Yannis Schumann
| Snapshot Date: 2026-03-31 13:45 -0400 (Tue, 31 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 2026-04-01 11:57 -0400 (Wed, 01 Apr 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" | 4896 |
| 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: 2026-03-31 21:21:52 -0400 (Tue, 31 Mar 2026) |
| EndedAt: 2026-03-31 21:23:22 -0400 (Tue, 31 Mar 2026) |
| EllapsedTime: 90.0 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 24.04.4 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 23.07 1.271 16.781
* 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")
2026-03-31 21:22:43.866517 INFO::Formatting Data.
2026-03-31 21:22:43.868069 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:43.879858 INFO::Removing potential empty rows and columns
2026-03-31 21:22:44.130807 INFO::Found 0 missing values.
2026-03-31 21:22:44.134625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:44.135375 INFO::Done
2026-03-31 21:22:44.135983 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:44.148357 INFO::Starting hierarchical adjustment
2026-03-31 21:22:44.149341 INFO::Found 3 batches.
2026-03-31 21:22:44.14992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:44.151213 INFO::Using default BPPARAM
2026-03-31 21:22:44.151826 INFO::Processing subtree level 1
2026-03-31 21:22:44.270882 INFO::Adjusting the last 1 batches sequentially
2026-03-31 21:22:44.273251 INFO::Done
2026-03-31 21:22:44.274131 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:44.277542 INFO::ASW Batch was 0.0468151808225741 prior to batch effect correction and is now 0.0468151808225741 .
2026-03-31 21:22:44.279321 INFO::Total function execution time is 0.413067579269409 s and adjustment time is 0.124056816101074 s ( 30.03 )
2026-03-31 21:22:44.296449 INFO::Formatting Data.
2026-03-31 21:22:44.297349 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:44.298369 INFO::Removing potential empty rows and columns
2026-03-31 21:22:44.299602 INFO::Found 0 missing values.
2026-03-31 21:22:44.300589 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.
2026-03-31 21:22:44.311834 INFO::Formatting Data.
2026-03-31 21:22:44.312569 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:44.31348 INFO::Removing potential empty rows and columns
2026-03-31 21:22:44.314579 INFO::Found 0 missing values.
2026-03-31 21:22:44.315565 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.
2026-03-31 21:22:44.332069 INFO::Formatting Data.
2026-03-31 21:22:44.332871 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:44.3338 INFO::Removing potential empty rows and columns
2026-03-31 21:22:44.334912 INFO::Found 0 missing values.
2026-03-31 21:22:44.335864 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.
2026-03-31 21:22:44.340423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:44.340976 INFO::Done
2026-03-31 21:22:44.341516 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:44.343717 INFO::Starting hierarchical adjustment
2026-03-31 21:22:44.34445 INFO::Found 2 batches.
2026-03-31 21:22:44.345005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:44.345667 INFO::Using default BPPARAM
2026-03-31 21:22:44.346193 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:44.347141 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 21:22:44.368949 INFO::Done
2026-03-31 21:22:44.369658 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:44.371827 INFO::ASW Batch was 0.126075488437536 prior to batch effect correction and is now -0.119951967806784 .
2026-03-31 21:22:44.372751 INFO::Total function execution time is 0.0407559871673584 s and adjustment time is 0.0246448516845703 s ( 60.47 )
2026-03-31 21:22:44.375681 INFO::Formatting Data.
2026-03-31 21:22:44.376338 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:44.385173 INFO::Formatting Data.
2026-03-31 21:22:44.385868 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:44.386763 INFO::Removing potential empty rows and columns
2026-03-31 21:22:44.387806 INFO::Found 0 missing values.
2026-03-31 21:22:44.390796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:44.391343 INFO::Done
2026-03-31 21:22:44.391883 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:44.416137 INFO::Starting hierarchical adjustment
2026-03-31 21:22:44.417407 INFO::Found 2 batches.
2026-03-31 21:22:44.417918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:44.418485 INFO::Using default BPPARAM
2026-03-31 21:22:44.418972 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:44.419854 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 21:22:44.433697 INFO::Done
2026-03-31 21:22:44.434345 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:44.436249 INFO::ASW Batch was 0.0467740992901643 prior to batch effect correction and is now -0.105285267671533 .
2026-03-31 21:22:44.43699 INFO::Total function execution time is 0.05185866355896 s and adjustment time is 0.0164577960968018 s ( 31.74 )
2026-03-31 21:22:44.438 INFO::Formatting Data.
2026-03-31 21:22:44.438578 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:44.439372 INFO::Removing potential empty rows and columns
2026-03-31 21:22:44.440303 INFO::Found 0 missing values.
2026-03-31 21:22:44.442854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:44.44336 INFO::Done
2026-03-31 21:22:44.443831 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:44.445689 INFO::Starting hierarchical adjustment
2026-03-31 21:22:44.446343 INFO::Found 2 batches.
2026-03-31 21:22:44.446828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:44.447413 INFO::Using default BPPARAM
2026-03-31 21:22:44.447893 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:44.448743 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 21:22:44.462289 INFO::Done
2026-03-31 21:22:44.462895 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:44.464752 INFO::ASW Batch was 0.0467740992901643 prior to batch effect correction and is now -0.105285267671533 .
2026-03-31 21:22:44.465496 INFO::Total function execution time is 0.0275008678436279 s and adjustment time is 0.0160567760467529 s ( 58.39 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-31 21:22:47.439094 INFO::Formatting Data.
2026-03-31 21:22:47.439888 INFO::Recognized SummarizedExperiment
2026-03-31 21:22:47.440381 INFO::Typecasting input to dataframe.
2026-03-31 21:22:47.470885 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:47.472203 INFO::Removing potential empty rows and columns
2026-03-31 21:22:47.475971 INFO::Found 0 missing values.
2026-03-31 21:22:47.483324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:47.4839 INFO::Done
2026-03-31 21:22:47.48445 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:47.488171 INFO::Starting hierarchical adjustment
2026-03-31 21:22:47.488891 INFO::Found 2 batches.
2026-03-31 21:22:47.489422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:47.490553 INFO::Using default BPPARAM
2026-03-31 21:22:47.49109 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:47.492063 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 21:22:47.550199 INFO::Done
2026-03-31 21:22:47.550915 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:47.554709 INFO::ASW Batch was -0.00122384574209286 prior to batch effect correction and is now -0.0966557269131501 .
2026-03-31 21:22:47.555547 INFO::Total function execution time is 0.116787433624268 s and adjustment time is 0.0614330768585205 s ( 52.6 )
Warning: stack imbalance in '{', 73 then 75
2026-03-31 21:22:47.574455 INFO::Formatting Data.
2026-03-31 21:22:47.57517 INFO::Recognized SummarizedExperiment
2026-03-31 21:22:47.575703 INFO::Typecasting input to dataframe.
2026-03-31 21:22:47.58538 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:47.586485 INFO::Removing potential empty rows and columns
2026-03-31 21:22:47.590159 INFO::Found 0 missing values.
2026-03-31 21:22:47.597212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:47.597787 INFO::Done
2026-03-31 21:22:47.598301 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:47.601801 INFO::Starting hierarchical adjustment
2026-03-31 21:22:47.602522 INFO::Found 2 batches.
2026-03-31 21:22:47.603034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:47.603643 INFO::Using default BPPARAM
2026-03-31 21:22:47.60415 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:47.605127 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 21:22:47.631049 INFO::Done
2026-03-31 21:22:47.63182 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:47.635476 INFO::ASW Batch was 0.0172736003333138 prior to batch effect correction and is now 0.0172736003333138 .
2026-03-31 21:22:47.636354 INFO::Total function execution time is 0.061861515045166 s and adjustment time is 0.028639554977417 s ( 46.3 )
2026-03-31 21:22:47.65541 INFO::Formatting Data.
2026-03-31 21:22:47.656227 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:47.657186 INFO::Removing potential empty rows and columns
2026-03-31 21:22:47.658231 INFO::Found 0 missing values.
2026-03-31 21:22:47.661566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:47.662102 INFO::Done
2026-03-31 21:22:47.662624 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:47.664674 INFO::Starting hierarchical adjustment
2026-03-31 21:22:47.665381 INFO::Found 3 batches.
2026-03-31 21:22:47.665897 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:47.666511 INFO::Using default BPPARAM
2026-03-31 21:22:47.667026 INFO::Processing subtree level 1
2026-03-31 21:22:47.813257 INFO::Adjusting the last 1 batches sequentially
2026-03-31 21:22:47.815432 INFO::Done
2026-03-31 21:22:47.816231 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:47.819107 INFO::ASW Batch was -0.0848484735246448 prior to batch effect correction and is now -0.15366755714668 .
2026-03-31 21:22:47.820183 INFO::Total function execution time is 0.164825201034546 s and adjustment time is 0.15012788772583 s ( 91.08 )
2026-03-31 21:22:47.836355 INFO::Skipping initial DF formatting
2026-03-31 21:22:47.837197 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:47.841609 INFO::Starting hierarchical adjustment
2026-03-31 21:22:47.842461 INFO::Found 5 batches.
2026-03-31 21:22:47.843003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:47.843658 INFO::Using default BPPARAM
2026-03-31 21:22:47.844203 INFO::Processing subtree level 1
2026-03-31 21:22:48.090985 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:48.092875 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 21:22:48.113775 INFO::Done
2026-03-31 21:22:48.114602 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:48.174719 INFO::ASW Batch was 0.553082126924269 prior to batch effect correction and is now 0.553082126924269 .
2026-03-31 21:22:48.175537 INFO::ASW Label was 0.390428988034638 prior to batch effect correction and is now 0.390428988034638 .
2026-03-31 21:22:48.176443 INFO::Total function execution time is 0.340257883071899 s and adjustment time is 0.27147102355957 s ( 79.78 )
2026-03-31 21:22:48.197367 INFO::Formatting Data.
2026-03-31 21:22:48.198214 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:48.199214 INFO::Removing potential empty rows and columns
2026-03-31 21:22:48.200299 INFO::Found 0 missing values.
2026-03-31 21:22:48.204814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:48.20544 INFO::Done
2026-03-31 21:22:48.205979 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:48.209424 INFO::Starting hierarchical adjustment
2026-03-31 21:22:48.210169 INFO::Found 5 batches.
2026-03-31 21:22:48.210736 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:48.211383 INFO::Using default BPPARAM
2026-03-31 21:22:48.211948 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.
2026-03-31 21:22:48.362536 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:48.364582 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 21:22:48.391013 INFO::Done
2026-03-31 21:22:48.392018 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:48.397366 INFO::ASW Batch was 0.680283510512879 prior to batch effect correction and is now -0.0661683038254246 .
2026-03-31 21:22:48.398418 INFO::ASW Label was 0.152344018149714 prior to batch effect correction and is now 0.686516560975699 .
2026-03-31 21:22:48.399604 INFO::Total function execution time is 0.202312231063843 s and adjustment time is 0.180908679962158 s ( 89.42 )
2026-03-31 21:22:48.400971 INFO::Formatting Data.
2026-03-31 21:22:48.402003 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:48.403432 INFO::Removing potential empty rows and columns
2026-03-31 21:22:48.405 INFO::Found 0 missing values.
2026-03-31 21:22:48.411527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:48.412253 INFO::Done
2026-03-31 21:22:48.413014 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:48.417384 INFO::Starting hierarchical adjustment
2026-03-31 21:22:48.418345 INFO::Found 5 batches.
2026-03-31 21:22:48.419017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:48.419891 INFO::Using default BPPARAM
2026-03-31 21:22:48.42051 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.
2026-03-31 21:22:48.575964 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:48.577894 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 21:22:48.595168 INFO::Done
2026-03-31 21:22:48.595877 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:48.599319 INFO::ASW Batch was 0.680283510512879 prior to batch effect correction and is now -0.0661683038254246 .
2026-03-31 21:22:48.599918 INFO::ASW Label was 0.152344018149714 prior to batch effect correction and is now 0.686516560975699 .
2026-03-31 21:22:48.600742 INFO::Total function execution time is 0.199866533279419 s and adjustment time is 0.177019357681274 s ( 88.57 )
2026-03-31 21:22:48.614876 INFO::Formatting Data.
2026-03-31 21:22:48.61571 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:48.616642 INFO::Removing potential empty rows and columns
2026-03-31 21:22:48.617666 INFO::Found 0 missing values.
2026-03-31 21:22:48.621721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:48.622292 INFO::Done
2026-03-31 21:22:48.622832 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:48.626042 INFO::Starting hierarchical adjustment
2026-03-31 21:22:48.62676 INFO::Found 5 batches.
2026-03-31 21:22:48.627257 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:48.627852 INFO::Using default BPPARAM
2026-03-31 21:22:48.628381 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.
2026-03-31 21:22:48.762293 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:48.764671 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 21:22:48.789656 INFO::Done
2026-03-31 21:22:48.790766 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:48.795919 INFO::ASW Batch was 0.327489088345269 prior to batch effect correction and is now -0.0361522318380852 .
2026-03-31 21:22:48.796823 INFO::ASW Label was 0.530410006911797 prior to batch effect correction and is now 0.736494820797971 .
2026-03-31 21:22:48.798178 INFO::Total function execution time is 0.183287620544434 s and adjustment time is 0.162945985794067 s ( 88.9 )
2026-03-31 21:22:48.799483 INFO::Formatting Data.
2026-03-31 21:22:48.800497 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:48.801842 INFO::Removing potential empty rows and columns
2026-03-31 21:22:48.803373 INFO::Found 0 missing values.
2026-03-31 21:22:48.807693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:48.808266 INFO::Done
2026-03-31 21:22:48.808848 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:48.812303 INFO::Starting hierarchical adjustment
2026-03-31 21:22:48.813066 INFO::Found 5 batches.
2026-03-31 21:22:48.813631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:48.814307 INFO::Using default BPPARAM
2026-03-31 21:22:48.8149 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.
2026-03-31 21:22:48.961352 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:48.963282 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 21:22:48.983403 INFO::Done
2026-03-31 21:22:48.9843 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:48.988153 INFO::ASW Batch was 0.327489088345269 prior to batch effect correction and is now -0.0361522318380852 .
2026-03-31 21:22:48.988924 INFO::ASW Label was 0.530410006911797 prior to batch effect correction and is now 0.736494820797971 .
2026-03-31 21:22:48.989955 INFO::Total function execution time is 0.190563201904297 s and adjustment time is 0.170436859130859 s ( 89.44 )
2026-03-31 21:22:49.006203 INFO::Formatting Data.
2026-03-31 21:22:49.007164 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:49.008261 INFO::Removing potential empty rows and columns
2026-03-31 21:22:49.009447 INFO::Found 0 missing values.
2026-03-31 21:22:49.01254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:49.013166 INFO::Done
2026-03-31 21:22:49.013778 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:49.017365 INFO::Starting hierarchical adjustment
2026-03-31 21:22:49.018194 INFO::Found 2 batches.
2026-03-31 21:22:49.018802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:49.019587 INFO::Using default BPPARAM
2026-03-31 21:22:49.020204 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:49.021318 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 21:22:49.038505 INFO::Done
2026-03-31 21:22:49.039262 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:49.042625 INFO::ASW Batch was 0.389460509014466 prior to batch effect correction and is now -0.0121304725367899 .
2026-03-31 21:22:49.043314 INFO::ASW Label was 0.512774451804461 prior to batch effect correction and is now 0.869243522836302 .
2026-03-31 21:22:49.044202 INFO::Total function execution time is 0.0381259918212891 s and adjustment time is 0.0204582214355469 s ( 53.66 )
2026-03-31 21:22:49.045144 INFO::Formatting Data.
2026-03-31 21:22:49.045828 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:49.046876 INFO::Removing potential empty rows and columns
2026-03-31 21:22:49.048029 INFO::Found 0 missing values.
2026-03-31 21:22:49.051049 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:49.051642 INFO::Done
2026-03-31 21:22:49.052206 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:49.055605 INFO::Starting hierarchical adjustment
2026-03-31 21:22:49.056385 INFO::Found 2 batches.
2026-03-31 21:22:49.056968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:49.057625 INFO::Using default BPPARAM
2026-03-31 21:22:49.058193 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:49.059151 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 21:22:49.089833 INFO::Done
2026-03-31 21:22:49.090808 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:49.095099 INFO::ASW Batch was 0.389460509014466 prior to batch effect correction and is now -0.0121304725367899 .
2026-03-31 21:22:49.095868 INFO::ASW Label was 0.512774451804461 prior to batch effect correction and is now 0.869243522836302 .
2026-03-31 21:22:49.096911 INFO::Total function execution time is 0.0517535209655762 s and adjustment time is 0.0335335731506348 s ( 64.79 )
2026-03-31 21:22:49.113347 INFO::Formatting Data.
2026-03-31 21:22:49.114451 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:49.115692 INFO::Removing potential empty rows and columns
2026-03-31 21:22:49.11693 INFO::Found 0 missing values.
2026-03-31 21:22:49.119941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:49.120646 INFO::Done
2026-03-31 21:22:49.121722 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:49.124336 INFO::Starting hierarchical adjustment
2026-03-31 21:22:49.125245 INFO::Found 2 batches.
2026-03-31 21:22:49.125941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:49.126786 INFO::Using default BPPARAM
2026-03-31 21:22:49.127488 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:49.128679 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 21:22:49.171488 INFO::Done
2026-03-31 21:22:49.172372 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:49.175065 INFO::ASW Batch was 0.0368971047703103 prior to batch effect correction and is now -0.125276066150478 .
2026-03-31 21:22:49.176049 INFO::Total function execution time is 0.0629167556762695 s and adjustment time is 0.0463931560516357 s ( 73.74 )
2026-03-31 21:22:49.19243 INFO::Formatting Data.
2026-03-31 21:22:49.193349 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:49.194423 INFO::Removing potential empty rows and columns
2026-03-31 21:22:49.195678 INFO::Found 0 missing values.
2026-03-31 21:22:49.197129 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.
2026-03-31 21:22:49.203007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:49.20366 INFO::Done
2026-03-31 21:22:49.204286 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:49.208092 INFO::Starting hierarchical adjustment
2026-03-31 21:22:49.208956 INFO::Found 2 batches.
2026-03-31 21:22:49.209625 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:49.210371 INFO::Using default BPPARAM
2026-03-31 21:22:49.211015 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:49.212153 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 21:22:49.233802 INFO::Done
2026-03-31 21:22:49.234646 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:49.238365 INFO::ASW Batch was 0.237057328153243 prior to batch effect correction and is now -0.019642088304032 .
2026-03-31 21:22:49.239111 INFO::ASW Label was 0.802809904847064 prior to batch effect correction and is now 0.948717935455757 .
2026-03-31 21:22:49.240092 INFO::Total function execution time is 0.0477962493896484 s and adjustment time is 0.0249683856964111 s ( 52.24 )
2026-03-31 21:22:49.241064 INFO::Formatting Data.
2026-03-31 21:22:49.241813 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:49.242892 INFO::Removing potential empty rows and columns
2026-03-31 21:22:49.244083 INFO::Found 0 missing values.
2026-03-31 21:22:49.245173 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.
2026-03-31 21:22:49.250731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:49.251377 INFO::Done
2026-03-31 21:22:49.251997 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:49.255609 INFO::Starting hierarchical adjustment
2026-03-31 21:22:49.256848 INFO::Found 2 batches.
2026-03-31 21:22:49.257491 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:49.258209 INFO::Using default BPPARAM
2026-03-31 21:22:49.258853 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:49.259982 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 21:22:49.280706 INFO::Done
2026-03-31 21:22:49.281578 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:49.285331 INFO::ASW Batch was 0.237057328153243 prior to batch effect correction and is now -0.019642088304032 .
2026-03-31 21:22:49.286012 INFO::ASW Label was 0.802809904847064 prior to batch effect correction and is now 0.948717935455757 .
2026-03-31 21:22:49.287017 INFO::Total function execution time is 0.0459859371185303 s and adjustment time is 0.0243194103240967 s ( 52.88 )
2026-03-31 21:22:49.549226 INFO::Formatting Data.
2026-03-31 21:22:49.55011 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:49.551181 INFO::Removing potential empty rows and columns
2026-03-31 21:22:49.552315 INFO::Found 0 missing values.
2026-03-31 21:22:49.555808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:49.556367 INFO::Done
2026-03-31 21:22:49.556893 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:49.55924 INFO::Starting hierarchical adjustment
2026-03-31 21:22:49.559975 INFO::Found 3 batches.
2026-03-31 21:22:49.560516 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:49.561154 INFO::Using default BPPARAM
2026-03-31 21:22:49.561689 INFO::Processing subtree level 1
2026-03-31 21:22:49.655499 INFO::Adjusting the last 1 batches sequentially
2026-03-31 21:22:49.657443 INFO::Done
2026-03-31 21:22:49.658135 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:49.660745 INFO::ASW Batch was 0.0726423380821399 prior to batch effect correction and is now 0.0726423380821399 .
2026-03-31 21:22:49.661711 INFO::Total function execution time is 0.112559795379639 s and adjustment time is 0.0976035594940186 s ( 86.71 )
2026-03-31 21:22:49.662836 INFO::Formatting Data.
2026-03-31 21:22:49.663523 INFO::Typecasting input to dataframe.
2026-03-31 21:22:49.664314 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:49.665296 INFO::Removing potential empty rows and columns
2026-03-31 21:22:49.666409 INFO::Found 0 missing values.
2026-03-31 21:22:49.669732 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:49.670318 INFO::Done
2026-03-31 21:22:49.67086 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:49.672905 INFO::Starting hierarchical adjustment
2026-03-31 21:22:49.673638 INFO::Found 3 batches.
2026-03-31 21:22:49.674179 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:49.674826 INFO::Using default BPPARAM
2026-03-31 21:22:49.675377 INFO::Processing subtree level 1
2026-03-31 21:22:49.76498 INFO::Adjusting the last 1 batches sequentially
2026-03-31 21:22:49.767084 INFO::Done
2026-03-31 21:22:49.767813 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:49.772478 INFO::ASW Batch was 0.0726423380821399 prior to batch effect correction and is now 0.0726423380821399 .
2026-03-31 21:22:49.773872 INFO::Total function execution time is 0.110982656478882 s and adjustment time is 0.093555212020874 s ( 84.3 )
2026-03-31 21:22:49.787699 INFO::Formatting Data.
2026-03-31 21:22:49.788531 INFO::Typecasting input to dataframe.
2026-03-31 21:22:49.789409 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:49.790356 INFO::Removing potential empty rows and columns
2026-03-31 21:22:49.791458 INFO::Found 0 missing values.
2026-03-31 21:22:49.794597 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:49.795135 INFO::Done
2026-03-31 21:22:49.795695 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:49.797788 INFO::Starting hierarchical adjustment
2026-03-31 21:22:49.798525 INFO::Found 3 batches.
2026-03-31 21:22:49.799055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:49.799692 INFO::Using default BPPARAM
2026-03-31 21:22:49.800236 INFO::Processing subtree level 1
2026-03-31 21:22:49.886503 INFO::Adjusting the last 1 batches sequentially
2026-03-31 21:22:49.888454 INFO::Done
2026-03-31 21:22:49.889076 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:49.89163 INFO::ASW Batch was -0.048643180153559 prior to batch effect correction and is now -0.048643180153559 .
2026-03-31 21:22:49.89257 INFO::Total function execution time is 0.10496973991394 s and adjustment time is 0.0900793075561523 s ( 85.81 )
2026-03-31 21:22:50.048061 INFO::Formatting Data.
2026-03-31 21:22:50.049026 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:50.050258 INFO::Removing potential empty rows and columns
2026-03-31 21:22:50.053206 INFO::Found 1000 missing values.
2026-03-31 21:22:50.072618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:50.073878 INFO::Done
2026-03-31 21:22:50.074694 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:50.080614 INFO::Starting hierarchical adjustment
2026-03-31 21:22:50.081401 INFO::Found 10 batches.
2026-03-31 21:22:50.081933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:50.082581 INFO::Using default BPPARAM
2026-03-31 21:22:50.083108 INFO::Processing subtree level 1
2026-03-31 21:22:50.216882 INFO::Processing subtree level 2
2026-03-31 21:22:50.359903 INFO::Adjusting the last 1 batches sequentially
2026-03-31 21:22:50.361782 INFO::Done
2026-03-31 21:22:50.36245 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:50.367934 INFO::ASW Batch was 0.476082766120513 prior to batch effect correction and is now 0.476082766120513 .
2026-03-31 21:22:50.3686 INFO::ASW Label was 0.349291332539975 prior to batch effect correction and is now 0.349291332539975 .
2026-03-31 21:22:50.36954 INFO::Total function execution time is 0.321614027023315 s and adjustment time is 0.280567169189453 s ( 87.24 )
2026-03-31 21:22:50.370397 INFO::Formatting Data.
2026-03-31 21:22:50.371029 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:50.372288 INFO::Removing potential empty rows and columns
2026-03-31 21:22:50.375137 INFO::Found 1000 missing values.
2026-03-31 21:22:50.394765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:50.395518 INFO::Done
2026-03-31 21:22:50.396074 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:50.401646 INFO::Starting hierarchical adjustment
2026-03-31 21:22:50.402414 INFO::Found 10 batches.
2026-03-31 21:22:51.612204 INFO::Set up parallel execution backend with 2 workers
2026-03-31 21:22:51.614434 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-31 21:22:52.908394 INFO::Adjusting the last 2 batches sequentially
2026-03-31 21:22:52.910672 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 21:22:52.928533 INFO::Done
2026-03-31 21:22:52.929323 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:52.934157 INFO::ASW Batch was 0.476082766120513 prior to batch effect correction and is now 0.476082766120513 .
2026-03-31 21:22:52.934785 INFO::ASW Label was 0.349291332539975 prior to batch effect correction and is now 0.349291332539975 .
2026-03-31 21:22:52.935545 INFO::Total function execution time is 2.56518912315369 s and adjustment time is 2.52621746063232 s ( 98.48 )
2026-03-31 21:22:53.118514 INFO::Formatting Data.
2026-03-31 21:22:53.119655 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.12083 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.122145 INFO::Found 0 missing values.
2026-03-31 21:22:53.12642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.127095 INFO::Done
2026-03-31 21:22:53.12771 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 21:22:53.131308 INFO::Starting hierarchical adjustment
2026-03-31 21:22:53.132196 INFO::Found 3 batches.
2026-03-31 21:22:53.132802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 21:22:53.133485 INFO::Using default BPPARAM
2026-03-31 21:22:53.134073 INFO::Processing subtree level 1
2026-03-31 21:22:53.26406 INFO::Adjusting the last 1 batches sequentially
2026-03-31 21:22:53.266199 INFO::Done
2026-03-31 21:22:53.266961 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 21:22:53.27071 INFO::ASW Batch was 0.129465643891111 prior to batch effect correction and is now -0.149155054580145 .
2026-03-31 21:22:53.271425 INFO::ASW Label was -0.128222484156952 prior to batch effect correction and is now 0.095086656646854 .
2026-03-31 21:22:53.272423 INFO::Total function execution time is 0.154154300689697 s and adjustment time is 0.134154081344604 s ( 87.03 )
2026-03-31 21:22:53.402926 INFO::Formatting Data.
2026-03-31 21:22:53.403959 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.405007 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.406146 INFO::Found 2 missing values.
2026-03-31 21:22:53.409178 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.409752 INFO::Done
2026-03-31 21:22:53.448812 INFO::Found NA in Reference column
2026-03-31 21:22:53.459891 INFO::Require at least two references per batch.
2026-03-31 21:22:53.482202 INFO::Formatting Data.
2026-03-31 21:22:53.48304 INFO::Recognized SummarizedExperiment
2026-03-31 21:22:53.483609 INFO::Typecasting input to dataframe.
2026-03-31 21:22:53.493818 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.495006 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.498538 INFO::Found 0 missing values.
2026-03-31 21:22:53.50507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.50567 INFO::Done
2026-03-31 21:22:53.521799 INFO::Formatting Data.
2026-03-31 21:22:53.522546 INFO::Recognized SummarizedExperiment
2026-03-31 21:22:53.52308 INFO::Typecasting input to dataframe.
2026-03-31 21:22:53.541416 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.542832 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.54639 INFO::Found 0 missing values.
2026-03-31 21:22:53.556786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.557434 INFO::Done
2026-03-31 21:22:53.572669 INFO::Formatting Data.
2026-03-31 21:22:53.573349 INFO::Recognized SummarizedExperiment
2026-03-31 21:22:53.573859 INFO::Typecasting input to dataframe.
2026-03-31 21:22:53.589653 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.590631 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.591671 INFO::Found 0 missing values.
2026-03-31 21:22:53.592553 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.
2026-03-31 21:22:53.596754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.597299 INFO::Done
2026-03-31 21:22:53.606954 INFO::Formatting Data.
2026-03-31 21:22:53.607728 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.608558 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.609497 INFO::Found 0 missing values.
2026-03-31 21:22:53.612147 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.612656 INFO::Done
2026-03-31 21:22:53.623815 INFO::Formatting Data.
2026-03-31 21:22:53.624763 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.625871 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.626975 INFO::Found 0 missing values.
2026-03-31 21:22:53.629941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.63052 INFO::Done
2026-03-31 21:22:53.662077 INFO::Formatting Data.
2026-03-31 21:22:53.663006 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.664174 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.665504 INFO::Found 1 missing values.
2026-03-31 21:22:53.66838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.66896 INFO::Done
2026-03-31 21:22:53.689129 INFO::Formatting Data.
2026-03-31 21:22:53.689964 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.690892 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.691892 INFO::Found 2 missing values.
2026-03-31 21:22:53.692877 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.
2026-03-31 21:22:53.69524 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.695817 INFO::Done
2026-03-31 21:22:53.706335 INFO::Formatting Data.
2026-03-31 21:22:53.707097 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.708023 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.708993 INFO::Found 2 missing values.
2026-03-31 21:22:53.710688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.711261 INFO::Done
2026-03-31 21:22:53.721818 INFO::Formatting Data.
2026-03-31 21:22:53.72255 INFO::Typecasting input to dataframe.
2026-03-31 21:22:53.723346 INFO::Replacing NaNs with NAs.
2026-03-31 21:22:53.724179 INFO::Removing potential empty rows and columns
2026-03-31 21:22:53.725178 INFO::Found 0 missing values.
2026-03-31 21:22:53.728133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 21:22:53.728692 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.022 4.043 21.553
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.070 | 1.271 | 16.781 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.009 | 0.001 | 0.011 | |