315 s ( 97.75 )
2026-03-26 22:18:12.070081 INFO::Formatting Data.
2026-03-26 22:18:12.070845 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.071731 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.072762 INFO::Found 0 missing values.
2026-03-26 22:18:12.076217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.076742 INFO::Done
2026-03-26 22:18:12.077222 INFO::Acquiring quality metrics before batch effect correction.
2026-03-26 22:18:12.07987 INFO::Starting hierarchical adjustment
2026-03-26 22:18:12.080558 INFO::Found 3 batches.
2026-03-26 22:18:12.081047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-26 22:18:12.081645 INFO::Using default BPPARAM
2026-03-26 22:18:12.082137 INFO::Processing subtree level 1
2026-03-26 22:18:12.183123 INFO::Adjusting the last 1 batches sequentially
2026-03-26 22:18:12.18501 INFO::Done
2026-03-26 22:18:12.185718 INFO::Acquiring quality metrics after batch effect correction.
2026-03-26 22:18:12.188913 INFO::ASW Batch was 0.223301273520989 prior to batch effect correction and is now -0.180179625011046 .
2026-03-26 22:18:12.189556 INFO::ASW Label was -0.201829615977488 prior to batch effect correction and is now 0.0128595766049542 .
2026-03-26 22:18:12.190465 INFO::Total function execution time is 0.120414972305298 s and adjustment time is 0.104558229446411 s ( 86.83 )
2026-03-26 22:18:12.309152 INFO::Formatting Data.
2026-03-26 22:18:12.309937 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.310811 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.311823 INFO::Found 2 missing values.
2026-03-26 22:18:12.314619 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.315134 INFO::Done
2026-03-26 22:18:12.341192 INFO::Found NA in Reference column
2026-03-26 22:18:12.350218 INFO::Require at least two references per batch.
2026-03-26 22:18:12.370491 INFO::Formatting Data.
2026-03-26 22:18:12.371201 INFO::Recognized SummarizedExperiment
2026-03-26 22:18:12.371719 INFO::Typecasting input to dataframe.
2026-03-26 22:18:12.38078 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.38184 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.385087 INFO::Found 0 missing values.
2026-03-26 22:18:12.39135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.39188 INFO::Done
2026-03-26 22:18:12.406413 INFO::Formatting Data.
2026-03-26 22:18:12.407084 INFO::Recognized SummarizedExperiment
2026-03-26 22:18:12.407599 INFO::Typecasting input to dataframe.
2026-03-26 22:18:12.423669 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.424828 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.428111 INFO::Found 0 missing values.
2026-03-26 22:18:12.438139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.438762 INFO::Done
2026-03-26 22:18:12.453838 INFO::Formatting Data.
2026-03-26 22:18:12.454541 INFO::Recognized SummarizedExperiment
2026-03-26 22:18:12.455036 INFO::Typecasting input to dataframe.
2026-03-26 22:18:12.470246 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.471202 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.472215 INFO::Found 0 missing values.
2026-03-26 22:18:12.473078 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-26 22:18:12.477128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.477633 INFO::Done
2026-03-26 22:18:12.486894 INFO::Formatting Data.
2026-03-26 22:18:12.487653 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.488476 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.489415 INFO::Found 0 missing values.
2026-03-26 22:18:12.492056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.492568 INFO::Done
2026-03-26 22:18:12.503268 INFO::Formatting Data.
2026-03-26 22:18:12.504132 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.505152 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.506179 INFO::Found 0 missing values.
2026-03-26 22:18:12.509063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.509624 INFO::Done
2026-03-26 22:18:12.539767 INFO::Formatting Data.
2026-03-26 22:18:12.540631 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.541721 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.542943 INFO::Found 1 missing values.
2026-03-26 22:18:12.545703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.546221 INFO::Done
2026-03-26 22:18:12.56606 INFO::Formatting Data.
2026-03-26 22:18:12.566928 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.567802 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.568791 INFO::Found 2 missing values.
2026-03-26 22:18:12.569721 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-26 22:18:12.572089 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.572664 INFO::Done
2026-03-26 22:18:12.583095 INFO::Formatting Data.
2026-03-26 22:18:12.583902 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.584807 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.58575 INFO::Found 2 missing values.
2026-03-26 22:18:12.587417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.587962 INFO::Done
2026-03-26 22:18:12.598654 INFO::Formatting Data.
2026-03-26 22:18:12.599389 INFO::Typecasting input to dataframe.
2026-03-26 22:18:12.600176 INFO::Replacing NaNs with NAs.
2026-03-26 22:18:12.601041 INFO::Removing potential empty rows and columns
2026-03-26 22:18:12.602046 INFO::Found 0 missing values.
2026-03-26 22:18:12.605035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-26 22:18:12.605593 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.231 3.320 20.300
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.811 | 1.676 | 17.780 | |
| compute_asw | 0.025 | 0.000 | 0.026 | |
| count_existing | 0.012 | 0.003 | 0.016 | |
| generate_data_covariables | 0.013 | 0.000 | 0.014 | |
| generate_dataset | 0.009 | 0.002 | 0.013 | |