Yannis Schumann
| Snapshot Date: 2026-02-22 13:40 -0500 (Sun, 22 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-23 11:32 -0500 (Mon, 23 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4871 |
| 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 169/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | 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: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-22 21:49:01 -0500 (Sun, 22 Feb 2026) |
| EndedAt: 2026-02-22 21:50:29 -0500 (Sun, 22 Feb 2026) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.7.0’
* 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 22.904 1.114 16.403
* 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-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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")
2026-02-22 21:49:51.824767 INFO::Formatting Data.
2026-02-22 21:49:51.826119 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:51.837081 INFO::Removing potential empty rows and columns
2026-02-22 21:49:52.076297 INFO::Found 0 missing values.
2026-02-22 21:49:52.079562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:52.080221 INFO::Done
2026-02-22 21:49:52.080771 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:52.092127 INFO::Starting hierarchical adjustment
2026-02-22 21:49:52.093047 INFO::Found 3 batches.
2026-02-22 21:49:52.093628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:52.094736 INFO::Using default BPPARAM
2026-02-22 21:49:52.095266 INFO::Processing subtree level 1
2026-02-22 21:49:52.190398 INFO::Adjusting the last 1 batches sequentially
2026-02-22 21:49:52.192153 INFO::Done
2026-02-22 21:49:52.192831 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:52.195355 INFO::ASW Batch was 0.0676786541537708 prior to batch effect correction and is now 0.0676786541537708 .
2026-02-22 21:49:52.196452 INFO::Total function execution time is 0.372296810150146 s and adjustment time is 0.0992813110351562 s ( 26.67 )
2026-02-22 21:49:52.209974 INFO::Formatting Data.
2026-02-22 21:49:52.210778 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:52.21177 INFO::Removing potential empty rows and columns
2026-02-22 21:49:52.212931 INFO::Found 0 missing values.
2026-02-22 21:49:52.213916 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.
2026-02-22 21:49:52.225006 INFO::Formatting Data.
2026-02-22 21:49:52.225813 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:52.226767 INFO::Removing potential empty rows and columns
2026-02-22 21:49:52.227863 INFO::Found 0 missing values.
2026-02-22 21:49:52.228832 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.
2026-02-22 21:49:52.246619 INFO::Formatting Data.
2026-02-22 21:49:52.24759 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:52.248627 INFO::Removing potential empty rows and columns
2026-02-22 21:49:52.249795 INFO::Found 0 missing values.
2026-02-22 21:49:52.250811 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.
2026-02-22 21:49:52.255777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:52.256423 INFO::Done
2026-02-22 21:49:52.256984 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:52.259154 INFO::Starting hierarchical adjustment
2026-02-22 21:49:52.259936 INFO::Found 2 batches.
2026-02-22 21:49:52.260511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:52.261171 INFO::Using default BPPARAM
2026-02-22 21:49:52.261734 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:52.262703 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-22 21:49:52.284223 INFO::Done
2026-02-22 21:49:52.285016 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:52.287355 INFO::ASW Batch was 0.0102304053450057 prior to batch effect correction and is now -0.111453978519131 .
2026-02-22 21:49:52.288221 INFO::Total function execution time is 0.0417726039886475 s and adjustment time is 0.0243997573852539 s ( 58.41 )
2026-02-22 21:49:52.291099 INFO::Formatting Data.
2026-02-22 21:49:52.291761 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:52.300693 INFO::Formatting Data.
2026-02-22 21:49:52.301515 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:52.302439 INFO::Removing potential empty rows and columns
2026-02-22 21:49:52.303513 INFO::Found 0 missing values.
2026-02-22 21:49:52.306525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:52.307093 INFO::Done
2026-02-22 21:49:52.307646 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:52.309706 INFO::Starting hierarchical adjustment
2026-02-22 21:49:52.310438 INFO::Found 2 batches.
2026-02-22 21:49:52.31098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:52.311625 INFO::Using default BPPARAM
2026-02-22 21:49:52.31217 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:52.313137 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-22 21:49:52.349854 INFO::Done
2026-02-22 21:49:52.35052 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:52.352421 INFO::ASW Batch was 0.00892686436010483 prior to batch effect correction and is now -0.122568243323792 .
2026-02-22 21:49:52.353196 INFO::Total function execution time is 0.0525705814361572 s and adjustment time is 0.0395445823669434 s ( 75.22 )
2026-02-22 21:49:52.354167 INFO::Formatting Data.
2026-02-22 21:49:52.354737 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:52.355549 INFO::Removing potential empty rows and columns
2026-02-22 21:49:52.356506 INFO::Found 0 missing values.
2026-02-22 21:49:52.359105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:52.359644 INFO::Done
2026-02-22 21:49:52.360133 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:52.361966 INFO::Starting hierarchical adjustment
2026-02-22 21:49:52.362639 INFO::Found 2 batches.
2026-02-22 21:49:52.36313 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:52.363709 INFO::Using default BPPARAM
2026-02-22 21:49:52.364191 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:52.365047 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-22 21:49:52.378803 INFO::Done
2026-02-22 21:49:52.37949 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:52.381453 INFO::ASW Batch was 0.00892686436010483 prior to batch effect correction and is now -0.122568243323792 .
2026-02-22 21:49:52.382247 INFO::Total function execution time is 0.0280623435974121 s and adjustment time is 0.0162723064422607 s ( 57.99 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-22 21:49:55.390923 INFO::Formatting Data.
2026-02-22 21:49:55.391648 INFO::Recognized SummarizedExperiment
2026-02-22 21:49:55.392554 INFO::Typecasting input to dataframe.
2026-02-22 21:49:55.42308 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:55.424508 INFO::Removing potential empty rows and columns
2026-02-22 21:49:55.42868 INFO::Found 0 missing values.
2026-02-22 21:49:55.436554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:55.437206 INFO::Done
2026-02-22 21:49:55.437756 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:55.441376 INFO::Starting hierarchical adjustment
2026-02-22 21:49:55.442098 INFO::Found 2 batches.
2026-02-22 21:49:55.442634 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:55.443744 INFO::Using default BPPARAM
2026-02-22 21:49:55.444285 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:55.445326 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-22 21:49:55.501254 INFO::Done
2026-02-22 21:49:55.501953 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:55.505552 INFO::ASW Batch was -0.00408970834583191 prior to batch effect correction and is now -0.0974421046751828 .
2026-02-22 21:49:55.506396 INFO::Total function execution time is 0.115756988525391 s and adjustment time is 0.059279203414917 s ( 51.21 )
Warning: stack imbalance in '{', 73 then 75
2026-02-22 21:49:55.524894 INFO::Formatting Data.
2026-02-22 21:49:55.525637 INFO::Recognized SummarizedExperiment
2026-02-22 21:49:55.52618 INFO::Typecasting input to dataframe.
2026-02-22 21:49:55.535311 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:55.536494 INFO::Removing potential empty rows and columns
2026-02-22 21:49:55.540339 INFO::Found 0 missing values.
2026-02-22 21:49:55.547846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:55.548524 INFO::Done
2026-02-22 21:49:55.549091 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:55.552671 INFO::Starting hierarchical adjustment
2026-02-22 21:49:55.553401 INFO::Found 2 batches.
2026-02-22 21:49:55.553936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:55.554566 INFO::Using default BPPARAM
2026-02-22 21:49:55.5551 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:55.55608 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-22 21:49:55.581677 INFO::Done
2026-02-22 21:49:55.5824 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:55.585994 INFO::ASW Batch was 0.00223859494507231 prior to batch effect correction and is now 0.00223859494507231 .
2026-02-22 21:49:55.586873 INFO::Total function execution time is 0.061964750289917 s and adjustment time is 0.0283904075622559 s ( 45.82 )
2026-02-22 21:49:55.605506 INFO::Formatting Data.
2026-02-22 21:49:55.606313 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:55.607233 INFO::Removing potential empty rows and columns
2026-02-22 21:49:55.60827 INFO::Found 0 missing values.
2026-02-22 21:49:55.611248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:55.611803 INFO::Done
2026-02-22 21:49:55.612317 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:55.614316 INFO::Starting hierarchical adjustment
2026-02-22 21:49:55.615029 INFO::Found 3 batches.
2026-02-22 21:49:55.615552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:55.616151 INFO::Using default BPPARAM
2026-02-22 21:49:55.616687 INFO::Processing subtree level 1
2026-02-22 21:49:55.74785 INFO::Adjusting the last 1 batches sequentially
2026-02-22 21:49:55.749798 INFO::Done
2026-02-22 21:49:55.750475 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:55.753006 INFO::ASW Batch was -0.0567496008969463 prior to batch effect correction and is now -0.162943276023502 .
2026-02-22 21:49:55.753951 INFO::Total function execution time is 0.148505210876465 s and adjustment time is 0.134886741638184 s ( 90.83 )
2026-02-22 21:49:55.768568 INFO::Skipping initial DF formatting
2026-02-22 21:49:55.769281 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:55.773417 INFO::Starting hierarchical adjustment
2026-02-22 21:49:55.774257 INFO::Found 5 batches.
2026-02-22 21:49:55.774844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:55.775493 INFO::Using default BPPARAM
2026-02-22 21:49:55.776049 INFO::Processing subtree level 1
2026-02-22 21:49:56.024071 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.025774 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-22 21:49:56.046224 INFO::Done
2026-02-22 21:49:56.046997 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.095714 INFO::ASW Batch was 0.512749780542745 prior to batch effect correction and is now 0.512749780542745 .
2026-02-22 21:49:56.096455 INFO::ASW Label was 0.382195034395456 prior to batch effect correction and is now 0.382195034395456 .
2026-02-22 21:49:56.097353 INFO::Total function execution time is 0.328885078430176 s and adjustment time is 0.272106885910034 s ( 82.74 )
2026-02-22 21:49:56.114791 INFO::Formatting Data.
2026-02-22 21:49:56.115571 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.116594 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.117623 INFO::Found 0 missing values.
2026-02-22 21:49:56.121814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.12238 INFO::Done
2026-02-22 21:49:56.122925 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.125957 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.126649 INFO::Found 5 batches.
2026-02-22 21:49:56.127191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.127846 INFO::Using default BPPARAM
2026-02-22 21:49:56.128454 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.
2026-02-22 21:49:56.251694 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.253315 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-22 21:49:56.270429 INFO::Done
2026-02-22 21:49:56.271164 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.274662 INFO::ASW Batch was 0.326647564817713 prior to batch effect correction and is now -0.0963644171283512 .
2026-02-22 21:49:56.275317 INFO::ASW Label was 0.293094933430883 prior to batch effect correction and is now 0.817165233733947 .
2026-02-22 21:49:56.276155 INFO::Total function execution time is 0.161418199539185 s and adjustment time is 0.14387845993042 s ( 89.13 )
2026-02-22 21:49:56.27708 INFO::Formatting Data.
2026-02-22 21:49:56.277734 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.278669 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.279736 INFO::Found 0 missing values.
2026-02-22 21:49:56.284074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.284631 INFO::Done
2026-02-22 21:49:56.285167 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.288252 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.288952 INFO::Found 5 batches.
2026-02-22 21:49:56.2895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.290101 INFO::Using default BPPARAM
2026-02-22 21:49:56.290645 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.
2026-02-22 21:49:56.407513 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.409058 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-22 21:49:56.424901 INFO::Done
2026-02-22 21:49:56.425604 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.428886 INFO::ASW Batch was 0.326647564817713 prior to batch effect correction and is now -0.0963644171283512 .
2026-02-22 21:49:56.429513 INFO::ASW Label was 0.293094933430883 prior to batch effect correction and is now 0.817165233733947 .
2026-02-22 21:49:56.430327 INFO::Total function execution time is 0.153259754180908 s and adjustment time is 0.136063814163208 s ( 88.78 )
2026-02-22 21:49:56.44346 INFO::Formatting Data.
2026-02-22 21:49:56.444181 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.445078 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.446145 INFO::Found 0 missing values.
2026-02-22 21:49:56.450151 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.450716 INFO::Done
2026-02-22 21:49:56.451222 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.454192 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.454896 INFO::Found 5 batches.
2026-02-22 21:49:56.455434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.456055 INFO::Using default BPPARAM
2026-02-22 21:49:56.456639 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.
2026-02-22 21:49:56.572391 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.573915 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-22 21:49:56.589294 INFO::Done
2026-02-22 21:49:56.589989 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.593199 INFO::ASW Batch was 0.502287947580109 prior to batch effect correction and is now -0.0979439216868933 .
2026-02-22 21:49:56.593791 INFO::ASW Label was 0.389255158162421 prior to batch effect correction and is now 0.768939141899913 .
2026-02-22 21:49:56.594599 INFO::Total function execution time is 0.151196718215942 s and adjustment time is 0.134517669677734 s ( 88.97 )
2026-02-22 21:49:56.595449 INFO::Formatting Data.
2026-02-22 21:49:56.596081 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.596965 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.597967 INFO::Found 0 missing values.
2026-02-22 21:49:56.602154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.602811 INFO::Done
2026-02-22 21:49:56.603332 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.606273 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.606989 INFO::Found 5 batches.
2026-02-22 21:49:56.607533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.608131 INFO::Using default BPPARAM
2026-02-22 21:49:56.60866 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.
2026-02-22 21:49:56.723877 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.725427 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-22 21:49:56.741802 INFO::Done
2026-02-22 21:49:56.742578 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.746272 INFO::ASW Batch was 0.502287947580109 prior to batch effect correction and is now -0.0979439216868933 .
2026-02-22 21:49:56.746915 INFO::ASW Label was 0.389255158162421 prior to batch effect correction and is now 0.768939141899913 .
2026-02-22 21:49:56.747791 INFO::Total function execution time is 0.152345180511475 s and adjustment time is 0.134923696517944 s ( 88.56 )
2026-02-22 21:49:56.760946 INFO::Formatting Data.
2026-02-22 21:49:56.76171 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.762614 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.763627 INFO::Found 0 missing values.
2026-02-22 21:49:56.766258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.766833 INFO::Done
2026-02-22 21:49:56.767344 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.770186 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.770891 INFO::Found 2 batches.
2026-02-22 21:49:56.77143 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.772027 INFO::Using default BPPARAM
2026-02-22 21:49:56.772575 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.773485 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-22 21:49:56.78756 INFO::Done
2026-02-22 21:49:56.788208 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.791074 INFO::ASW Batch was 0.718565018556781 prior to batch effect correction and is now -0.0256370351807107 .
2026-02-22 21:49:56.791706 INFO::ASW Label was 0.353049092558852 prior to batch effect correction and is now 0.919987314387085 .
2026-02-22 21:49:56.79248 INFO::Total function execution time is 0.0316054821014404 s and adjustment time is 0.0168023109436035 s ( 53.16 )
2026-02-22 21:49:56.793257 INFO::Formatting Data.
2026-02-22 21:49:56.793864 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.794701 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.795662 INFO::Found 0 missing values.
2026-02-22 21:49:56.798239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.798771 INFO::Done
2026-02-22 21:49:56.79927 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.802115 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.802802 INFO::Found 2 batches.
2026-02-22 21:49:56.803316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.803903 INFO::Using default BPPARAM
2026-02-22 21:49:56.804442 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.805312 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-22 21:49:56.819278 INFO::Done
2026-02-22 21:49:56.81994 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.822857 INFO::ASW Batch was 0.718565018556781 prior to batch effect correction and is now -0.0256370351807107 .
2026-02-22 21:49:56.823486 INFO::ASW Label was 0.353049092558852 prior to batch effect correction and is now 0.919987314387085 .
2026-02-22 21:49:56.824249 INFO::Total function execution time is 0.0310091972351074 s and adjustment time is 0.0165972709655762 s ( 53.52 )
2026-02-22 21:49:56.835392 INFO::Formatting Data.
2026-02-22 21:49:56.836114 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.836985 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.837866 INFO::Found 0 missing values.
2026-02-22 21:49:56.839916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.840448 INFO::Done
2026-02-22 21:49:56.840943 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.842767 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.84344 INFO::Found 2 batches.
2026-02-22 21:49:56.843943 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.844555 INFO::Using default BPPARAM
2026-02-22 21:49:56.845074 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.845962 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-22 21:49:56.875684 INFO::Done
2026-02-22 21:49:56.876374 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.878257 INFO::ASW Batch was -0.124172433393271 prior to batch effect correction and is now -0.129728523575475 .
2026-02-22 21:49:56.879047 INFO::Total function execution time is 0.043736457824707 s and adjustment time is 0.0323567390441895 s ( 73.98 )
2026-02-22 21:49:56.891073 INFO::Formatting Data.
2026-02-22 21:49:56.892016 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.893017 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.894149 INFO::Found 0 missing values.
2026-02-22 21:49:56.895466 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.
2026-02-22 21:49:56.900362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.900965 INFO::Done
2026-02-22 21:49:56.901509 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.904536 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.90527 INFO::Found 2 batches.
2026-02-22 21:49:56.905828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.906476 INFO::Using default BPPARAM
2026-02-22 21:49:56.906993 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.907947 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-22 21:49:56.923853 INFO::Done
2026-02-22 21:49:56.92453 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.927338 INFO::ASW Batch was 0.728260298726054 prior to batch effect correction and is now -0.0362755800254314 .
2026-02-22 21:49:56.927923 INFO::ASW Label was 0.347819678373607 prior to batch effect correction and is now 0.931011011931867 .
2026-02-22 21:49:56.928698 INFO::Total function execution time is 0.0377922058105469 s and adjustment time is 0.0187246799468994 s ( 49.55 )
2026-02-22 21:49:56.929449 INFO::Formatting Data.
2026-02-22 21:49:56.93004 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:56.930901 INFO::Removing potential empty rows and columns
2026-02-22 21:49:56.931828 INFO::Found 0 missing values.
2026-02-22 21:49:56.932684 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.
2026-02-22 21:49:56.936917 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:56.937446 INFO::Done
2026-02-22 21:49:56.937946 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:56.940629 INFO::Starting hierarchical adjustment
2026-02-22 21:49:56.941281 INFO::Found 2 batches.
2026-02-22 21:49:56.941813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:56.942397 INFO::Using default BPPARAM
2026-02-22 21:49:56.942898 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:49:56.943755 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-22 21:49:56.958868 INFO::Done
2026-02-22 21:49:56.959488 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:56.962204 INFO::ASW Batch was 0.728260298726054 prior to batch effect correction and is now -0.0362755800254314 .
2026-02-22 21:49:56.962786 INFO::ASW Label was 0.347819678373607 prior to batch effect correction and is now 0.931011011931867 .
2026-02-22 21:49:56.963544 INFO::Total function execution time is 0.0341198444366455 s and adjustment time is 0.017707347869873 s ( 51.9 )
2026-02-22 21:49:57.18217 INFO::Formatting Data.
2026-02-22 21:49:57.183068 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:57.184005 INFO::Removing potential empty rows and columns
2026-02-22 21:49:57.185104 INFO::Found 0 missing values.
2026-02-22 21:49:57.188485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:57.189026 INFO::Done
2026-02-22 21:49:57.189564 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:57.191648 INFO::Starting hierarchical adjustment
2026-02-22 21:49:57.192349 INFO::Found 3 batches.
2026-02-22 21:49:57.192882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:57.193522 INFO::Using default BPPARAM
2026-02-22 21:49:57.19404 INFO::Processing subtree level 1
2026-02-22 21:49:57.277079 INFO::Adjusting the last 1 batches sequentially
2026-02-22 21:49:57.278865 INFO::Done
2026-02-22 21:49:57.279526 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:57.28196 INFO::ASW Batch was -0.110206820987997 prior to batch effect correction and is now -0.110206820987997 .
2026-02-22 21:49:57.282947 INFO::Total function execution time is 0.100857496261597 s and adjustment time is 0.0866467952728271 s ( 85.91 )
2026-02-22 21:49:57.283976 INFO::Formatting Data.
2026-02-22 21:49:57.284626 INFO::Typecasting input to dataframe.
2026-02-22 21:49:57.285391 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:57.28629 INFO::Removing potential empty rows and columns
2026-02-22 21:49:57.287606 INFO::Found 0 missing values.
2026-02-22 21:49:57.29071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:57.291292 INFO::Done
2026-02-22 21:49:57.29186 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:57.29389 INFO::Starting hierarchical adjustment
2026-02-22 21:49:57.294625 INFO::Found 3 batches.
2026-02-22 21:49:57.295161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:57.295794 INFO::Using default BPPARAM
2026-02-22 21:49:57.296347 INFO::Processing subtree level 1
2026-02-22 21:49:57.376423 INFO::Adjusting the last 1 batches sequentially
2026-02-22 21:49:57.378146 INFO::Done
2026-02-22 21:49:57.378814 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:57.381222 INFO::ASW Batch was -0.110206820987997 prior to batch effect correction and is now -0.110206820987997 .
2026-02-22 21:49:57.382166 INFO::Total function execution time is 0.0981812477111816 s and adjustment time is 0.0836606025695801 s ( 85.21 )
2026-02-22 21:49:57.395175 INFO::Formatting Data.
2026-02-22 21:49:57.395947 INFO::Typecasting input to dataframe.
2026-02-22 21:49:57.396802 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:57.397736 INFO::Removing potential empty rows and columns
2026-02-22 21:49:57.398829 INFO::Found 0 missing values.
2026-02-22 21:49:57.401861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:57.402415 INFO::Done
2026-02-22 21:49:57.40295 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:57.404982 INFO::Starting hierarchical adjustment
2026-02-22 21:49:57.405692 INFO::Found 3 batches.
2026-02-22 21:49:57.406233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:57.406881 INFO::Using default BPPARAM
2026-02-22 21:49:57.407449 INFO::Processing subtree level 1
2026-02-22 21:49:57.49053 INFO::Adjusting the last 1 batches sequentially
2026-02-22 21:49:57.492319 INFO::Done
2026-02-22 21:49:57.492967 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:57.495586 INFO::ASW Batch was -0.0387694990680257 prior to batch effect correction and is now -0.0387694990680257 .
2026-02-22 21:49:57.496503 INFO::Total function execution time is 0.101369380950928 s and adjustment time is 0.0867440700531006 s ( 85.57 )
2026-02-22 21:49:57.632147 INFO::Formatting Data.
2026-02-22 21:49:57.63301 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:57.634169 INFO::Removing potential empty rows and columns
2026-02-22 21:49:57.637028 INFO::Found 1000 missing values.
2026-02-22 21:49:57.657296 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:57.658141 INFO::Done
2026-02-22 21:49:57.658742 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:57.664485 INFO::Starting hierarchical adjustment
2026-02-22 21:49:57.665252 INFO::Found 10 batches.
2026-02-22 21:49:57.665812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:49:57.666487 INFO::Using default BPPARAM
2026-02-22 21:49:57.667045 INFO::Processing subtree level 1
2026-02-22 21:49:57.794823 INFO::Processing subtree level 2
2026-02-22 21:49:57.935693 INFO::Adjusting the last 1 batches sequentially
2026-02-22 21:49:57.937632 INFO::Done
2026-02-22 21:49:57.938288 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:49:57.943712 INFO::ASW Batch was 0.501316284184837 prior to batch effect correction and is now 0.501316284184837 .
2026-02-22 21:49:57.944384 INFO::ASW Label was 0.343871509055932 prior to batch effect correction and is now 0.343871509055932 .
2026-02-22 21:49:57.945284 INFO::Total function execution time is 0.313204526901245 s and adjustment time is 0.272523164749146 s ( 87.01 )
2026-02-22 21:49:57.946144 INFO::Formatting Data.
2026-02-22 21:49:57.9468 INFO::Replacing NaNs with NAs.
2026-02-22 21:49:57.948064 INFO::Removing potential empty rows and columns
2026-02-22 21:49:57.950953 INFO::Found 1000 missing values.
2026-02-22 21:49:57.970782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:49:57.971537 INFO::Done
2026-02-22 21:49:57.972104 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:49:57.977738 INFO::Starting hierarchical adjustment
2026-02-22 21:49:57.978858 INFO::Found 10 batches.
2026-02-22 21:49:58.865832 INFO::Set up parallel execution backend with 2 workers
2026-02-22 21:49:58.86808 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-22 21:50:00.041101 INFO::Adjusting the last 2 batches sequentially
2026-02-22 21:50:00.0431 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-22 21:50:00.059692 INFO::Done
2026-02-22 21:50:00.060396 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:50:00.06497 INFO::ASW Batch was 0.501316284184837 prior to batch effect correction and is now 0.501316284184837 .
2026-02-22 21:50:00.065573 INFO::ASW Label was 0.343871509055932 prior to batch effect correction and is now 0.343871509055932 .
2026-02-22 21:50:00.066317 INFO::Total function execution time is 2.12019872665405 s and adjustment time is 2.08100032806396 s ( 98.15 )
2026-02-22 21:50:00.204717 INFO::Formatting Data.
2026-02-22 21:50:00.20546 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.206324 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.207383 INFO::Found 0 missing values.
2026-02-22 21:50:00.211003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.211538 INFO::Done
2026-02-22 21:50:00.21205 INFO::Acquiring quality metrics before batch effect correction.
2026-02-22 21:50:00.214692 INFO::Starting hierarchical adjustment
2026-02-22 21:50:00.215364 INFO::Found 3 batches.
2026-02-22 21:50:00.215889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-22 21:50:00.216535 INFO::Using default BPPARAM
2026-02-22 21:50:00.217062 INFO::Processing subtree level 1
2026-02-22 21:50:00.316041 INFO::Adjusting the last 1 batches sequentially
2026-02-22 21:50:00.317846 INFO::Done
2026-02-22 21:50:00.318526 INFO::Acquiring quality metrics after batch effect correction.
2026-02-22 21:50:00.321714 INFO::ASW Batch was 0.148859245959928 prior to batch effect correction and is now -0.137189703176565 .
2026-02-22 21:50:00.322323 INFO::ASW Label was -0.13722768024626 prior to batch effect correction and is now 0.0531695769105363 .
2026-02-22 21:50:00.323271 INFO::Total function execution time is 0.118586540222168 s and adjustment time is 0.102591753005981 s ( 86.51 )
2026-02-22 21:50:00.436551 INFO::Formatting Data.
2026-02-22 21:50:00.437345 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.438245 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.439263 INFO::Found 2 missing values.
2026-02-22 21:50:00.442021 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.442579 INFO::Done
2026-02-22 21:50:00.468381 INFO::Found NA in Reference column
2026-02-22 21:50:00.477247 INFO::Require at least two references per batch.
2026-02-22 21:50:00.496434 INFO::Formatting Data.
2026-02-22 21:50:00.497137 INFO::Recognized SummarizedExperiment
2026-02-22 21:50:00.497675 INFO::Typecasting input to dataframe.
2026-02-22 21:50:00.506699 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.507789 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.511239 INFO::Found 0 missing values.
2026-02-22 21:50:00.517858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.518412 INFO::Done
2026-02-22 21:50:00.532998 INFO::Formatting Data.
2026-02-22 21:50:00.533691 INFO::Recognized SummarizedExperiment
2026-02-22 21:50:00.534204 INFO::Typecasting input to dataframe.
2026-02-22 21:50:00.551911 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.553287 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.556955 INFO::Found 0 missing values.
2026-02-22 21:50:00.568425 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.5691 INFO::Done
2026-02-22 21:50:00.584349 INFO::Formatting Data.
2026-02-22 21:50:00.585157 INFO::Recognized SummarizedExperiment
2026-02-22 21:50:00.585698 INFO::Typecasting input to dataframe.
2026-02-22 21:50:00.601835 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.602861 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.603969 INFO::Found 0 missing values.
2026-02-22 21:50:00.60489 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.
2026-02-22 21:50:00.60919 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.609734 INFO::Done
2026-02-22 21:50:00.628151 INFO::Formatting Data.
2026-02-22 21:50:00.629215 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.630196 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.631262 INFO::Found 0 missing values.
2026-02-22 21:50:00.634171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.634702 INFO::Done
2026-02-22 21:50:00.646046 INFO::Formatting Data.
2026-02-22 21:50:00.646772 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.64763 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.648626 INFO::Found 0 missing values.
2026-02-22 21:50:00.651448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.651965 INFO::Done
2026-02-22 21:50:00.680438 INFO::Formatting Data.
2026-02-22 21:50:00.681233 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.682229 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.683389 INFO::Found 1 missing values.
2026-02-22 21:50:00.685928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.686486 INFO::Done
2026-02-22 21:50:00.704535 INFO::Formatting Data.
2026-02-22 21:50:00.705312 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.706201 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.707134 INFO::Found 2 missing values.
2026-02-22 21:50:00.708013 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.
2026-02-22 21:50:00.710419 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.710938 INFO::Done
2026-02-22 21:50:00.720205 INFO::Formatting Data.
2026-02-22 21:50:00.720896 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.721731 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.722604 INFO::Found 2 missing values.
2026-02-22 21:50:00.724077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.724629 INFO::Done
2026-02-22 21:50:00.73418 INFO::Formatting Data.
2026-02-22 21:50:00.734865 INFO::Typecasting input to dataframe.
2026-02-22 21:50:00.73563 INFO::Replacing NaNs with NAs.
2026-02-22 21:50:00.736432 INFO::Removing potential empty rows and columns
2026-02-22 21:50:00.737384 INFO::Found 0 missing values.
2026-02-22 21:50:00.740109 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-22 21:50:00.740629 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.650 3.409 19.695
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 22.904 | 1.114 | 16.403 | |
| compute_asw | 0.025 | 0.001 | 0.027 | |
| count_existing | 0.014 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |