Yannis Schumann
| Snapshot Date: 2026-03-03 13:45 -0500 (Tue, 03 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 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-04 11:57 -0500 (Wed, 04 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" | 4892 |
| 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: 2026-03-03 21:28:36 -0500 (Tue, 03 Mar 2026) |
| EndedAt: 2026-03-03 21:30:07 -0500 (Tue, 03 Mar 2026) |
| EllapsedTime: 91.1 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.907 1.521 17.971
* 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")
2026-03-03 21:29:29.19046 INFO::Formatting Data.
2026-03-03 21:29:29.192033 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:29.204033 INFO::Removing potential empty rows and columns
2026-03-03 21:29:29.441498 INFO::Found 0 missing values.
2026-03-03 21:29:29.445009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:29.445703 INFO::Done
2026-03-03 21:29:29.44625 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:29.457143 INFO::Starting hierarchical adjustment
2026-03-03 21:29:29.457968 INFO::Found 3 batches.
2026-03-03 21:29:29.458504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:29.459682 INFO::Using default BPPARAM
2026-03-03 21:29:29.460219 INFO::Processing subtree level 1
2026-03-03 21:29:29.563993 INFO::Adjusting the last 1 batches sequentially
2026-03-03 21:29:29.56615 INFO::Done
2026-03-03 21:29:29.566916 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:29.569757 INFO::ASW Batch was -0.116502287977548 prior to batch effect correction and is now -0.116502287977548 .
2026-03-03 21:29:29.570944 INFO::Total function execution time is 0.381279468536377 s and adjustment time is 0.1083083152771 s ( 28.41 )
2026-03-03 21:29:29.586973 INFO::Formatting Data.
2026-03-03 21:29:29.588209 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:29.589697 INFO::Removing potential empty rows and columns
2026-03-03 21:29:29.591447 INFO::Found 0 missing values.
2026-03-03 21:29:29.592875 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.
2026-03-03 21:29:29.607573 INFO::Formatting Data.
2026-03-03 21:29:29.608373 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:29.609345 INFO::Removing potential empty rows and columns
2026-03-03 21:29:29.610445 INFO::Found 0 missing values.
2026-03-03 21:29:29.611407 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.
2026-03-03 21:29:29.62735 INFO::Formatting Data.
2026-03-03 21:29:29.628081 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:29.62896 INFO::Removing potential empty rows and columns
2026-03-03 21:29:29.629979 INFO::Found 0 missing values.
2026-03-03 21:29:29.639459 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.
2026-03-03 21:29:29.644807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:29.64541 INFO::Done
2026-03-03 21:29:29.646023 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:29.648753 INFO::Starting hierarchical adjustment
2026-03-03 21:29:29.649478 INFO::Found 2 batches.
2026-03-03 21:29:29.650036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:29.650768 INFO::Using default BPPARAM
2026-03-03 21:29:29.651304 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:29.652264 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-03 21:29:29.675086 INFO::Done
2026-03-03 21:29:29.675802 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:29.678218 INFO::ASW Batch was -0.0235334063565627 prior to batch effect correction and is now -0.116290131530085 .
2026-03-03 21:29:29.679107 INFO::Total function execution time is 0.051774263381958 s and adjustment time is 0.0257389545440674 s ( 49.71 )
2026-03-03 21:29:29.682336 INFO::Formatting Data.
2026-03-03 21:29:29.683006 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:29.69238 INFO::Formatting Data.
2026-03-03 21:29:29.693391 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:29.694781 INFO::Removing potential empty rows and columns
2026-03-03 21:29:29.696606 INFO::Found 0 missing values.
2026-03-03 21:29:29.701108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:29.701915 INFO::Done
2026-03-03 21:29:29.702674 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:29.752424 INFO::Starting hierarchical adjustment
2026-03-03 21:29:29.754394 INFO::Found 2 batches.
2026-03-03 21:29:29.75535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:29.756327 INFO::Using default BPPARAM
2026-03-03 21:29:29.757161 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:29.758656 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-03 21:29:29.784043 INFO::Done
2026-03-03 21:29:29.785113 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:29.78831 INFO::ASW Batch was -0.0119087188003833 prior to batch effect correction and is now -0.116311562125361 .
2026-03-03 21:29:29.789529 INFO::Total function execution time is 0.0970890522003174 s and adjustment time is 0.0298740863800049 s ( 30.77 )
2026-03-03 21:29:29.79117 INFO::Formatting Data.
2026-03-03 21:29:29.792117 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:29.793457 INFO::Removing potential empty rows and columns
2026-03-03 21:29:29.795093 INFO::Found 0 missing values.
2026-03-03 21:29:29.799814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:29.800712 INFO::Done
2026-03-03 21:29:29.801313 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:29.803488 INFO::Starting hierarchical adjustment
2026-03-03 21:29:29.8042 INFO::Found 2 batches.
2026-03-03 21:29:29.804724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:29.805312 INFO::Using default BPPARAM
2026-03-03 21:29:29.805849 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:29.806748 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-03 21:29:29.82137 INFO::Done
2026-03-03 21:29:29.822033 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:29.824028 INFO::ASW Batch was -0.0119087188003833 prior to batch effect correction and is now -0.116311562125361 .
2026-03-03 21:29:29.824811 INFO::Total function execution time is 0.0337245464324951 s and adjustment time is 0.0172958374023438 s ( 51.29 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-03 21:29:32.764045 INFO::Formatting Data.
2026-03-03 21:29:32.764735 INFO::Recognized SummarizedExperiment
2026-03-03 21:29:32.76521 INFO::Typecasting input to dataframe.
2026-03-03 21:29:32.797433 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:32.798751 INFO::Removing potential empty rows and columns
2026-03-03 21:29:32.802666 INFO::Found 0 missing values.
2026-03-03 21:29:32.810009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:32.810646 INFO::Done
2026-03-03 21:29:32.811171 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:32.814793 INFO::Starting hierarchical adjustment
2026-03-03 21:29:32.815501 INFO::Found 2 batches.
2026-03-03 21:29:32.816036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:32.817108 INFO::Using default BPPARAM
2026-03-03 21:29:32.817655 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:32.818621 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-03 21:29:32.875324 INFO::Done
2026-03-03 21:29:32.876148 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:32.879889 INFO::ASW Batch was 0.00926502764797268 prior to batch effect correction and is now -0.105202560769356 .
2026-03-03 21:29:32.8808 INFO::Total function execution time is 0.116992712020874 s and adjustment time is 0.0598978996276855 s ( 51.2 )
Warning: stack imbalance in '{', 73 then 75
2026-03-03 21:29:32.900039 INFO::Formatting Data.
2026-03-03 21:29:32.900757 INFO::Recognized SummarizedExperiment
2026-03-03 21:29:32.901283 INFO::Typecasting input to dataframe.
2026-03-03 21:29:32.910435 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:32.911547 INFO::Removing potential empty rows and columns
2026-03-03 21:29:32.915344 INFO::Found 0 missing values.
2026-03-03 21:29:32.922352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:32.922949 INFO::Done
2026-03-03 21:29:32.923456 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:32.926961 INFO::Starting hierarchical adjustment
2026-03-03 21:29:32.927674 INFO::Found 2 batches.
2026-03-03 21:29:32.92819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:32.928805 INFO::Using default BPPARAM
2026-03-03 21:29:32.929308 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:32.930255 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-03 21:29:32.95494 INFO::Done
2026-03-03 21:29:32.955637 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:32.959237 INFO::ASW Batch was -0.0100559307732865 prior to batch effect correction and is now -0.0100559307732865 .
2026-03-03 21:29:32.960124 INFO::Total function execution time is 0.0600640773773193 s and adjustment time is 0.0273947715759277 s ( 45.61 )
2026-03-03 21:29:32.978382 INFO::Formatting Data.
2026-03-03 21:29:32.979157 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:32.98006 INFO::Removing potential empty rows and columns
2026-03-03 21:29:32.981075 INFO::Found 0 missing values.
2026-03-03 21:29:32.983988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:32.984524 INFO::Done
2026-03-03 21:29:32.985029 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:32.986995 INFO::Starting hierarchical adjustment
2026-03-03 21:29:32.987683 INFO::Found 3 batches.
2026-03-03 21:29:32.988202 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:32.988961 INFO::Using default BPPARAM
2026-03-03 21:29:32.989472 INFO::Processing subtree level 1
2026-03-03 21:29:33.126862 INFO::Adjusting the last 1 batches sequentially
2026-03-03 21:29:33.128766 INFO::Done
2026-03-03 21:29:33.129434 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:33.131937 INFO::ASW Batch was -0.00573001873724378 prior to batch effect correction and is now -0.167946752311602 .
2026-03-03 21:29:33.13287 INFO::Total function execution time is 0.154514312744141 s and adjustment time is 0.141197919845581 s ( 91.38 )
2026-03-03 21:29:33.147072 INFO::Skipping initial DF formatting
2026-03-03 21:29:33.147792 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:33.151813 INFO::Starting hierarchical adjustment
2026-03-03 21:29:33.152556 INFO::Found 5 batches.
2026-03-03 21:29:33.153093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:33.153715 INFO::Using default BPPARAM
2026-03-03 21:29:33.154257 INFO::Processing subtree level 1
2026-03-03 21:29:33.462546 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:33.464417 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-03 21:29:33.485068 INFO::Done
2026-03-03 21:29:33.485951 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:33.54777 INFO::ASW Batch was 0.527134099368911 prior to batch effect correction and is now 0.527134099368911 .
2026-03-03 21:29:33.548634 INFO::ASW Label was 0.380563993366947 prior to batch effect correction and is now 0.380563993366947 .
2026-03-03 21:29:33.549603 INFO::Total function execution time is 0.40255069732666 s and adjustment time is 0.332596063613892 s ( 82.62 )
2026-03-03 21:29:33.567979 INFO::Formatting Data.
2026-03-03 21:29:33.568879 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:33.569889 INFO::Removing potential empty rows and columns
2026-03-03 21:29:33.570982 INFO::Found 0 missing values.
2026-03-03 21:29:33.575454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:33.576078 INFO::Done
2026-03-03 21:29:33.576651 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:33.579979 INFO::Starting hierarchical adjustment
2026-03-03 21:29:33.580738 INFO::Found 5 batches.
2026-03-03 21:29:33.581317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:33.582075 INFO::Using default BPPARAM
2026-03-03 21:29:33.582842 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.
2026-03-03 21:29:33.739093 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:33.740965 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-03 21:29:33.760673 INFO::Done
2026-03-03 21:29:33.761537 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:33.765641 INFO::ASW Batch was 0.377273691039846 prior to batch effect correction and is now -0.0717359331628862 .
2026-03-03 21:29:33.766357 INFO::ASW Label was 0.386594838723924 prior to batch effect correction and is now 0.858149087327116 .
2026-03-03 21:29:33.767317 INFO::Total function execution time is 0.199409484863281 s and adjustment time is 0.180019617080688 s ( 90.28 )
2026-03-03 21:29:33.768327 INFO::Formatting Data.
2026-03-03 21:29:33.769029 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:33.77005 INFO::Removing potential empty rows and columns
2026-03-03 21:29:33.77124 INFO::Found 0 missing values.
2026-03-03 21:29:33.775853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:33.776481 INFO::Done
2026-03-03 21:29:33.777045 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:33.780487 INFO::Starting hierarchical adjustment
2026-03-03 21:29:33.781248 INFO::Found 5 batches.
2026-03-03 21:29:33.781829 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:33.782464 INFO::Using default BPPARAM
2026-03-03 21:29:33.78302 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.
2026-03-03 21:29:33.936197 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:33.938193 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-03 21:29:33.957603 INFO::Done
2026-03-03 21:29:33.958606 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:33.962883 INFO::ASW Batch was 0.377273691039846 prior to batch effect correction and is now -0.0717359331628862 .
2026-03-03 21:29:33.963643 INFO::ASW Label was 0.386594838723924 prior to batch effect correction and is now 0.858149087327116 .
2026-03-03 21:29:33.964622 INFO::Total function execution time is 0.196268081665039 s and adjustment time is 0.176418781280518 s ( 89.89 )
2026-03-03 21:29:33.980103 INFO::Formatting Data.
2026-03-03 21:29:33.980983 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:33.982016 INFO::Removing potential empty rows and columns
2026-03-03 21:29:33.983132 INFO::Found 0 missing values.
2026-03-03 21:29:33.987536 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:33.98821 INFO::Done
2026-03-03 21:29:33.98883 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:33.992463 INFO::Starting hierarchical adjustment
2026-03-03 21:29:33.993277 INFO::Found 5 batches.
2026-03-03 21:29:33.993851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:33.994491 INFO::Using default BPPARAM
2026-03-03 21:29:33.99506 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.
2026-03-03 21:29:34.151168 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:34.153146 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-03 21:29:34.171766 INFO::Done
2026-03-03 21:29:34.172701 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:34.176627 INFO::ASW Batch was 0.418401957141198 prior to batch effect correction and is now -0.0871126703723592 .
2026-03-03 21:29:34.17733 INFO::ASW Label was 0.433606711558129 prior to batch effect correction and is now 0.818883983182999 .
2026-03-03 21:29:34.178235 INFO::Total function execution time is 0.198222160339355 s and adjustment time is 0.178573846817017 s ( 90.09 )
2026-03-03 21:29:34.179174 INFO::Formatting Data.
2026-03-03 21:29:34.179864 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:34.180819 INFO::Removing potential empty rows and columns
2026-03-03 21:29:34.181895 INFO::Found 0 missing values.
2026-03-03 21:29:34.186235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:34.186839 INFO::Done
2026-03-03 21:29:34.187375 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:34.190736 INFO::Starting hierarchical adjustment
2026-03-03 21:29:34.19155 INFO::Found 5 batches.
2026-03-03 21:29:34.192135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:34.192945 INFO::Using default BPPARAM
2026-03-03 21:29:34.193501 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.
2026-03-03 21:29:34.332516 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:34.334756 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-03 21:29:34.355329 INFO::Done
2026-03-03 21:29:34.356261 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:34.360198 INFO::ASW Batch was 0.418401957141198 prior to batch effect correction and is now -0.0871126703723592 .
2026-03-03 21:29:34.360988 INFO::ASW Label was 0.433606711558129 prior to batch effect correction and is now 0.818883983182999 .
2026-03-03 21:29:34.36194 INFO::Total function execution time is 0.182772636413574 s and adjustment time is 0.163898706436157 s ( 89.67 )
2026-03-03 21:29:34.378306 INFO::Formatting Data.
2026-03-03 21:29:34.3793 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:34.3804 INFO::Removing potential empty rows and columns
2026-03-03 21:29:34.381602 INFO::Found 0 missing values.
2026-03-03 21:29:34.384697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:34.385352 INFO::Done
2026-03-03 21:29:34.385943 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:34.38947 INFO::Starting hierarchical adjustment
2026-03-03 21:29:34.390272 INFO::Found 2 batches.
2026-03-03 21:29:34.390847 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:34.391519 INFO::Using default BPPARAM
2026-03-03 21:29:34.392085 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:34.393102 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-03 21:29:34.409483 INFO::Done
2026-03-03 21:29:34.410298 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:34.413793 INFO::ASW Batch was 0.489470191740089 prior to batch effect correction and is now 0.0705192604415287 .
2026-03-03 21:29:34.414481 INFO::ASW Label was 0.671451970061715 prior to batch effect correction and is now 0.90670659253679 .
2026-03-03 21:29:34.415333 INFO::Total function execution time is 0.0371880531311035 s and adjustment time is 0.0193328857421875 s ( 51.99 )
2026-03-03 21:29:34.416191 INFO::Formatting Data.
2026-03-03 21:29:34.416862 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:34.417811 INFO::Removing potential empty rows and columns
2026-03-03 21:29:34.418875 INFO::Found 0 missing values.
2026-03-03 21:29:34.421723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:34.422285 INFO::Done
2026-03-03 21:29:34.422842 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:34.42606 INFO::Starting hierarchical adjustment
2026-03-03 21:29:34.426811 INFO::Found 2 batches.
2026-03-03 21:29:34.427375 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:34.428036 INFO::Using default BPPARAM
2026-03-03 21:29:34.428591 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:34.429582 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-03 21:29:34.445348 INFO::Done
2026-03-03 21:29:34.446115 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:34.449441 INFO::ASW Batch was 0.489470191740089 prior to batch effect correction and is now 0.0705192604415287 .
2026-03-03 21:29:34.450097 INFO::ASW Label was 0.671451970061715 prior to batch effect correction and is now 0.90670659253679 .
2026-03-03 21:29:34.450933 INFO::Total function execution time is 0.0347576141357422 s and adjustment time is 0.018651008605957 s ( 53.66 )
2026-03-03 21:29:34.462979 INFO::Formatting Data.
2026-03-03 21:29:34.463965 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:34.464973 INFO::Removing potential empty rows and columns
2026-03-03 21:29:34.46598 INFO::Found 0 missing values.
2026-03-03 21:29:34.468241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:34.468822 INFO::Done
2026-03-03 21:29:34.469361 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:34.471491 INFO::Starting hierarchical adjustment
2026-03-03 21:29:34.472264 INFO::Found 2 batches.
2026-03-03 21:29:34.472828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:34.47345 INFO::Using default BPPARAM
2026-03-03 21:29:34.474008 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:34.474967 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-03 21:29:34.508828 INFO::Done
2026-03-03 21:29:34.50965 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:34.511901 INFO::ASW Batch was -0.125639937683413 prior to batch effect correction and is now -0.154376804959651 .
2026-03-03 21:29:34.512818 INFO::Total function execution time is 0.0499348640441895 s and adjustment time is 0.0366785526275635 s ( 73.45 )
2026-03-03 21:29:34.526256 INFO::Formatting Data.
2026-03-03 21:29:34.527155 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:34.528145 INFO::Removing potential empty rows and columns
2026-03-03 21:29:34.529244 INFO::Found 0 missing values.
2026-03-03 21:29:34.530529 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.
2026-03-03 21:29:34.53538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:34.535997 INFO::Done
2026-03-03 21:29:34.536538 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:34.539755 INFO::Starting hierarchical adjustment
2026-03-03 21:29:34.540542 INFO::Found 2 batches.
2026-03-03 21:29:34.54109 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:34.541741 INFO::Using default BPPARAM
2026-03-03 21:29:34.542272 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:34.543273 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-03 21:29:34.561215 INFO::Done
2026-03-03 21:29:34.562033 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:34.565327 INFO::ASW Batch was 0.476436112081411 prior to batch effect correction and is now -0.0280289315048332 .
2026-03-03 21:29:34.565997 INFO::ASW Label was 0.608111448131649 prior to batch effect correction and is now 0.947566924619299 .
2026-03-03 21:29:34.566819 INFO::Total function execution time is 0.0406997203826904 s and adjustment time is 0.0207962989807129 s ( 51.1 )
2026-03-03 21:29:34.567664 INFO::Formatting Data.
2026-03-03 21:29:34.56831 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:34.56931 INFO::Removing potential empty rows and columns
2026-03-03 21:29:34.57038 INFO::Found 0 missing values.
2026-03-03 21:29:34.571351 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.
2026-03-03 21:29:34.576082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:34.576689 INFO::Done
2026-03-03 21:29:34.57723 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:34.58054 INFO::Starting hierarchical adjustment
2026-03-03 21:29:34.581321 INFO::Found 2 batches.
2026-03-03 21:29:34.581889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:34.582533 INFO::Using default BPPARAM
2026-03-03 21:29:34.583071 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:34.584063 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-03 21:29:34.602025 INFO::Done
2026-03-03 21:29:34.60289 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:34.606209 INFO::ASW Batch was 0.476436112081411 prior to batch effect correction and is now -0.0280289315048332 .
2026-03-03 21:29:34.606898 INFO::ASW Label was 0.608111448131649 prior to batch effect correction and is now 0.947566924619299 .
2026-03-03 21:29:34.607745 INFO::Total function execution time is 0.0401179790496826 s and adjustment time is 0.0207951068878174 s ( 51.83 )
2026-03-03 21:29:34.84037 INFO::Formatting Data.
2026-03-03 21:29:34.841244 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:34.842165 INFO::Removing potential empty rows and columns
2026-03-03 21:29:34.843243 INFO::Found 0 missing values.
2026-03-03 21:29:34.846276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:34.846819 INFO::Done
2026-03-03 21:29:34.847326 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:34.849526 INFO::Starting hierarchical adjustment
2026-03-03 21:29:34.850239 INFO::Found 3 batches.
2026-03-03 21:29:34.850778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:34.851378 INFO::Using default BPPARAM
2026-03-03 21:29:34.851903 INFO::Processing subtree level 1
2026-03-03 21:29:34.943225 INFO::Adjusting the last 1 batches sequentially
2026-03-03 21:29:34.945241 INFO::Done
2026-03-03 21:29:34.945941 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:34.948614 INFO::ASW Batch was -0.0607800810564811 prior to batch effect correction and is now -0.0607800810564811 .
2026-03-03 21:29:34.949627 INFO::Total function execution time is 0.109339475631714 s and adjustment time is 0.0951166152954102 s ( 86.99 )
2026-03-03 21:29:34.950739 INFO::Formatting Data.
2026-03-03 21:29:34.951411 INFO::Typecasting input to dataframe.
2026-03-03 21:29:34.952221 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:34.953212 INFO::Removing potential empty rows and columns
2026-03-03 21:29:34.954359 INFO::Found 0 missing values.
2026-03-03 21:29:34.957688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:34.958234 INFO::Done
2026-03-03 21:29:34.958785 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:34.960982 INFO::Starting hierarchical adjustment
2026-03-03 21:29:34.961725 INFO::Found 3 batches.
2026-03-03 21:29:34.962273 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:34.962912 INFO::Using default BPPARAM
2026-03-03 21:29:34.963459 INFO::Processing subtree level 1
2026-03-03 21:29:35.053159 INFO::Adjusting the last 1 batches sequentially
2026-03-03 21:29:35.055142 INFO::Done
2026-03-03 21:29:35.055864 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:35.05853 INFO::ASW Batch was -0.0607800810564811 prior to batch effect correction and is now -0.0607800810564811 .
2026-03-03 21:29:35.059546 INFO::Total function execution time is 0.108785390853882 s and adjustment time is 0.0935428142547607 s ( 85.99 )
2026-03-03 21:29:35.073939 INFO::Formatting Data.
2026-03-03 21:29:35.074882 INFO::Typecasting input to dataframe.
2026-03-03 21:29:35.075784 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:35.076752 INFO::Removing potential empty rows and columns
2026-03-03 21:29:35.077872 INFO::Found 0 missing values.
2026-03-03 21:29:35.081003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:35.081585 INFO::Done
2026-03-03 21:29:35.082111 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:35.084317 INFO::Starting hierarchical adjustment
2026-03-03 21:29:35.085076 INFO::Found 3 batches.
2026-03-03 21:29:35.085624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:35.086278 INFO::Using default BPPARAM
2026-03-03 21:29:35.086834 INFO::Processing subtree level 1
2026-03-03 21:29:35.180987 INFO::Adjusting the last 1 batches sequentially
2026-03-03 21:29:35.183006 INFO::Done
2026-03-03 21:29:35.183745 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:35.186503 INFO::ASW Batch was -0.14096420175071 prior to batch effect correction and is now -0.14096420175071 .
2026-03-03 21:29:35.187566 INFO::Total function execution time is 0.113697528839111 s and adjustment time is 0.0980257987976074 s ( 86.22 )
2026-03-03 21:29:35.332333 INFO::Formatting Data.
2026-03-03 21:29:35.333227 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:35.334404 INFO::Removing potential empty rows and columns
2026-03-03 21:29:35.337275 INFO::Found 1000 missing values.
2026-03-03 21:29:35.361 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:35.362173 INFO::Done
2026-03-03 21:29:35.363145 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:35.372183 INFO::Starting hierarchical adjustment
2026-03-03 21:29:35.373572 INFO::Found 10 batches.
2026-03-03 21:29:35.374468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:35.375479 INFO::Using default BPPARAM
2026-03-03 21:29:35.376338 INFO::Processing subtree level 1
2026-03-03 21:29:35.565938 INFO::Processing subtree level 2
2026-03-03 21:29:35.710172 INFO::Adjusting the last 1 batches sequentially
2026-03-03 21:29:35.712324 INFO::Done
2026-03-03 21:29:35.713074 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:35.718928 INFO::ASW Batch was 0.447385689305297 prior to batch effect correction and is now 0.447385689305297 .
2026-03-03 21:29:35.719692 INFO::ASW Label was 0.3845715351463 prior to batch effect correction and is now 0.3845715351463 .
2026-03-03 21:29:35.720659 INFO::Total function execution time is 0.388400077819824 s and adjustment time is 0.339085340499878 s ( 87.3 )
2026-03-03 21:29:35.721528 INFO::Formatting Data.
2026-03-03 21:29:35.722179 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:35.723479 INFO::Removing potential empty rows and columns
2026-03-03 21:29:35.726328 INFO::Found 1000 missing values.
2026-03-03 21:29:35.745745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:35.7466 INFO::Done
2026-03-03 21:29:35.747196 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:35.762469 INFO::Starting hierarchical adjustment
2026-03-03 21:29:35.763451 INFO::Found 10 batches.
2026-03-03 21:29:37.179368 INFO::Set up parallel execution backend with 2 workers
2026-03-03 21:29:37.181824 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-03 21:29:38.46631 INFO::Adjusting the last 2 batches sequentially
2026-03-03 21:29:38.468381 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-03 21:29:38.485555 INFO::Done
2026-03-03 21:29:38.486215 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:38.490952 INFO::ASW Batch was 0.447385689305297 prior to batch effect correction and is now 0.447385689305297 .
2026-03-03 21:29:38.491533 INFO::ASW Label was 0.3845715351463 prior to batch effect correction and is now 0.3845715351463 .
2026-03-03 21:29:38.492293 INFO::Total function execution time is 2.77081346511841 s and adjustment time is 2.7222683429718 s ( 98.25 )
2026-03-03 21:29:38.651111 INFO::Formatting Data.
2026-03-03 21:29:38.652026 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:38.652962 INFO::Removing potential empty rows and columns
2026-03-03 21:29:38.65403 INFO::Found 0 missing values.
2026-03-03 21:29:38.657742 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:38.658269 INFO::Done
2026-03-03 21:29:38.658777 INFO::Acquiring quality metrics before batch effect correction.
2026-03-03 21:29:38.661579 INFO::Starting hierarchical adjustment
2026-03-03 21:29:38.662271 INFO::Found 3 batches.
2026-03-03 21:29:38.662796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-03 21:29:38.66339 INFO::Using default BPPARAM
2026-03-03 21:29:38.66391 INFO::Processing subtree level 1
2026-03-03 21:29:38.774332 INFO::Adjusting the last 1 batches sequentially
2026-03-03 21:29:38.776141 INFO::Done
2026-03-03 21:29:38.776802 INFO::Acquiring quality metrics after batch effect correction.
2026-03-03 21:29:38.780025 INFO::ASW Batch was 0.16204791130083 prior to batch effect correction and is now -0.165907786501807 .
2026-03-03 21:29:38.780647 INFO::ASW Label was -0.19816180798155 prior to batch effect correction and is now 0.103110842614411 .
2026-03-03 21:29:38.781593 INFO::Total function execution time is 0.130539655685425 s and adjustment time is 0.113989353179932 s ( 87.32 )
2026-03-03 21:29:38.906112 INFO::Formatting Data.
2026-03-03 21:29:38.906988 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:38.907937 INFO::Removing potential empty rows and columns
2026-03-03 21:29:38.909003 INFO::Found 2 missing values.
2026-03-03 21:29:38.9119 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:38.912412 INFO::Done
2026-03-03 21:29:38.940214 INFO::Found NA in Reference column
2026-03-03 21:29:38.949629 INFO::Require at least two references per batch.
2026-03-03 21:29:38.969801 INFO::Formatting Data.
2026-03-03 21:29:38.970584 INFO::Recognized SummarizedExperiment
2026-03-03 21:29:38.9711 INFO::Typecasting input to dataframe.
2026-03-03 21:29:38.980536 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:38.981756 INFO::Removing potential empty rows and columns
2026-03-03 21:29:38.985133 INFO::Found 0 missing values.
2026-03-03 21:29:38.991848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:38.992443 INFO::Done
2026-03-03 21:29:39.008128 INFO::Formatting Data.
2026-03-03 21:29:39.008913 INFO::Recognized SummarizedExperiment
2026-03-03 21:29:39.009422 INFO::Typecasting input to dataframe.
2026-03-03 21:29:39.0267 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:39.028026 INFO::Removing potential empty rows and columns
2026-03-03 21:29:39.031423 INFO::Found 0 missing values.
2026-03-03 21:29:39.041861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:39.04255 INFO::Done
2026-03-03 21:29:39.058262 INFO::Formatting Data.
2026-03-03 21:29:39.059047 INFO::Recognized SummarizedExperiment
2026-03-03 21:29:39.059568 INFO::Typecasting input to dataframe.
2026-03-03 21:29:39.075994 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:39.077127 INFO::Removing potential empty rows and columns
2026-03-03 21:29:39.078231 INFO::Found 0 missing values.
2026-03-03 21:29:39.079158 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.
2026-03-03 21:29:39.083477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:39.084028 INFO::Done
2026-03-03 21:29:39.094477 INFO::Formatting Data.
2026-03-03 21:29:39.09532 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:39.096184 INFO::Removing potential empty rows and columns
2026-03-03 21:29:39.09715 INFO::Found 0 missing values.
2026-03-03 21:29:39.099963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:39.100469 INFO::Done
2026-03-03 21:29:39.112153 INFO::Formatting Data.
2026-03-03 21:29:39.113037 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:39.114038 INFO::Removing potential empty rows and columns
2026-03-03 21:29:39.115051 INFO::Found 0 missing values.
2026-03-03 21:29:39.11791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:39.118425 INFO::Done
2026-03-03 21:29:39.149848 INFO::Formatting Data.
2026-03-03 21:29:39.150728 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:39.151847 INFO::Removing potential empty rows and columns
2026-03-03 21:29:39.153048 INFO::Found 1 missing values.
2026-03-03 21:29:39.155794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:39.156311 INFO::Done
2026-03-03 21:29:39.176671 INFO::Formatting Data.
2026-03-03 21:29:39.17748 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:39.178356 INFO::Removing potential empty rows and columns
2026-03-03 21:29:39.1793 INFO::Found 2 missing values.
2026-03-03 21:29:39.18019 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.
2026-03-03 21:29:39.182436 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:39.182976 INFO::Done
2026-03-03 21:29:39.193243 INFO::Formatting Data.
2026-03-03 21:29:39.19408 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:39.19521 INFO::Removing potential empty rows and columns
2026-03-03 21:29:39.196147 INFO::Found 2 missing values.
2026-03-03 21:29:39.197798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:39.198314 INFO::Done
2026-03-03 21:29:39.208831 INFO::Formatting Data.
2026-03-03 21:29:39.20962 INFO::Typecasting input to dataframe.
2026-03-03 21:29:39.210421 INFO::Replacing NaNs with NAs.
2026-03-03 21:29:39.211268 INFO::Removing potential empty rows and columns
2026-03-03 21:29:39.212249 INFO::Found 0 missing values.
2026-03-03 21:29:39.215146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-03 21:29:39.215675 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.908 4.286 21.626
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.907 | 1.521 | 17.971 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.012 | 0.002 | 0.014 | |
| generate_dataset | 0.012 | 0.001 | 0.013 | |