Yannis Schumann
| Snapshot Date: 2026-03-19 13:45 -0400 (Thu, 19 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-20 11:57 -0400 (Fri, 20 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: 2026-03-19 21:23:44 -0400 (Thu, 19 Mar 2026) |
| EndedAt: 2026-03-19 21:25:12 -0400 (Thu, 19 Mar 2026) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.524 1.191 17.062
* 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")
2026-03-19 21:24:35.674563 INFO::Formatting Data.
2026-03-19 21:24:35.675972 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:35.68798 INFO::Removing potential empty rows and columns
2026-03-19 21:24:35.946366 INFO::Found 0 missing values.
2026-03-19 21:24:35.95002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:35.950724 INFO::Done
2026-03-19 21:24:35.951332 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:35.963337 INFO::Starting hierarchical adjustment
2026-03-19 21:24:35.9643 INFO::Found 3 batches.
2026-03-19 21:24:35.964882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:35.966063 INFO::Using default BPPARAM
2026-03-19 21:24:35.966679 INFO::Processing subtree level 1
2026-03-19 21:24:36.094437 INFO::Adjusting the last 1 batches sequentially
2026-03-19 21:24:36.096598 INFO::Done
2026-03-19 21:24:36.097384 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:36.100556 INFO::ASW Batch was 0.00708222318253308 prior to batch effect correction and is now 0.00708222318253308 .
2026-03-19 21:24:36.101852 INFO::Total function execution time is 0.427974224090576 s and adjustment time is 0.132444143295288 s ( 30.95 )
2026-03-19 21:24:36.117599 INFO::Formatting Data.
2026-03-19 21:24:36.1185 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:36.119634 INFO::Removing potential empty rows and columns
2026-03-19 21:24:36.120936 INFO::Found 0 missing values.
2026-03-19 21:24:36.122088 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.
2026-03-19 21:24:36.134676 INFO::Formatting Data.
2026-03-19 21:24:36.135602 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:36.136627 INFO::Removing potential empty rows and columns
2026-03-19 21:24:36.137778 INFO::Found 0 missing values.
2026-03-19 21:24:36.138842 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.
2026-03-19 21:24:36.157925 INFO::Formatting Data.
2026-03-19 21:24:36.15894 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:36.160204 INFO::Removing potential empty rows and columns
2026-03-19 21:24:36.161695 INFO::Found 0 missing values.
2026-03-19 21:24:36.163001 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.
2026-03-19 21:24:36.169745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:36.170673 INFO::Done
2026-03-19 21:24:36.171396 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:36.174224 INFO::Starting hierarchical adjustment
2026-03-19 21:24:36.175201 INFO::Found 2 batches.
2026-03-19 21:24:36.175885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:36.176697 INFO::Using default BPPARAM
2026-03-19 21:24:36.177355 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:36.178625 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-19 21:24:36.206649 INFO::Done
2026-03-19 21:24:36.207534 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:36.210744 INFO::ASW Batch was -0.0629774500440776 prior to batch effect correction and is now -0.0964801128693698 .
2026-03-19 21:24:36.211829 INFO::Total function execution time is 0.0540549755096436 s and adjustment time is 0.0316190719604492 s ( 58.49 )
2026-03-19 21:24:36.215377 INFO::Formatting Data.
2026-03-19 21:24:36.216261 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:36.227237 INFO::Formatting Data.
2026-03-19 21:24:36.228271 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:36.229392 INFO::Removing potential empty rows and columns
2026-03-19 21:24:36.230583 INFO::Found 0 missing values.
2026-03-19 21:24:36.234129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:36.234747 INFO::Done
2026-03-19 21:24:36.235318 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:36.274009 INFO::Starting hierarchical adjustment
2026-03-19 21:24:36.276144 INFO::Found 2 batches.
2026-03-19 21:24:36.276986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:36.277727 INFO::Using default BPPARAM
2026-03-19 21:24:36.27834 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:36.279526 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-19 21:24:36.297123 INFO::Done
2026-03-19 21:24:36.298115 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:36.300661 INFO::ASW Batch was 0.0427785501219366 prior to batch effect correction and is now -0.108328064569608 .
2026-03-19 21:24:36.301596 INFO::Total function execution time is 0.0744659900665283 s and adjustment time is 0.0211913585662842 s ( 28.46 )
2026-03-19 21:24:36.302786 INFO::Formatting Data.
2026-03-19 21:24:36.303421 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:36.304369 INFO::Removing potential empty rows and columns
2026-03-19 21:24:36.305485 INFO::Found 0 missing values.
2026-03-19 21:24:36.308549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:36.309101 INFO::Done
2026-03-19 21:24:36.309629 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:36.311849 INFO::Starting hierarchical adjustment
2026-03-19 21:24:36.312568 INFO::Found 2 batches.
2026-03-19 21:24:36.313087 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:36.313675 INFO::Using default BPPARAM
2026-03-19 21:24:36.314166 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:36.315076 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-19 21:24:36.330944 INFO::Done
2026-03-19 21:24:36.331753 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:36.334003 INFO::ASW Batch was 0.0427785501219366 prior to batch effect correction and is now -0.108328064569608 .
2026-03-19 21:24:36.334871 INFO::Total function execution time is 0.0320718288421631 s and adjustment time is 0.0184752941131592 s ( 57.61 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-19 21:24:39.568079 INFO::Formatting Data.
2026-03-19 21:24:39.568849 INFO::Recognized SummarizedExperiment
2026-03-19 21:24:39.569328 INFO::Typecasting input to dataframe.
2026-03-19 21:24:39.602143 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:39.603653 INFO::Removing potential empty rows and columns
2026-03-19 21:24:39.607711 INFO::Found 0 missing values.
2026-03-19 21:24:39.615533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:39.616292 INFO::Done
2026-03-19 21:24:39.616859 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:39.630329 INFO::Starting hierarchical adjustment
2026-03-19 21:24:39.633502 INFO::Found 2 batches.
2026-03-19 21:24:39.634149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:39.637804 INFO::Using default BPPARAM
2026-03-19 21:24:39.638398 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:39.64 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-19 21:24:39.705028 INFO::Done
2026-03-19 21:24:39.705756 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:39.709735 INFO::ASW Batch was -0.0125771807632942 prior to batch effect correction and is now -0.0981780208316214 .
2026-03-19 21:24:39.710793 INFO::Total function execution time is 0.142954349517822 s and adjustment time is 0.0724220275878906 s ( 50.66 )
Warning: stack imbalance in '{', 73 then 75
2026-03-19 21:24:39.735317 INFO::Formatting Data.
2026-03-19 21:24:39.736066 INFO::Recognized SummarizedExperiment
2026-03-19 21:24:39.736626 INFO::Typecasting input to dataframe.
2026-03-19 21:24:39.747786 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:39.749039 INFO::Removing potential empty rows and columns
2026-03-19 21:24:39.752995 INFO::Found 0 missing values.
2026-03-19 21:24:39.760176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:39.760842 INFO::Done
2026-03-19 21:24:39.761375 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:39.764906 INFO::Starting hierarchical adjustment
2026-03-19 21:24:39.765658 INFO::Found 2 batches.
2026-03-19 21:24:39.766204 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:39.766827 INFO::Using default BPPARAM
2026-03-19 21:24:39.767337 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:39.768344 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-19 21:24:39.793538 INFO::Done
2026-03-19 21:24:39.794245 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:39.798032 INFO::ASW Batch was 0.0218607425844004 prior to batch effect correction and is now 0.0218607425844004 .
2026-03-19 21:24:39.798922 INFO::Total function execution time is 0.0635876655578613 s and adjustment time is 0.0279979705810547 s ( 44.03 )
2026-03-19 21:24:39.817688 INFO::Formatting Data.
2026-03-19 21:24:39.818452 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:39.819349 INFO::Removing potential empty rows and columns
2026-03-19 21:24:39.820396 INFO::Found 0 missing values.
2026-03-19 21:24:39.823323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:39.823864 INFO::Done
2026-03-19 21:24:39.82439 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:39.82637 INFO::Starting hierarchical adjustment
2026-03-19 21:24:39.827059 INFO::Found 3 batches.
2026-03-19 21:24:39.827604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:39.828202 INFO::Using default BPPARAM
2026-03-19 21:24:39.828742 INFO::Processing subtree level 1
2026-03-19 21:24:39.963222 INFO::Adjusting the last 1 batches sequentially
2026-03-19 21:24:39.964941 INFO::Done
2026-03-19 21:24:39.965595 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:39.968283 INFO::ASW Batch was -0.0857957189872229 prior to batch effect correction and is now -0.164132818563219 .
2026-03-19 21:24:39.969243 INFO::Total function execution time is 0.151627779006958 s and adjustment time is 0.13799524307251 s ( 91.01 )
2026-03-19 21:24:39.983579 INFO::Skipping initial DF formatting
2026-03-19 21:24:39.984299 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:39.988289 INFO::Starting hierarchical adjustment
2026-03-19 21:24:39.989111 INFO::Found 5 batches.
2026-03-19 21:24:39.989676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:39.990287 INFO::Using default BPPARAM
2026-03-19 21:24:39.990815 INFO::Processing subtree level 1
2026-03-19 21:24:40.232132 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:40.233672 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-19 21:24:40.25293 INFO::Done
2026-03-19 21:24:40.253647 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:40.257837 INFO::ASW Batch was 0.40524181835787 prior to batch effect correction and is now 0.40524181835787 .
2026-03-19 21:24:40.258429 INFO::ASW Label was 0.460481783501643 prior to batch effect correction and is now 0.460481783501643 .
2026-03-19 21:24:40.259252 INFO::Total function execution time is 0.275745868682861 s and adjustment time is 0.263956069946289 s ( 95.72 )
2026-03-19 21:24:40.324541 INFO::Formatting Data.
2026-03-19 21:24:40.325305 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:40.326188 INFO::Removing potential empty rows and columns
2026-03-19 21:24:40.327111 INFO::Found 0 missing values.
2026-03-19 21:24:40.330954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:40.331486 INFO::Done
2026-03-19 21:24:40.332 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:40.334834 INFO::Starting hierarchical adjustment
2026-03-19 21:24:40.335528 INFO::Found 5 batches.
2026-03-19 21:24:40.336041 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:40.336637 INFO::Using default BPPARAM
2026-03-19 21:24:40.337137 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.
2026-03-19 21:24:40.471618 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:40.473172 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-19 21:24:40.490022 INFO::Done
2026-03-19 21:24:40.490753 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:40.494134 INFO::ASW Batch was 0.393030159629907 prior to batch effect correction and is now -0.0573650486450181 .
2026-03-19 21:24:40.494743 INFO::ASW Label was 0.432186482974833 prior to batch effect correction and is now 0.795928326491066 .
2026-03-19 21:24:40.495553 INFO::Total function execution time is 0.171075105667114 s and adjustment time is 0.154616594314575 s ( 90.38 )
2026-03-19 21:24:40.496423 INFO::Formatting Data.
2026-03-19 21:24:40.497053 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:40.498021 INFO::Removing potential empty rows and columns
2026-03-19 21:24:40.499012 INFO::Found 0 missing values.
2026-03-19 21:24:40.503269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:40.503858 INFO::Done
2026-03-19 21:24:40.504368 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:40.507383 INFO::Starting hierarchical adjustment
2026-03-19 21:24:40.508112 INFO::Found 5 batches.
2026-03-19 21:24:40.508623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:40.509229 INFO::Using default BPPARAM
2026-03-19 21:24:40.509787 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.
2026-03-19 21:24:40.635489 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:40.637181 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-19 21:24:40.654495 INFO::Done
2026-03-19 21:24:40.655241 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:40.658531 INFO::ASW Batch was 0.393030159629907 prior to batch effect correction and is now -0.0573650486450181 .
2026-03-19 21:24:40.659126 INFO::ASW Label was 0.432186482974833 prior to batch effect correction and is now 0.795928326491066 .
2026-03-19 21:24:40.660005 INFO::Total function execution time is 0.163572549819946 s and adjustment time is 0.146504878997803 s ( 89.57 )
2026-03-19 21:24:40.674124 INFO::Formatting Data.
2026-03-19 21:24:40.674886 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:40.675796 INFO::Removing potential empty rows and columns
2026-03-19 21:24:40.676779 INFO::Found 0 missing values.
2026-03-19 21:24:40.680704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:40.681222 INFO::Done
2026-03-19 21:24:40.681748 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:40.684644 INFO::Starting hierarchical adjustment
2026-03-19 21:24:40.685358 INFO::Found 5 batches.
2026-03-19 21:24:40.685909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:40.686568 INFO::Using default BPPARAM
2026-03-19 21:24:40.687081 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.
2026-03-19 21:24:40.828967 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:40.830775 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-19 21:24:40.84831 INFO::Done
2026-03-19 21:24:40.849161 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:40.852845 INFO::ASW Batch was 0.546139955370858 prior to batch effect correction and is now -0.0555720648434019 .
2026-03-19 21:24:40.853516 INFO::ASW Label was 0.0969885475486365 prior to batch effect correction and is now 0.705679228703028 .
2026-03-19 21:24:40.854392 INFO::Total function execution time is 0.180307626724243 s and adjustment time is 0.163030862808228 s ( 90.42 )
2026-03-19 21:24:40.855306 INFO::Formatting Data.
2026-03-19 21:24:40.855988 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:40.856928 INFO::Removing potential empty rows and columns
2026-03-19 21:24:40.858014 INFO::Found 0 missing values.
2026-03-19 21:24:40.862195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:40.862764 INFO::Done
2026-03-19 21:24:40.863309 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:40.866561 INFO::Starting hierarchical adjustment
2026-03-19 21:24:40.867316 INFO::Found 5 batches.
2026-03-19 21:24:40.867885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:40.868543 INFO::Using default BPPARAM
2026-03-19 21:24:40.869099 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.
2026-03-19 21:24:41.003213 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:41.004913 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-19 21:24:41.022598 INFO::Done
2026-03-19 21:24:41.023562 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.027119 INFO::ASW Batch was 0.546139955370858 prior to batch effect correction and is now -0.0555720648434019 .
2026-03-19 21:24:41.027786 INFO::ASW Label was 0.0969885475486365 prior to batch effect correction and is now 0.705679228703028 .
2026-03-19 21:24:41.028668 INFO::Total function execution time is 0.17335319519043 s and adjustment time is 0.155353546142578 s ( 89.62 )
2026-03-19 21:24:41.042401 INFO::Formatting Data.
2026-03-19 21:24:41.043212 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.04426 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.045305 INFO::Found 0 missing values.
2026-03-19 21:24:41.048074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.048639 INFO::Done
2026-03-19 21:24:41.049151 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.052176 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.052916 INFO::Found 2 batches.
2026-03-19 21:24:41.053451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.054093 INFO::Using default BPPARAM
2026-03-19 21:24:41.054634 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:41.055519 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-19 21:24:41.069799 INFO::Done
2026-03-19 21:24:41.07044 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.073273 INFO::ASW Batch was 0.656033409204604 prior to batch effect correction and is now 0.0509073038502313 .
2026-03-19 21:24:41.073844 INFO::ASW Label was 0.442083266848685 prior to batch effect correction and is now 0.86849628191573 .
2026-03-19 21:24:41.074579 INFO::Total function execution time is 0.0322706699371338 s and adjustment time is 0.01702880859375 s ( 52.77 )
2026-03-19 21:24:41.075328 INFO::Formatting Data.
2026-03-19 21:24:41.075945 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.076776 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.0777 INFO::Found 0 missing values.
2026-03-19 21:24:41.080209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.080737 INFO::Done
2026-03-19 21:24:41.081227 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.083985 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.084658 INFO::Found 2 batches.
2026-03-19 21:24:41.085162 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.085747 INFO::Using default BPPARAM
2026-03-19 21:24:41.086239 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:41.087107 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-19 21:24:41.101138 INFO::Done
2026-03-19 21:24:41.101797 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.104606 INFO::ASW Batch was 0.656033409204604 prior to batch effect correction and is now 0.0509073038502313 .
2026-03-19 21:24:41.105161 INFO::ASW Label was 0.442083266848685 prior to batch effect correction and is now 0.86849628191573 .
2026-03-19 21:24:41.105912 INFO::Total function execution time is 0.0305924415588379 s and adjustment time is 0.0165989398956299 s ( 54.26 )
2026-03-19 21:24:41.11677 INFO::Formatting Data.
2026-03-19 21:24:41.117474 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.118339 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.11922 INFO::Found 0 missing values.
2026-03-19 21:24:41.121289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.121808 INFO::Done
2026-03-19 21:24:41.122304 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.124137 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.12482 INFO::Found 2 batches.
2026-03-19 21:24:41.125318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.125897 INFO::Using default BPPARAM
2026-03-19 21:24:41.1264 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:41.127256 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-19 21:24:41.157173 INFO::Done
2026-03-19 21:24:41.157859 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.159765 INFO::ASW Batch was 0.0368573404856752 prior to batch effect correction and is now -0.0978866406613712 .
2026-03-19 21:24:41.160553 INFO::Total function execution time is 0.0439217090606689 s and adjustment time is 0.0324649810791016 s ( 73.92 )
2026-03-19 21:24:41.171956 INFO::Formatting Data.
2026-03-19 21:24:41.172697 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.173537 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.174475 INFO::Found 0 missing values.
2026-03-19 21:24:41.175589 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.
2026-03-19 21:24:41.179881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.180408 INFO::Done
2026-03-19 21:24:41.18091 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.183722 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.184394 INFO::Found 2 batches.
2026-03-19 21:24:41.184912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.185488 INFO::Using default BPPARAM
2026-03-19 21:24:41.185987 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:41.186898 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-19 21:24:41.210913 INFO::Done
2026-03-19 21:24:41.21169 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.21474 INFO::ASW Batch was 0.456244882279567 prior to batch effect correction and is now -0.0341110836940611 .
2026-03-19 21:24:41.21534 INFO::ASW Label was 0.606995369564633 prior to batch effect correction and is now 0.912972496262618 .
2026-03-19 21:24:41.216119 INFO::Total function execution time is 0.0442311763763428 s and adjustment time is 0.0266017913818359 s ( 60.14 )
2026-03-19 21:24:41.216934 INFO::Formatting Data.
2026-03-19 21:24:41.217531 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.218407 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.219361 INFO::Found 0 missing values.
2026-03-19 21:24:41.22023 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.
2026-03-19 21:24:41.22447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.225022 INFO::Done
2026-03-19 21:24:41.225511 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.228279 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.228952 INFO::Found 2 batches.
2026-03-19 21:24:41.229458 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.230087 INFO::Using default BPPARAM
2026-03-19 21:24:41.230597 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:41.231477 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-19 21:24:41.247106 INFO::Done
2026-03-19 21:24:41.247767 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.250559 INFO::ASW Batch was 0.456244882279567 prior to batch effect correction and is now -0.0341110836940611 .
2026-03-19 21:24:41.251126 INFO::ASW Label was 0.606995369564633 prior to batch effect correction and is now 0.912972496262618 .
2026-03-19 21:24:41.251879 INFO::Total function execution time is 0.0349671840667725 s and adjustment time is 0.0182690620422363 s ( 52.25 )
2026-03-19 21:24:41.451497 INFO::Formatting Data.
2026-03-19 21:24:41.452369 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.453282 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.4543 INFO::Found 0 missing values.
2026-03-19 21:24:41.457307 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.457868 INFO::Done
2026-03-19 21:24:41.458379 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.460395 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.461103 INFO::Found 3 batches.
2026-03-19 21:24:41.461624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.462228 INFO::Using default BPPARAM
2026-03-19 21:24:41.462754 INFO::Processing subtree level 1
2026-03-19 21:24:41.549602 INFO::Adjusting the last 1 batches sequentially
2026-03-19 21:24:41.551251 INFO::Done
2026-03-19 21:24:41.551871 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.55424 INFO::ASW Batch was -0.11537454315667 prior to batch effect correction and is now -0.11537454315667 .
2026-03-19 21:24:41.555185 INFO::Total function execution time is 0.103738784790039 s and adjustment time is 0.0902845859527588 s ( 87.03 )
2026-03-19 21:24:41.556257 INFO::Formatting Data.
2026-03-19 21:24:41.556918 INFO::Typecasting input to dataframe.
2026-03-19 21:24:41.557681 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.558624 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.5597 INFO::Found 0 missing values.
2026-03-19 21:24:41.562759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.563297 INFO::Done
2026-03-19 21:24:41.563847 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.565831 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.566557 INFO::Found 3 batches.
2026-03-19 21:24:41.567104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.567718 INFO::Using default BPPARAM
2026-03-19 21:24:41.568239 INFO::Processing subtree level 1
2026-03-19 21:24:41.657025 INFO::Adjusting the last 1 batches sequentially
2026-03-19 21:24:41.65943 INFO::Done
2026-03-19 21:24:41.660174 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.662874 INFO::ASW Batch was -0.11537454315667 prior to batch effect correction and is now -0.11537454315667 .
2026-03-19 21:24:41.664468 INFO::Total function execution time is 0.108081579208374 s and adjustment time is 0.0929980278015137 s ( 86.04 )
2026-03-19 21:24:41.678386 INFO::Formatting Data.
2026-03-19 21:24:41.679255 INFO::Typecasting input to dataframe.
2026-03-19 21:24:41.680156 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.681078 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.68214 INFO::Found 0 missing values.
2026-03-19 21:24:41.685169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.685728 INFO::Done
2026-03-19 21:24:41.686243 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.688396 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.68911 INFO::Found 3 batches.
2026-03-19 21:24:41.689661 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.690284 INFO::Using default BPPARAM
2026-03-19 21:24:41.69081 INFO::Processing subtree level 1
2026-03-19 21:24:41.776462 INFO::Adjusting the last 1 batches sequentially
2026-03-19 21:24:41.778255 INFO::Done
2026-03-19 21:24:41.778892 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:41.78144 INFO::ASW Batch was -0.0392919178313109 prior to batch effect correction and is now -0.0392919178313109 .
2026-03-19 21:24:41.782382 INFO::Total function execution time is 0.104067325592041 s and adjustment time is 0.089285135269165 s ( 85.8 )
2026-03-19 21:24:41.928526 INFO::Formatting Data.
2026-03-19 21:24:41.929361 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:41.930481 INFO::Removing potential empty rows and columns
2026-03-19 21:24:41.933261 INFO::Found 1000 missing values.
2026-03-19 21:24:41.952204 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:41.952963 INFO::Done
2026-03-19 21:24:41.953514 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:41.95902 INFO::Starting hierarchical adjustment
2026-03-19 21:24:41.95979 INFO::Found 10 batches.
2026-03-19 21:24:41.960331 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:41.960952 INFO::Using default BPPARAM
2026-03-19 21:24:41.961489 INFO::Processing subtree level 1
2026-03-19 21:24:42.096926 INFO::Processing subtree level 2
2026-03-19 21:24:42.243842 INFO::Adjusting the last 1 batches sequentially
2026-03-19 21:24:42.246118 INFO::Done
2026-03-19 21:24:42.24683 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:42.252304 INFO::ASW Batch was 0.518066955466035 prior to batch effect correction and is now 0.518066955466035 .
2026-03-19 21:24:42.252943 INFO::ASW Label was 0.327672344041611 prior to batch effect correction and is now 0.327672344041611 .
2026-03-19 21:24:42.25386 INFO::Total function execution time is 0.325414180755615 s and adjustment time is 0.286413669586182 s ( 88.02 )
2026-03-19 21:24:42.254697 INFO::Formatting Data.
2026-03-19 21:24:42.25533 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:42.256537 INFO::Removing potential empty rows and columns
2026-03-19 21:24:42.259288 INFO::Found 1000 missing values.
2026-03-19 21:24:42.278202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:42.278952 INFO::Done
2026-03-19 21:24:42.279498 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:42.2849 INFO::Starting hierarchical adjustment
2026-03-19 21:24:42.285674 INFO::Found 10 batches.
2026-03-19 21:24:43.25853 INFO::Set up parallel execution backend with 2 workers
2026-03-19 21:24:43.26024 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-19 21:24:44.394157 INFO::Adjusting the last 2 batches sequentially
2026-03-19 21:24:44.396235 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-19 21:24:44.411627 INFO::Done
2026-03-19 21:24:44.412225 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:44.416518 INFO::ASW Batch was 0.518066955466035 prior to batch effect correction and is now 0.518066955466035 .
2026-03-19 21:24:44.417041 INFO::ASW Label was 0.327672344041611 prior to batch effect correction and is now 0.327672344041611 .
2026-03-19 21:24:44.417727 INFO::Total function execution time is 2.1630585193634 s and adjustment time is 2.1261031627655 s ( 98.29 )
2026-03-19 21:24:44.564926 INFO::Formatting Data.
2026-03-19 21:24:44.565875 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:44.566843 INFO::Removing potential empty rows and columns
2026-03-19 21:24:44.567959 INFO::Found 0 missing values.
2026-03-19 21:24:44.57157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:44.572112 INFO::Done
2026-03-19 21:24:44.572634 INFO::Acquiring quality metrics before batch effect correction.
2026-03-19 21:24:44.575548 INFO::Starting hierarchical adjustment
2026-03-19 21:24:44.576267 INFO::Found 3 batches.
2026-03-19 21:24:44.576794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-19 21:24:44.577404 INFO::Using default BPPARAM
2026-03-19 21:24:44.577962 INFO::Processing subtree level 1
2026-03-19 21:24:44.685763 INFO::Adjusting the last 1 batches sequentially
2026-03-19 21:24:44.687738 INFO::Done
2026-03-19 21:24:44.688438 INFO::Acquiring quality metrics after batch effect correction.
2026-03-19 21:24:44.69191 INFO::ASW Batch was 0.143877048391589 prior to batch effect correction and is now -0.127422909432408 .
2026-03-19 21:24:44.692578 INFO::ASW Label was -0.179564436440946 prior to batch effect correction and is now -0.189991359096542 .
2026-03-19 21:24:44.693575 INFO::Total function execution time is 0.128750324249268 s and adjustment time is 0.111584424972534 s ( 86.67 )
2026-03-19 21:24:44.827946 INFO::Formatting Data.
2026-03-19 21:24:44.828861 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:44.829806 INFO::Removing potential empty rows and columns
2026-03-19 21:24:44.830901 INFO::Found 2 missing values.
2026-03-19 21:24:44.833647 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:44.834159 INFO::Done
2026-03-19 21:24:44.861087 INFO::Found NA in Reference column
2026-03-19 21:24:44.870373 INFO::Require at least two references per batch.
2026-03-19 21:24:44.889896 INFO::Formatting Data.
2026-03-19 21:24:44.890627 INFO::Recognized SummarizedExperiment
2026-03-19 21:24:44.891131 INFO::Typecasting input to dataframe.
2026-03-19 21:24:44.900275 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:44.901366 INFO::Removing potential empty rows and columns
2026-03-19 21:24:44.904632 INFO::Found 0 missing values.
2026-03-19 21:24:44.910923 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:44.911484 INFO::Done
2026-03-19 21:24:44.926242 INFO::Formatting Data.
2026-03-19 21:24:44.926928 INFO::Recognized SummarizedExperiment
2026-03-19 21:24:44.927424 INFO::Typecasting input to dataframe.
2026-03-19 21:24:44.943785 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:44.944931 INFO::Removing potential empty rows and columns
2026-03-19 21:24:44.948198 INFO::Found 0 missing values.
2026-03-19 21:24:44.958198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:44.95884 INFO::Done
2026-03-19 21:24:44.973826 INFO::Formatting Data.
2026-03-19 21:24:44.974522 INFO::Recognized SummarizedExperiment
2026-03-19 21:24:44.975029 INFO::Typecasting input to dataframe.
2026-03-19 21:24:45.00111 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:45.00253 INFO::Removing potential empty rows and columns
2026-03-19 21:24:45.003666 INFO::Found 0 missing values.
2026-03-19 21:24:45.004638 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.
2026-03-19 21:24:45.008909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:45.009434 INFO::Done
2026-03-19 21:24:45.02071 INFO::Formatting Data.
2026-03-19 21:24:45.021481 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:45.022312 INFO::Removing potential empty rows and columns
2026-03-19 21:24:45.023252 INFO::Found 0 missing values.
2026-03-19 21:24:45.025931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:45.026433 INFO::Done
2026-03-19 21:24:45.037322 INFO::Formatting Data.
2026-03-19 21:24:45.03822 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:45.039189 INFO::Removing potential empty rows and columns
2026-03-19 21:24:45.040165 INFO::Found 0 missing values.
2026-03-19 21:24:45.042855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:45.043369 INFO::Done
2026-03-19 21:24:45.071719 INFO::Formatting Data.
2026-03-19 21:24:45.072525 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:45.073561 INFO::Removing potential empty rows and columns
2026-03-19 21:24:45.074689 INFO::Found 1 missing values.
2026-03-19 21:24:45.077334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:45.077863 INFO::Done
2026-03-19 21:24:45.096482 INFO::Formatting Data.
2026-03-19 21:24:45.097315 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:45.098145 INFO::Removing potential empty rows and columns
2026-03-19 21:24:45.099059 INFO::Found 2 missing values.
2026-03-19 21:24:45.099915 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.
2026-03-19 21:24:45.102067 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:45.102593 INFO::Done
2026-03-19 21:24:45.112149 INFO::Formatting Data.
2026-03-19 21:24:45.112969 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:45.113811 INFO::Removing potential empty rows and columns
2026-03-19 21:24:45.114702 INFO::Found 2 missing values.
2026-03-19 21:24:45.116228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:45.11674 INFO::Done
2026-03-19 21:24:45.126605 INFO::Formatting Data.
2026-03-19 21:24:45.127301 INFO::Typecasting input to dataframe.
2026-03-19 21:24:45.12813 INFO::Replacing NaNs with NAs.
2026-03-19 21:24:45.12893 INFO::Removing potential empty rows and columns
2026-03-19 21:24:45.129848 INFO::Found 0 missing values.
2026-03-19 21:24:45.132538 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-19 21:24:45.133046 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.942 3.878 20.442
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.524 | 1.191 | 17.062 | |
| compute_asw | 0.025 | 0.001 | 0.026 | |
| count_existing | 0.014 | 0.000 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.000 | 0.012 | |