Yannis Schumann
| Snapshot Date: 2026-04-29 13:45 -0400 (Wed, 29 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 072dd1e |
| git_last_commit_date: 2026-04-28 09:02:01 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-04-30 11:32 -0400 (Thu, 30 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4843 |
| 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 167/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.9.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.4 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: 1.9.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz |
| StartedAt: 2026-04-29 21:45:22 -0400 (Wed, 29 Apr 2026) |
| EndedAt: 2026-04-29 21:46:57 -0400 (Wed, 29 Apr 2026) |
| EllapsedTime: 95.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BERT_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-30 01:45:22 UTC
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.9.0’
* 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 26.877 1.544 20.858
* 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-3.24-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.9.0’ ** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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")
2026-04-29 21:46:17.995039 INFO::Formatting Data.
2026-04-29 21:46:17.996411 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:18.007319 INFO::Removing potential empty rows and columns
2026-04-29 21:46:18.247818 INFO::Found 0 missing values.
2026-04-29 21:46:18.251064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:18.251679 INFO::Done
2026-04-29 21:46:18.252227 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:18.264007 INFO::Starting hierarchical adjustment
2026-04-29 21:46:18.264813 INFO::Found 3 batches.
2026-04-29 21:46:18.265367 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:18.26646 INFO::Using default BPPARAM
2026-04-29 21:46:18.267009 INFO::Processing subtree level 1
2026-04-29 21:46:18.363118 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:46:18.364883 INFO::Done
2026-04-29 21:46:18.365586 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:18.368052 INFO::ASW Batch was -0.146532094043528 prior to batch effect correction and is now -0.146532094043528 .
2026-04-29 21:46:18.369072 INFO::Total function execution time is 0.374735593795776 s and adjustment time is 0.100216865539551 s ( 26.74 )
2026-04-29 21:46:18.382134 INFO::Formatting Data.
2026-04-29 21:46:18.382857 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:18.383761 INFO::Removing potential empty rows and columns
2026-04-29 21:46:18.384837 INFO::Found 0 missing values.
2026-04-29 21:46:18.385771 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.
2026-04-29 21:46:18.39622 INFO::Formatting Data.
2026-04-29 21:46:18.396935 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:18.397833 INFO::Removing potential empty rows and columns
2026-04-29 21:46:18.398939 INFO::Found 0 missing values.
2026-04-29 21:46:18.399853 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.
2026-04-29 21:46:18.415187 INFO::Formatting Data.
2026-04-29 21:46:18.41593 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:18.416783 INFO::Removing potential empty rows and columns
2026-04-29 21:46:18.417781 INFO::Found 0 missing values.
2026-04-29 21:46:18.418663 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.
2026-04-29 21:46:18.422967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:18.423533 INFO::Done
2026-04-29 21:46:18.424076 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:18.426101 INFO::Starting hierarchical adjustment
2026-04-29 21:46:18.426816 INFO::Found 2 batches.
2026-04-29 21:46:18.427386 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:18.428055 INFO::Using default BPPARAM
2026-04-29 21:46:18.428643 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:18.429616 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:46:18.449821 INFO::Done
2026-04-29 21:46:18.450511 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:18.452454 INFO::ASW Batch was 0.0578063678909402 prior to batch effect correction and is now -0.120314444823864 .
2026-04-29 21:46:18.4532 INFO::Total function execution time is 0.0380592346191406 s and adjustment time is 0.0231282711029053 s ( 60.77 )
2026-04-29 21:46:18.455969 INFO::Formatting Data.
2026-04-29 21:46:18.456628 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:18.465189 INFO::Formatting Data.
2026-04-29 21:46:18.465877 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:18.466758 INFO::Removing potential empty rows and columns
2026-04-29 21:46:18.467819 INFO::Found 0 missing values.
2026-04-29 21:46:18.470744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:18.4713 INFO::Done
2026-04-29 21:46:18.471852 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:18.47388 INFO::Starting hierarchical adjustment
2026-04-29 21:46:18.474609 INFO::Found 2 batches.
2026-04-29 21:46:18.475172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:18.475817 INFO::Using default BPPARAM
2026-04-29 21:46:18.476367 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:18.477287 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:46:18.492688 INFO::Done
2026-04-29 21:46:18.493355 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:18.495465 INFO::ASW Batch was -0.0235438088802025 prior to batch effect correction and is now -0.0817629384901289 .
2026-04-29 21:46:18.496337 INFO::Total function execution time is 0.0311543941497803 s and adjustment time is 0.018226146697998 s ( 58.5 )
2026-04-29 21:46:18.497521 INFO::Formatting Data.
2026-04-29 21:46:18.49816 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:18.499072 INFO::Removing potential empty rows and columns
2026-04-29 21:46:18.5002 INFO::Found 0 missing values.
2026-04-29 21:46:18.503202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:18.503783 INFO::Done
2026-04-29 21:46:18.50435 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:18.506427 INFO::Starting hierarchical adjustment
2026-04-29 21:46:18.507262 INFO::Found 2 batches.
2026-04-29 21:46:18.507862 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:18.508539 INFO::Using default BPPARAM
2026-04-29 21:46:18.509133 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:18.510054 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:46:18.525034 INFO::Done
2026-04-29 21:46:18.525708 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:18.5277 INFO::ASW Batch was -0.0235438088802025 prior to batch effect correction and is now -0.0817629384901289 .
2026-04-29 21:46:18.528501 INFO::Total function execution time is 0.0309722423553467 s and adjustment time is 0.0179259777069092 s ( 57.88 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-29 21:46:21.609022 INFO::Formatting Data.
2026-04-29 21:46:21.609774 INFO::Recognized SummarizedExperiment
2026-04-29 21:46:21.610285 INFO::Typecasting input to dataframe.
2026-04-29 21:46:21.639333 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:21.640583 INFO::Removing potential empty rows and columns
2026-04-29 21:46:21.643874 INFO::Found 0 missing values.
2026-04-29 21:46:21.650057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:21.650656 INFO::Done
2026-04-29 21:46:21.651155 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:21.654305 INFO::Starting hierarchical adjustment
2026-04-29 21:46:21.655002 INFO::Found 2 batches.
2026-04-29 21:46:21.655541 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:21.656575 INFO::Using default BPPARAM
2026-04-29 21:46:21.657086 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:21.658005 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:46:21.706781 INFO::Done
2026-04-29 21:46:21.707497 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:21.710696 INFO::ASW Batch was 0.0120708471778147 prior to batch effect correction and is now -0.0909983744177831 .
2026-04-29 21:46:21.711487 INFO::Total function execution time is 0.102723598480225 s and adjustment time is 0.0518887042999268 s ( 50.51 )
Warning: stack imbalance in '{', 73 then 75
2026-04-29 21:46:21.728007 INFO::Formatting Data.
2026-04-29 21:46:21.728731 INFO::Recognized SummarizedExperiment
2026-04-29 21:46:21.729242 INFO::Typecasting input to dataframe.
2026-04-29 21:46:21.737472 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:21.738575 INFO::Removing potential empty rows and columns
2026-04-29 21:46:21.74178 INFO::Found 0 missing values.
2026-04-29 21:46:21.747987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:21.748592 INFO::Done
2026-04-29 21:46:21.7491 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:21.752296 INFO::Starting hierarchical adjustment
2026-04-29 21:46:21.752982 INFO::Found 2 batches.
2026-04-29 21:46:21.7535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:21.75415 INFO::Using default BPPARAM
2026-04-29 21:46:21.754665 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:21.755583 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:46:21.779908 INFO::Done
2026-04-29 21:46:21.780732 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:21.784446 INFO::ASW Batch was 0.00883304855434753 prior to batch effect correction and is now 0.00883304855434753 .
2026-04-29 21:46:21.78534 INFO::Total function execution time is 0.0572984218597412 s and adjustment time is 0.0270004272460938 s ( 47.12 )
2026-04-29 21:46:21.8041 INFO::Formatting Data.
2026-04-29 21:46:21.805046 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:21.806015 INFO::Removing potential empty rows and columns
2026-04-29 21:46:21.807242 INFO::Found 0 missing values.
2026-04-29 21:46:21.810977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:21.811598 INFO::Done
2026-04-29 21:46:21.812147 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:21.814248 INFO::Starting hierarchical adjustment
2026-04-29 21:46:21.81498 INFO::Found 3 batches.
2026-04-29 21:46:21.815576 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:21.816212 INFO::Using default BPPARAM
2026-04-29 21:46:21.816792 INFO::Processing subtree level 1
2026-04-29 21:46:21.99164 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:46:21.99361 INFO::Done
2026-04-29 21:46:21.994329 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:21.996942 INFO::ASW Batch was -0.0851279256061934 prior to batch effect correction and is now -0.176955415092454 .
2026-04-29 21:46:21.998153 INFO::Total function execution time is 0.194082736968994 s and adjustment time is 0.178753137588501 s ( 92.1 )
2026-04-29 21:46:22.013435 INFO::Skipping initial DF formatting
2026-04-29 21:46:22.014304 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:22.019012 INFO::Starting hierarchical adjustment
2026-04-29 21:46:22.019921 INFO::Found 5 batches.
2026-04-29 21:46:22.020533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:22.021215 INFO::Using default BPPARAM
2026-04-29 21:46:22.021808 INFO::Processing subtree level 1
2026-04-29 21:46:22.146963 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:22.148978 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:46:22.170476 INFO::Done
2026-04-29 21:46:22.171341 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:22.1761 INFO::ASW Batch was 0.518872683916514 prior to batch effect correction and is now 0.518872683916514 .
2026-04-29 21:46:22.176827 INFO::ASW Label was 0.37352492394131 prior to batch effect correction and is now 0.37352492394131 .
2026-04-29 21:46:22.1778 INFO::Total function execution time is 0.164507627487183 s and adjustment time is 0.150688886642456 s ( 91.6 )
2026-04-29 21:46:22.198573 INFO::Formatting Data.
2026-04-29 21:46:22.199603 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:22.20069 INFO::Removing potential empty rows and columns
2026-04-29 21:46:22.20184 INFO::Found 0 missing values.
2026-04-29 21:46:22.206261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:22.206921 INFO::Done
2026-04-29 21:46:22.207524 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:22.211313 INFO::Starting hierarchical adjustment
2026-04-29 21:46:22.212549 INFO::Found 5 batches.
2026-04-29 21:46:22.213478 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:22.214543 INFO::Using default BPPARAM
2026-04-29 21:46:22.215465 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.
2026-04-29 21:46:22.343213 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:22.344934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:46:22.361957 INFO::Done
2026-04-29 21:46:22.362788 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:22.366132 INFO::ASW Batch was 0.428597926232723 prior to batch effect correction and is now -0.0552472258934996 .
2026-04-29 21:46:22.366793 INFO::ASW Label was 0.311589896848615 prior to batch effect correction and is now 0.823988959437534 .
2026-04-29 21:46:22.367685 INFO::Total function execution time is 0.16929292678833 s and adjustment time is 0.149663686752319 s ( 88.41 )
2026-04-29 21:46:22.368581 INFO::Formatting Data.
2026-04-29 21:46:22.36937 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:22.370317 INFO::Removing potential empty rows and columns
2026-04-29 21:46:22.37138 INFO::Found 0 missing values.
2026-04-29 21:46:22.375556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:22.37617 INFO::Done
2026-04-29 21:46:22.376752 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:22.379839 INFO::Starting hierarchical adjustment
2026-04-29 21:46:22.380626 INFO::Found 5 batches.
2026-04-29 21:46:22.381202 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:22.381877 INFO::Using default BPPARAM
2026-04-29 21:46:22.382454 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.
2026-04-29 21:46:22.490732 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:22.49259 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:46:22.509765 INFO::Done
2026-04-29 21:46:22.510624 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:22.514217 INFO::ASW Batch was 0.428597926232723 prior to batch effect correction and is now -0.0552472258934996 .
2026-04-29 21:46:22.514912 INFO::ASW Label was 0.311589896848615 prior to batch effect correction and is now 0.823988959437534 .
2026-04-29 21:46:22.515841 INFO::Total function execution time is 0.14725661277771 s and adjustment time is 0.129231691360474 s ( 87.76 )
2026-04-29 21:46:22.530824 INFO::Formatting Data.
2026-04-29 21:46:22.531827 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:22.53291 INFO::Removing potential empty rows and columns
2026-04-29 21:46:22.53403 INFO::Found 0 missing values.
2026-04-29 21:46:22.538456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:22.539075 INFO::Done
2026-04-29 21:46:22.539659 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:22.542984 INFO::Starting hierarchical adjustment
2026-04-29 21:46:22.543785 INFO::Found 5 batches.
2026-04-29 21:46:22.54437 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:22.545051 INFO::Using default BPPARAM
2026-04-29 21:46:22.545635 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.
2026-04-29 21:46:22.668339 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:22.670244 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:46:22.696498 INFO::Done
2026-04-29 21:46:22.697784 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:22.703487 INFO::ASW Batch was 0.369098872404824 prior to batch effect correction and is now -0.047602545958752 .
2026-04-29 21:46:22.704452 INFO::ASW Label was 0.370321748429874 prior to batch effect correction and is now 0.817740410014938 .
2026-04-29 21:46:22.705753 INFO::Total function execution time is 0.174970626831055 s and adjustment time is 0.152753114700317 s ( 87.3 )
2026-04-29 21:46:22.707091 INFO::Formatting Data.
2026-04-29 21:46:22.708143 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:22.709648 INFO::Removing potential empty rows and columns
2026-04-29 21:46:22.711253 INFO::Found 0 missing values.
2026-04-29 21:46:22.718237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:22.71918 INFO::Done
2026-04-29 21:46:22.720042 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:22.724784 INFO::Starting hierarchical adjustment
2026-04-29 21:46:22.725944 INFO::Found 5 batches.
2026-04-29 21:46:22.726832 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:22.727843 INFO::Using default BPPARAM
2026-04-29 21:46:22.728725 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.
2026-04-29 21:46:22.863102 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:22.864796 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:46:22.880864 INFO::Done
2026-04-29 21:46:22.881636 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:22.884887 INFO::ASW Batch was 0.369098872404824 prior to batch effect correction and is now -0.047602545958752 .
2026-04-29 21:46:22.885538 INFO::ASW Label was 0.370321748429874 prior to batch effect correction and is now 0.817740410014938 .
2026-04-29 21:46:22.886415 INFO::Total function execution time is 0.179407596588135 s and adjustment time is 0.155150651931763 s ( 86.48 )
2026-04-29 21:46:22.900569 INFO::Formatting Data.
2026-04-29 21:46:22.901477 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:22.902472 INFO::Removing potential empty rows and columns
2026-04-29 21:46:22.903533 INFO::Found 0 missing values.
2026-04-29 21:46:22.906334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:22.906945 INFO::Done
2026-04-29 21:46:22.907525 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:22.910603 INFO::Starting hierarchical adjustment
2026-04-29 21:46:22.911354 INFO::Found 2 batches.
2026-04-29 21:46:22.911941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:22.912605 INFO::Using default BPPARAM
2026-04-29 21:46:22.913172 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:22.914131 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:46:22.92897 INFO::Done
2026-04-29 21:46:22.929689 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:22.932671 INFO::ASW Batch was 0.501295339084949 prior to batch effect correction and is now -0.0351784232919696 .
2026-04-29 21:46:22.933272 INFO::ASW Label was 0.52296070159739 prior to batch effect correction and is now 0.916644382237274 .
2026-04-29 21:46:22.934089 INFO::Total function execution time is 0.0336253643035889 s and adjustment time is 0.0177679061889648 s ( 52.84 )
2026-04-29 21:46:22.934917 INFO::Formatting Data.
2026-04-29 21:46:22.935586 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:22.93649 INFO::Removing potential empty rows and columns
2026-04-29 21:46:22.937503 INFO::Found 0 missing values.
2026-04-29 21:46:22.940238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:22.940825 INFO::Done
2026-04-29 21:46:22.941389 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:22.944296 INFO::Starting hierarchical adjustment
2026-04-29 21:46:22.945049 INFO::Found 2 batches.
2026-04-29 21:46:22.945631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:22.946268 INFO::Using default BPPARAM
2026-04-29 21:46:22.946839 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:22.947771 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-29 21:46:22.962581 INFO::Done
2026-04-29 21:46:22.963284 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:22.966274 INFO::ASW Batch was 0.501295339084949 prior to batch effect correction and is now -0.0351784232919696 .
2026-04-29 21:46:22.966897 INFO::ASW Label was 0.52296070159739 prior to batch effect correction and is now 0.916644382237274 .
2026-04-29 21:46:22.967709 INFO::Total function execution time is 0.0328068733215332 s and adjustment time is 0.01766037940979 s ( 53.83 )
2026-04-29 21:46:22.979351 INFO::Formatting Data.
2026-04-29 21:46:22.980174 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:22.981093 INFO::Removing potential empty rows and columns
2026-04-29 21:46:22.98206 INFO::Found 0 missing values.
2026-04-29 21:46:22.984243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:22.984835 INFO::Done
2026-04-29 21:46:22.985397 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:22.987344 INFO::Starting hierarchical adjustment
2026-04-29 21:46:22.988098 INFO::Found 2 batches.
2026-04-29 21:46:22.988684 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:22.989316 INFO::Using default BPPARAM
2026-04-29 21:46:22.989903 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:22.99083 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:46:23.022393 INFO::Done
2026-04-29 21:46:23.023155 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:23.025232 INFO::ASW Batch was 0.0156493388420654 prior to batch effect correction and is now 0.0129480975907955 .
2026-04-29 21:46:23.0261 INFO::Total function execution time is 0.0468087196350098 s and adjustment time is 0.0343976020812988 s ( 73.49 )
2026-04-29 21:46:23.038654 INFO::Formatting Data.
2026-04-29 21:46:23.039515 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:23.040475 INFO::Removing potential empty rows and columns
2026-04-29 21:46:23.041528 INFO::Found 0 missing values.
2026-04-29 21:46:23.042749 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.
2026-04-29 21:46:23.047551 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:23.048133 INFO::Done
2026-04-29 21:46:23.04871 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:23.051725 INFO::Starting hierarchical adjustment
2026-04-29 21:46:23.052474 INFO::Found 2 batches.
2026-04-29 21:46:23.05303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:23.053696 INFO::Using default BPPARAM
2026-04-29 21:46:23.054254 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:23.055214 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:46:23.072089 INFO::Done
2026-04-29 21:46:23.072857 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:23.075924 INFO::ASW Batch was 0.720624223528659 prior to batch effect correction and is now -0.0219906809238279 .
2026-04-29 21:46:23.076564 INFO::ASW Label was 0.288713937004405 prior to batch effect correction and is now 0.80197588239334 .
2026-04-29 21:46:23.077385 INFO::Total function execution time is 0.0388150215148926 s and adjustment time is 0.0197460651397705 s ( 50.87 )
2026-04-29 21:46:23.078212 INFO::Formatting Data.
2026-04-29 21:46:23.078873 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:23.079836 INFO::Removing potential empty rows and columns
2026-04-29 21:46:23.080881 INFO::Found 0 missing values.
2026-04-29 21:46:23.081841 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.
2026-04-29 21:46:23.086608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:23.087219 INFO::Done
2026-04-29 21:46:23.087798 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:23.090909 INFO::Starting hierarchical adjustment
2026-04-29 21:46:23.091669 INFO::Found 2 batches.
2026-04-29 21:46:23.092239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:23.092891 INFO::Using default BPPARAM
2026-04-29 21:46:23.093465 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:23.094446 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:46:23.111461 INFO::Done
2026-04-29 21:46:23.112209 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:23.115348 INFO::ASW Batch was 0.720624223528659 prior to batch effect correction and is now -0.0219906809238279 .
2026-04-29 21:46:23.116013 INFO::ASW Label was 0.288713937004405 prior to batch effect correction and is now 0.80197588239334 .
2026-04-29 21:46:23.116879 INFO::Total function execution time is 0.0386910438537598 s and adjustment time is 0.0198984146118164 s ( 51.43 )
2026-04-29 21:46:23.329229 INFO::Formatting Data.
2026-04-29 21:46:23.330148 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:23.331119 INFO::Removing potential empty rows and columns
2026-04-29 21:46:23.332223 INFO::Found 0 missing values.
2026-04-29 21:46:23.335451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:23.336046 INFO::Done
2026-04-29 21:46:23.336616 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:23.338758 INFO::Starting hierarchical adjustment
2026-04-29 21:46:23.33951 INFO::Found 3 batches.
2026-04-29 21:46:23.340074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:23.34074 INFO::Using default BPPARAM
2026-04-29 21:46:23.341312 INFO::Processing subtree level 1
2026-04-29 21:46:23.430748 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:46:23.432713 INFO::Done
2026-04-29 21:46:23.433478 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:23.436305 INFO::ASW Batch was 0.0278269109133585 prior to batch effect correction and is now 0.0278269109133585 .
2026-04-29 21:46:23.437344 INFO::Total function execution time is 0.108166217803955 s and adjustment time is 0.0933401584625244 s ( 86.29 )
2026-04-29 21:46:23.438498 INFO::Formatting Data.
2026-04-29 21:46:23.439243 INFO::Typecasting input to dataframe.
2026-04-29 21:46:23.440092 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:23.441081 INFO::Removing potential empty rows and columns
2026-04-29 21:46:23.442246 INFO::Found 0 missing values.
2026-04-29 21:46:23.445479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:23.446071 INFO::Done
2026-04-29 21:46:23.446659 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:23.448817 INFO::Starting hierarchical adjustment
2026-04-29 21:46:23.449583 INFO::Found 3 batches.
2026-04-29 21:46:23.450418 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:23.451081 INFO::Using default BPPARAM
2026-04-29 21:46:23.451711 INFO::Processing subtree level 1
2026-04-29 21:46:23.53791 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:46:23.539845 INFO::Done
2026-04-29 21:46:23.540612 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:23.543264 INFO::ASW Batch was 0.0278269109133585 prior to batch effect correction and is now 0.0278269109133585 .
2026-04-29 21:46:23.544336 INFO::Total function execution time is 0.105818748474121 s and adjustment time is 0.0903975963592529 s ( 85.43 )
2026-04-29 21:46:23.558497 INFO::Formatting Data.
2026-04-29 21:46:23.559413 INFO::Typecasting input to dataframe.
2026-04-29 21:46:23.560326 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:23.561323 INFO::Removing potential empty rows and columns
2026-04-29 21:46:23.562507 INFO::Found 0 missing values.
2026-04-29 21:46:23.565815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:23.566411 INFO::Done
2026-04-29 21:46:23.566976 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:23.569113 INFO::Starting hierarchical adjustment
2026-04-29 21:46:23.569874 INFO::Found 3 batches.
2026-04-29 21:46:23.570457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:23.571126 INFO::Using default BPPARAM
2026-04-29 21:46:23.571716 INFO::Processing subtree level 1
2026-04-29 21:46:23.659218 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:46:23.661256 INFO::Done
2026-04-29 21:46:23.662027 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:23.664908 INFO::ASW Batch was -0.11810569860635 prior to batch effect correction and is now -0.11810569860635 .
2026-04-29 21:46:23.665992 INFO::Total function execution time is 0.107555389404297 s and adjustment time is 0.0914986133575439 s ( 85.07 )
2026-04-29 21:46:23.812834 INFO::Formatting Data.
2026-04-29 21:46:23.813856 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:23.815191 INFO::Removing potential empty rows and columns
2026-04-29 21:46:23.818287 INFO::Found 1000 missing values.
2026-04-29 21:46:23.838951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:23.839906 INFO::Done
2026-04-29 21:46:23.840581 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:23.846767 INFO::Starting hierarchical adjustment
2026-04-29 21:46:23.84767 INFO::Found 10 batches.
2026-04-29 21:46:23.84828 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:23.848989 INFO::Using default BPPARAM
2026-04-29 21:46:23.849613 INFO::Processing subtree level 1
2026-04-29 21:46:23.99536 INFO::Processing subtree level 2
2026-04-29 21:46:24.155422 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:46:24.157779 INFO::Done
2026-04-29 21:46:24.158612 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:24.165015 INFO::ASW Batch was 0.463073956902946 prior to batch effect correction and is now 0.463073956902946 .
2026-04-29 21:46:24.165876 INFO::ASW Label was 0.349013508188025 prior to batch effect correction and is now 0.349013508188025 .
2026-04-29 21:46:24.16698 INFO::Total function execution time is 0.354242086410522 s and adjustment time is 0.310290336608887 s ( 87.59 )
2026-04-29 21:46:24.167984 INFO::Formatting Data.
2026-04-29 21:46:24.168739 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:24.170151 INFO::Removing potential empty rows and columns
2026-04-29 21:46:24.173342 INFO::Found 1000 missing values.
2026-04-29 21:46:24.195163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:24.196105 INFO::Done
2026-04-29 21:46:24.196783 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:24.203035 INFO::Starting hierarchical adjustment
2026-04-29 21:46:24.204015 INFO::Found 10 batches.
2026-04-29 21:46:25.654756 INFO::Set up parallel execution backend with 2 workers
2026-04-29 21:46:25.657742 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-29 21:46:27.126424 INFO::Adjusting the last 2 batches sequentially
2026-04-29 21:46:27.129932 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-29 21:46:27.148172 INFO::Done
2026-04-29 21:46:27.149007 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:27.15384 INFO::ASW Batch was 0.463073956902946 prior to batch effect correction and is now 0.463073956902946 .
2026-04-29 21:46:27.154469 INFO::ASW Label was 0.349013508188025 prior to batch effect correction and is now 0.349013508188025 .
2026-04-29 21:46:27.155257 INFO::Total function execution time is 2.98732566833496 s and adjustment time is 2.9443085193634 s ( 98.56 )
2026-04-29 21:46:27.318727 INFO::Formatting Data.
2026-04-29 21:46:27.319854 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.320982 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.32221 INFO::Found 0 missing values.
2026-04-29 21:46:27.326336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.326969 INFO::Done
2026-04-29 21:46:27.327565 INFO::Acquiring quality metrics before batch effect correction.
2026-04-29 21:46:27.330779 INFO::Starting hierarchical adjustment
2026-04-29 21:46:27.33159 INFO::Found 3 batches.
2026-04-29 21:46:27.33219 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-29 21:46:27.332888 INFO::Using default BPPARAM
2026-04-29 21:46:27.333503 INFO::Processing subtree level 1
2026-04-29 21:46:27.447639 INFO::Adjusting the last 1 batches sequentially
2026-04-29 21:46:27.449939 INFO::Done
2026-04-29 21:46:27.450782 INFO::Acquiring quality metrics after batch effect correction.
2026-04-29 21:46:27.454705 INFO::ASW Batch was 0.171293272260995 prior to batch effect correction and is now -0.155915087425636 .
2026-04-29 21:46:27.455487 INFO::ASW Label was -0.160505276454661 prior to batch effect correction and is now 0.0492858796481453 .
2026-04-29 21:46:27.456573 INFO::Total function execution time is 0.137971162796021 s and adjustment time is 0.11849308013916 s ( 85.88 )
2026-04-29 21:46:27.595553 INFO::Formatting Data.
2026-04-29 21:46:27.596642 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.597703 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.598923 INFO::Found 2 missing values.
2026-04-29 21:46:27.602075 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.6027 INFO::Done
2026-04-29 21:46:27.632475 INFO::Found NA in Reference column
2026-04-29 21:46:27.643459 INFO::Require at least two references per batch.
2026-04-29 21:46:27.665999 INFO::Formatting Data.
2026-04-29 21:46:27.666924 INFO::Recognized SummarizedExperiment
2026-04-29 21:46:27.66756 INFO::Typecasting input to dataframe.
2026-04-29 21:46:27.677925 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.67923 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.68305 INFO::Found 0 missing values.
2026-04-29 21:46:27.690207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.69085 INFO::Done
2026-04-29 21:46:27.707226 INFO::Formatting Data.
2026-04-29 21:46:27.708076 INFO::Recognized SummarizedExperiment
2026-04-29 21:46:27.708671 INFO::Typecasting input to dataframe.
2026-04-29 21:46:27.726648 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.728024 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.731766 INFO::Found 0 missing values.
2026-04-29 21:46:27.74289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.743686 INFO::Done
2026-04-29 21:46:27.759556 INFO::Formatting Data.
2026-04-29 21:46:27.760405 INFO::Recognized SummarizedExperiment
2026-04-29 21:46:27.760995 INFO::Typecasting input to dataframe.
2026-04-29 21:46:27.777807 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.778963 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.780057 INFO::Found 0 missing values.
2026-04-29 21:46:27.781015 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.
2026-04-29 21:46:27.785473 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.78606 INFO::Done
2026-04-29 21:46:27.79633 INFO::Formatting Data.
2026-04-29 21:46:27.797222 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.798125 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.799153 INFO::Found 0 missing values.
2026-04-29 21:46:27.802012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.802569 INFO::Done
2026-04-29 21:46:27.81382 INFO::Formatting Data.
2026-04-29 21:46:27.814666 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.815562 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.816578 INFO::Found 0 missing values.
2026-04-29 21:46:27.819448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.82 INFO::Done
2026-04-29 21:46:27.85056 INFO::Formatting Data.
2026-04-29 21:46:27.851509 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.852643 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.85386 INFO::Found 1 missing values.
2026-04-29 21:46:27.856594 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.857165 INFO::Done
2026-04-29 21:46:27.877215 INFO::Formatting Data.
2026-04-29 21:46:27.878187 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.879204 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.880239 INFO::Found 2 missing values.
2026-04-29 21:46:27.881268 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.
2026-04-29 21:46:27.883782 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.88436 INFO::Done
2026-04-29 21:46:27.895035 INFO::Formatting Data.
2026-04-29 21:46:27.895944 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.896931 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.897954 INFO::Found 2 missing values.
2026-04-29 21:46:27.899843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.900581 INFO::Done
2026-04-29 21:46:27.912028 INFO::Formatting Data.
2026-04-29 21:46:27.912944 INFO::Typecasting input to dataframe.
2026-04-29 21:46:27.913823 INFO::Replacing NaNs with NAs.
2026-04-29 21:46:27.914764 INFO::Removing potential empty rows and columns
2026-04-29 21:46:27.915817 INFO::Found 0 missing values.
2026-04-29 21:46:27.918806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-29 21:46:27.919362 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.486 3.618 21.799
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.877 | 1.544 | 20.858 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.000 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.000 | 0.012 | |