Yannis Schumann
| Snapshot Date: 2026-02-23 13:40 -0500 (Mon, 23 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 2026-02-24 11:32 -0500 (Tue, 24 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" | 4872 |
| 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: 2026-02-23 21:33:10 -0500 (Mon, 23 Feb 2026) |
| EndedAt: 2026-02-23 21:34:40 -0500 (Mon, 23 Feb 2026) |
| EllapsedTime: 90.1 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 23.451 1.161 16.888
* 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")
2026-02-23 21:34:01.246514 INFO::Formatting Data.
2026-02-23 21:34:01.24781 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:01.258584 INFO::Removing potential empty rows and columns
2026-02-23 21:34:01.504746 INFO::Found 0 missing values.
2026-02-23 21:34:01.508285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:01.508942 INFO::Done
2026-02-23 21:34:01.509508 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:01.521415 INFO::Starting hierarchical adjustment
2026-02-23 21:34:01.522338 INFO::Found 3 batches.
2026-02-23 21:34:01.522933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:01.524184 INFO::Using default BPPARAM
2026-02-23 21:34:01.524761 INFO::Processing subtree level 1
2026-02-23 21:34:01.636318 INFO::Adjusting the last 1 batches sequentially
2026-02-23 21:34:01.638341 INFO::Done
2026-02-23 21:34:01.63911 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:01.641973 INFO::ASW Batch was -0.152599481259809 prior to batch effect correction and is now -0.152599481259809 .
2026-02-23 21:34:01.643182 INFO::Total function execution time is 0.397260665893555 s and adjustment time is 0.116168260574341 s ( 29.24 )
2026-02-23 21:34:01.660963 INFO::Formatting Data.
2026-02-23 21:34:01.661865 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:01.662876 INFO::Removing potential empty rows and columns
2026-02-23 21:34:01.664087 INFO::Found 0 missing values.
2026-02-23 21:34:01.665134 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.
2026-02-23 21:34:01.676981 INFO::Formatting Data.
2026-02-23 21:34:01.677731 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:01.678668 INFO::Removing potential empty rows and columns
2026-02-23 21:34:01.679789 INFO::Found 0 missing values.
2026-02-23 21:34:01.680743 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.
2026-02-23 21:34:01.697457 INFO::Formatting Data.
2026-02-23 21:34:01.698223 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:01.699144 INFO::Removing potential empty rows and columns
2026-02-23 21:34:01.700227 INFO::Found 0 missing values.
2026-02-23 21:34:01.701211 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.
2026-02-23 21:34:01.706017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:01.706621 INFO::Done
2026-02-23 21:34:01.70717 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:01.709445 INFO::Starting hierarchical adjustment
2026-02-23 21:34:01.710196 INFO::Found 2 batches.
2026-02-23 21:34:01.710772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:01.711438 INFO::Using default BPPARAM
2026-02-23 21:34:01.711995 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:01.712958 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-23 21:34:01.736184 INFO::Done
2026-02-23 21:34:01.736993 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:01.73946 INFO::ASW Batch was -0.0553453824936095 prior to batch effect correction and is now -0.128547572080604 .
2026-02-23 21:34:01.740304 INFO::Total function execution time is 0.0429294109344482 s and adjustment time is 0.0260922908782959 s ( 60.78 )
2026-02-23 21:34:01.743491 INFO::Formatting Data.
2026-02-23 21:34:01.744145 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:01.753752 INFO::Formatting Data.
2026-02-23 21:34:01.754589 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:01.755559 INFO::Removing potential empty rows and columns
2026-02-23 21:34:01.756662 INFO::Found 0 missing values.
2026-02-23 21:34:01.759768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:01.760322 INFO::Done
2026-02-23 21:34:01.760886 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:01.763094 INFO::Starting hierarchical adjustment
2026-02-23 21:34:01.763834 INFO::Found 2 batches.
2026-02-23 21:34:01.764396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:01.765044 INFO::Using default BPPARAM
2026-02-23 21:34:01.765614 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:01.766652 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-23 21:34:01.835999 INFO::Done
2026-02-23 21:34:01.836795 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:01.839054 INFO::ASW Batch was 0.0228761025105317 prior to batch effect correction and is now -0.126919040732907 .
2026-02-23 21:34:01.839898 INFO::Total function execution time is 0.0862009525299072 s and adjustment time is 0.072268009185791 s ( 83.84 )
2026-02-23 21:34:01.841031 INFO::Formatting Data.
2026-02-23 21:34:01.841681 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:01.842585 INFO::Removing potential empty rows and columns
2026-02-23 21:34:01.843632 INFO::Found 0 missing values.
2026-02-23 21:34:01.846435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:01.846987 INFO::Done
2026-02-23 21:34:01.847545 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:01.862258 INFO::Starting hierarchical adjustment
2026-02-23 21:34:01.863796 INFO::Found 2 batches.
2026-02-23 21:34:01.864567 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:01.865513 INFO::Using default BPPARAM
2026-02-23 21:34:01.866254 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:01.867727 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-23 21:34:01.89293 INFO::Done
2026-02-23 21:34:01.894199 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:01.897195 INFO::ASW Batch was 0.0228761025105317 prior to batch effect correction and is now -0.126919040732907 .
2026-02-23 21:34:01.89835 INFO::Total function execution time is 0.0572118759155273 s and adjustment time is 0.0294029712677002 s ( 51.39 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-23 21:34:05.452622 INFO::Formatting Data.
2026-02-23 21:34:05.453444 INFO::Recognized SummarizedExperiment
2026-02-23 21:34:05.453953 INFO::Typecasting input to dataframe.
2026-02-23 21:34:05.485982 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:05.487435 INFO::Removing potential empty rows and columns
2026-02-23 21:34:05.491653 INFO::Found 0 missing values.
2026-02-23 21:34:05.499473 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:05.500232 INFO::Done
2026-02-23 21:34:05.500805 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:05.5047 INFO::Starting hierarchical adjustment
2026-02-23 21:34:05.505466 INFO::Found 2 batches.
2026-02-23 21:34:05.506004 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:05.507205 INFO::Using default BPPARAM
2026-02-23 21:34:05.507762 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:05.50883 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-23 21:34:05.568922 INFO::Done
2026-02-23 21:34:05.569839 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:05.573811 INFO::ASW Batch was -0.00531188482622529 prior to batch effect correction and is now -0.0893474636362601 .
2026-02-23 21:34:05.57483 INFO::Total function execution time is 0.122480630874634 s and adjustment time is 0.0635478496551514 s ( 51.88 )
Warning: stack imbalance in '{', 73 then 75
2026-02-23 21:34:05.59509 INFO::Formatting Data.
2026-02-23 21:34:05.59598 INFO::Recognized SummarizedExperiment
2026-02-23 21:34:05.596582 INFO::Typecasting input to dataframe.
2026-02-23 21:34:05.606552 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:05.607923 INFO::Removing potential empty rows and columns
2026-02-23 21:34:05.612013 INFO::Found 0 missing values.
2026-02-23 21:34:05.619971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:05.620771 INFO::Done
2026-02-23 21:34:05.621375 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:05.625252 INFO::Starting hierarchical adjustment
2026-02-23 21:34:05.626084 INFO::Found 2 batches.
2026-02-23 21:34:05.626649 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:05.627297 INFO::Using default BPPARAM
2026-02-23 21:34:05.627846 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:05.628896 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-23 21:34:05.656024 INFO::Done
2026-02-23 21:34:05.656875 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:05.660698 INFO::ASW Batch was 0.00707842291057027 prior to batch effect correction and is now 0.00707842291057027 .
2026-02-23 21:34:05.661672 INFO::Total function execution time is 0.0665667057037354 s and adjustment time is 0.0300562381744385 s ( 45.15 )
2026-02-23 21:34:05.681618 INFO::Formatting Data.
2026-02-23 21:34:05.68255 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:05.683547 INFO::Removing potential empty rows and columns
2026-02-23 21:34:05.684626 INFO::Found 0 missing values.
2026-02-23 21:34:05.687697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:05.688249 INFO::Done
2026-02-23 21:34:05.688776 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:05.690965 INFO::Starting hierarchical adjustment
2026-02-23 21:34:05.691686 INFO::Found 3 batches.
2026-02-23 21:34:05.692215 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:05.692823 INFO::Using default BPPARAM
2026-02-23 21:34:05.693354 INFO::Processing subtree level 1
2026-02-23 21:34:05.839348 INFO::Adjusting the last 1 batches sequentially
2026-02-23 21:34:05.841302 INFO::Done
2026-02-23 21:34:05.842034 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:05.844677 INFO::ASW Batch was -0.0606777896855534 prior to batch effect correction and is now -0.172689140957793 .
2026-02-23 21:34:05.845716 INFO::Total function execution time is 0.164196968078613 s and adjustment time is 0.149746417999268 s ( 91.2 )
2026-02-23 21:34:05.861005 INFO::Skipping initial DF formatting
2026-02-23 21:34:05.861828 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:05.866066 INFO::Starting hierarchical adjustment
2026-02-23 21:34:05.866965 INFO::Found 5 batches.
2026-02-23 21:34:05.867554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:05.868195 INFO::Using default BPPARAM
2026-02-23 21:34:05.868745 INFO::Processing subtree level 1
2026-02-23 21:34:06.115529 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:06.117482 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-23 21:34:06.138673 INFO::Done
2026-02-23 21:34:06.139604 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:06.144472 INFO::ASW Batch was 0.553505696653052 prior to batch effect correction and is now 0.553505696653052 .
2026-02-23 21:34:06.145144 INFO::ASW Label was 0.322952543867588 prior to batch effect correction and is now 0.322952543867588 .
2026-02-23 21:34:06.202099 INFO::Total function execution time is 0.341110467910767 s and adjustment time is 0.27182674407959 s ( 79.69 )
2026-02-23 21:34:06.222322 INFO::Formatting Data.
2026-02-23 21:34:06.223194 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:06.224164 INFO::Removing potential empty rows and columns
2026-02-23 21:34:06.225213 INFO::Found 0 missing values.
2026-02-23 21:34:06.229645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:06.230302 INFO::Done
2026-02-23 21:34:06.230937 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:06.234243 INFO::Starting hierarchical adjustment
2026-02-23 21:34:06.235027 INFO::Found 5 batches.
2026-02-23 21:34:06.2356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:06.236303 INFO::Using default BPPARAM
2026-02-23 21:34:06.236885 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.
2026-02-23 21:34:06.383483 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:06.385298 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-23 21:34:06.404464 INFO::Done
2026-02-23 21:34:06.405372 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:06.40958 INFO::ASW Batch was 0.339879194754054 prior to batch effect correction and is now -0.0235520231371431 .
2026-02-23 21:34:06.410345 INFO::ASW Label was 0.410746864998819 prior to batch effect correction and is now 0.764453388544646 .
2026-02-23 21:34:06.41133 INFO::Total function execution time is 0.189087390899658 s and adjustment time is 0.169497489929199 s ( 89.64 )
2026-02-23 21:34:06.412306 INFO::Formatting Data.
2026-02-23 21:34:06.413014 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:06.414047 INFO::Removing potential empty rows and columns
2026-02-23 21:34:06.415346 INFO::Found 0 missing values.
2026-02-23 21:34:06.420079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:06.420727 INFO::Done
2026-02-23 21:34:06.421323 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:06.424912 INFO::Starting hierarchical adjustment
2026-02-23 21:34:06.425713 INFO::Found 5 batches.
2026-02-23 21:34:06.426297 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:06.427099 INFO::Using default BPPARAM
2026-02-23 21:34:06.427699 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.
2026-02-23 21:34:06.557774 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:06.559553 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-23 21:34:06.576499 INFO::Done
2026-02-23 21:34:06.57725 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:06.580693 INFO::ASW Batch was 0.339879194754054 prior to batch effect correction and is now -0.0235520231371431 .
2026-02-23 21:34:06.581328 INFO::ASW Label was 0.410746864998819 prior to batch effect correction and is now 0.764453388544646 .
2026-02-23 21:34:06.582208 INFO::Total function execution time is 0.169920206069946 s and adjustment time is 0.150887489318848 s ( 88.8 )
2026-02-23 21:34:06.596634 INFO::Formatting Data.
2026-02-23 21:34:06.597485 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:06.598456 INFO::Removing potential empty rows and columns
2026-02-23 21:34:06.599509 INFO::Found 0 missing values.
2026-02-23 21:34:06.603744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:06.604322 INFO::Done
2026-02-23 21:34:06.604843 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:06.607951 INFO::Starting hierarchical adjustment
2026-02-23 21:34:06.608688 INFO::Found 5 batches.
2026-02-23 21:34:06.609216 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:06.609835 INFO::Using default BPPARAM
2026-02-23 21:34:06.610394 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.
2026-02-23 21:34:06.743834 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:06.745548 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-23 21:34:06.762076 INFO::Done
2026-02-23 21:34:06.762898 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:06.766536 INFO::ASW Batch was 0.410416128025161 prior to batch effect correction and is now -0.0930896248056144 .
2026-02-23 21:34:06.76722 INFO::ASW Label was 0.210699080736954 prior to batch effect correction and is now 0.825469109841978 .
2026-02-23 21:34:06.768132 INFO::Total function execution time is 0.171610593795776 s and adjustment time is 0.15349292755127 s ( 89.44 )
2026-02-23 21:34:06.769043 INFO::Formatting Data.
2026-02-23 21:34:06.769751 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:06.770698 INFO::Removing potential empty rows and columns
2026-02-23 21:34:06.771778 INFO::Found 0 missing values.
2026-02-23 21:34:06.77613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:06.776749 INFO::Done
2026-02-23 21:34:06.77734 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:06.78093 INFO::Starting hierarchical adjustment
2026-02-23 21:34:06.781695 INFO::Found 5 batches.
2026-02-23 21:34:06.782296 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:06.782993 INFO::Using default BPPARAM
2026-02-23 21:34:06.783571 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.
2026-02-23 21:34:06.918982 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:06.920706 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-23 21:34:06.93895 INFO::Done
2026-02-23 21:34:06.939837 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:06.943611 INFO::ASW Batch was 0.410416128025161 prior to batch effect correction and is now -0.0930896248056144 .
2026-02-23 21:34:06.944387 INFO::ASW Label was 0.210699080736954 prior to batch effect correction and is now 0.825469109841978 .
2026-02-23 21:34:06.945654 INFO::Total function execution time is 0.176522970199585 s and adjustment time is 0.157344102859497 s ( 89.14 )
2026-02-23 21:34:06.960806 INFO::Formatting Data.
2026-02-23 21:34:06.961714 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:06.962749 INFO::Removing potential empty rows and columns
2026-02-23 21:34:06.963827 INFO::Found 0 missing values.
2026-02-23 21:34:06.966773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:06.967419 INFO::Done
2026-02-23 21:34:06.967993 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:06.971318 INFO::Starting hierarchical adjustment
2026-02-23 21:34:06.972138 INFO::Found 2 batches.
2026-02-23 21:34:06.972722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:06.973437 INFO::Using default BPPARAM
2026-02-23 21:34:06.974047 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:06.975067 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-23 21:34:06.990592 INFO::Done
2026-02-23 21:34:06.991362 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:06.994459 INFO::ASW Batch was 0.359736573980678 prior to batch effect correction and is now -0.0232455952261908 .
2026-02-23 21:34:06.995129 INFO::ASW Label was 0.697609244175854 prior to batch effect correction and is now 0.945845791562141 .
2026-02-23 21:34:06.995947 INFO::Total function execution time is 0.0353004932403564 s and adjustment time is 0.0185854434967041 s ( 52.65 )
2026-02-23 21:34:06.996741 INFO::Formatting Data.
2026-02-23 21:34:06.997347 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:06.99824 INFO::Removing potential empty rows and columns
2026-02-23 21:34:06.999246 INFO::Found 0 missing values.
2026-02-23 21:34:07.002052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:07.002611 INFO::Done
2026-02-23 21:34:07.003124 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:07.006101 INFO::Starting hierarchical adjustment
2026-02-23 21:34:07.006828 INFO::Found 2 batches.
2026-02-23 21:34:07.007364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:07.007983 INFO::Using default BPPARAM
2026-02-23 21:34:07.008542 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:07.009488 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-23 21:34:07.024883 INFO::Done
2026-02-23 21:34:07.025671 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:07.028813 INFO::ASW Batch was 0.359736573980678 prior to batch effect correction and is now -0.0232455952261908 .
2026-02-23 21:34:07.029541 INFO::ASW Label was 0.697609244175854 prior to batch effect correction and is now 0.945845791562141 .
2026-02-23 21:34:07.030398 INFO::Total function execution time is 0.0336425304412842 s and adjustment time is 0.0181479454040527 s ( 53.94 )
2026-02-23 21:34:07.042834 INFO::Formatting Data.
2026-02-23 21:34:07.043752 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:07.044762 INFO::Removing potential empty rows and columns
2026-02-23 21:34:07.045749 INFO::Found 0 missing values.
2026-02-23 21:34:07.04798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:07.048569 INFO::Done
2026-02-23 21:34:07.0491 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:07.051081 INFO::Starting hierarchical adjustment
2026-02-23 21:34:07.051774 INFO::Found 2 batches.
2026-02-23 21:34:07.052284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:07.052884 INFO::Using default BPPARAM
2026-02-23 21:34:07.053426 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:07.054319 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-23 21:34:07.087744 INFO::Done
2026-02-23 21:34:07.088585 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:07.090787 INFO::ASW Batch was 0.248011839451699 prior to batch effect correction and is now -0.119902667545287 .
2026-02-23 21:34:07.091666 INFO::Total function execution time is 0.048961877822876 s and adjustment time is 0.0360462665557861 s ( 73.62 )
2026-02-23 21:34:07.104345 INFO::Formatting Data.
2026-02-23 21:34:07.10516 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:07.106122 INFO::Removing potential empty rows and columns
2026-02-23 21:34:07.107189 INFO::Found 0 missing values.
2026-02-23 21:34:07.108426 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.
2026-02-23 21:34:07.113217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:07.113827 INFO::Done
2026-02-23 21:34:07.114406 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:07.117517 INFO::Starting hierarchical adjustment
2026-02-23 21:34:07.118251 INFO::Found 2 batches.
2026-02-23 21:34:07.118819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:07.1195 INFO::Using default BPPARAM
2026-02-23 21:34:07.120075 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:07.121052 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-23 21:34:07.138428 INFO::Done
2026-02-23 21:34:07.139199 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:07.142409 INFO::ASW Batch was 0.213164351050699 prior to batch effect correction and is now -0.0285747841484965 .
2026-02-23 21:34:07.143052 INFO::ASW Label was 0.779648349124533 prior to batch effect correction and is now 0.922559567994463 .
2026-02-23 21:34:07.143918 INFO::Total function execution time is 0.0396466255187988 s and adjustment time is 0.0202775001525879 s ( 51.15 )
2026-02-23 21:34:07.14477 INFO::Formatting Data.
2026-02-23 21:34:07.145449 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:07.146423 INFO::Removing potential empty rows and columns
2026-02-23 21:34:07.147455 INFO::Found 0 missing values.
2026-02-23 21:34:07.148418 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.
2026-02-23 21:34:07.153195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:07.153796 INFO::Done
2026-02-23 21:34:07.154351 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:07.157509 INFO::Starting hierarchical adjustment
2026-02-23 21:34:07.158251 INFO::Found 2 batches.
2026-02-23 21:34:07.158856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:07.159522 INFO::Using default BPPARAM
2026-02-23 21:34:07.160091 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:07.161075 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-23 21:34:07.178532 INFO::Done
2026-02-23 21:34:07.179281 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:07.182449 INFO::ASW Batch was 0.213164351050699 prior to batch effect correction and is now -0.0285747841484965 .
2026-02-23 21:34:07.183099 INFO::ASW Label was 0.779648349124533 prior to batch effect correction and is now 0.922559567994463 .
2026-02-23 21:34:07.183955 INFO::Total function execution time is 0.039193868637085 s and adjustment time is 0.0204033851623535 s ( 52.06 )
2026-02-23 21:34:07.389231 INFO::Formatting Data.
2026-02-23 21:34:07.390088 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:07.391053 INFO::Removing potential empty rows and columns
2026-02-23 21:34:07.392202 INFO::Found 0 missing values.
2026-02-23 21:34:07.395292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:07.395845 INFO::Done
2026-02-23 21:34:07.396392 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:07.398552 INFO::Starting hierarchical adjustment
2026-02-23 21:34:07.399266 INFO::Found 3 batches.
2026-02-23 21:34:07.399819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:07.400499 INFO::Using default BPPARAM
2026-02-23 21:34:07.401035 INFO::Processing subtree level 1
2026-02-23 21:34:07.493922 INFO::Adjusting the last 1 batches sequentially
2026-02-23 21:34:07.495812 INFO::Done
2026-02-23 21:34:07.496516 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:07.499053 INFO::ASW Batch was -0.0541197180687549 prior to batch effect correction and is now -0.0541197180687549 .
2026-02-23 21:34:07.500056 INFO::Total function execution time is 0.110904693603516 s and adjustment time is 0.0966734886169434 s ( 87.17 )
2026-02-23 21:34:07.501129 INFO::Formatting Data.
2026-02-23 21:34:07.501812 INFO::Typecasting input to dataframe.
2026-02-23 21:34:07.502616 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:07.503574 INFO::Removing potential empty rows and columns
2026-02-23 21:34:07.504725 INFO::Found 0 missing values.
2026-02-23 21:34:07.507887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:07.508494 INFO::Done
2026-02-23 21:34:07.509044 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:07.511137 INFO::Starting hierarchical adjustment
2026-02-23 21:34:07.511908 INFO::Found 3 batches.
2026-02-23 21:34:07.51247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:07.513112 INFO::Using default BPPARAM
2026-02-23 21:34:07.513701 INFO::Processing subtree level 1
2026-02-23 21:34:07.604506 INFO::Adjusting the last 1 batches sequentially
2026-02-23 21:34:07.606496 INFO::Done
2026-02-23 21:34:07.607228 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:07.609934 INFO::ASW Batch was -0.0541197180687549 prior to batch effect correction and is now -0.0541197180687549 .
2026-02-23 21:34:07.610975 INFO::Total function execution time is 0.109811782836914 s and adjustment time is 0.0947167873382568 s ( 86.25 )
2026-02-23 21:34:07.625145 INFO::Formatting Data.
2026-02-23 21:34:07.626038 INFO::Typecasting input to dataframe.
2026-02-23 21:34:07.626971 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:07.627951 INFO::Removing potential empty rows and columns
2026-02-23 21:34:07.629075 INFO::Found 0 missing values.
2026-02-23 21:34:07.632242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:07.632813 INFO::Done
2026-02-23 21:34:07.633345 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:07.635505 INFO::Starting hierarchical adjustment
2026-02-23 21:34:07.636218 INFO::Found 3 batches.
2026-02-23 21:34:07.636776 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:07.637413 INFO::Using default BPPARAM
2026-02-23 21:34:07.637967 INFO::Processing subtree level 1
2026-02-23 21:34:07.728126 INFO::Adjusting the last 1 batches sequentially
2026-02-23 21:34:07.730332 INFO::Done
2026-02-23 21:34:07.731102 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:07.733874 INFO::ASW Batch was -0.0980255143776566 prior to batch effect correction and is now -0.0980255143776566 .
2026-02-23 21:34:07.734939 INFO::Total function execution time is 0.109878301620483 s and adjustment time is 0.0942192077636719 s ( 85.75 )
2026-02-23 21:34:07.875869 INFO::Formatting Data.
2026-02-23 21:34:07.876793 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:07.878037 INFO::Removing potential empty rows and columns
2026-02-23 21:34:07.880987 INFO::Found 1000 missing values.
2026-02-23 21:34:07.9123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:07.913348 INFO::Done
2026-02-23 21:34:07.914017 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:07.920298 INFO::Starting hierarchical adjustment
2026-02-23 21:34:07.921193 INFO::Found 10 batches.
2026-02-23 21:34:07.921797 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:07.922689 INFO::Using default BPPARAM
2026-02-23 21:34:07.923256 INFO::Processing subtree level 1
2026-02-23 21:34:08.069345 INFO::Processing subtree level 2
2026-02-23 21:34:08.221896 INFO::Adjusting the last 1 batches sequentially
2026-02-23 21:34:08.224192 INFO::Done
2026-02-23 21:34:08.224966 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:08.230932 INFO::ASW Batch was 0.502660773294007 prior to batch effect correction and is now 0.502660773294007 .
2026-02-23 21:34:08.231679 INFO::ASW Label was 0.336604789212729 prior to batch effect correction and is now 0.336604789212729 .
2026-02-23 21:34:08.232768 INFO::Total function execution time is 0.356955289840698 s and adjustment time is 0.303185701370239 s ( 84.94 )
2026-02-23 21:34:08.233794 INFO::Formatting Data.
2026-02-23 21:34:08.234483 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:08.235838 INFO::Removing potential empty rows and columns
2026-02-23 21:34:08.238918 INFO::Found 1000 missing values.
2026-02-23 21:34:08.259464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:08.260307 INFO::Done
2026-02-23 21:34:08.260938 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:08.266664 INFO::Starting hierarchical adjustment
2026-02-23 21:34:08.267493 INFO::Found 10 batches.
2026-02-23 21:34:09.666217 INFO::Set up parallel execution backend with 2 workers
2026-02-23 21:34:09.668782 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-23 21:34:10.911963 INFO::Adjusting the last 2 batches sequentially
2026-02-23 21:34:10.913792 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-23 21:34:10.930528 INFO::Done
2026-02-23 21:34:10.931203 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:10.935839 INFO::ASW Batch was 0.502660773294007 prior to batch effect correction and is now 0.502660773294007 .
2026-02-23 21:34:10.936479 INFO::ASW Label was 0.336604789212729 prior to batch effect correction and is now 0.336604789212729 .
2026-02-23 21:34:10.937226 INFO::Total function execution time is 2.70347380638123 s and adjustment time is 2.66319179534912 s ( 98.51 )
2026-02-23 21:34:11.082967 INFO::Formatting Data.
2026-02-23 21:34:11.083754 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.084648 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.085687 INFO::Found 0 missing values.
2026-02-23 21:34:11.08922 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.089769 INFO::Done
2026-02-23 21:34:11.090267 INFO::Acquiring quality metrics before batch effect correction.
2026-02-23 21:34:11.092916 INFO::Starting hierarchical adjustment
2026-02-23 21:34:11.09361 INFO::Found 3 batches.
2026-02-23 21:34:11.094118 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-23 21:34:11.094751 INFO::Using default BPPARAM
2026-02-23 21:34:11.095261 INFO::Processing subtree level 1
2026-02-23 21:34:11.199959 INFO::Adjusting the last 1 batches sequentially
2026-02-23 21:34:11.201765 INFO::Done
2026-02-23 21:34:11.202404 INFO::Acquiring quality metrics after batch effect correction.
2026-02-23 21:34:11.205502 INFO::ASW Batch was 0.189309926652352 prior to batch effect correction and is now -0.138987195425714 .
2026-02-23 21:34:11.206134 INFO::ASW Label was -0.195998677566852 prior to batch effect correction and is now -0.172532393874978 .
2026-02-23 21:34:11.207052 INFO::Total function execution time is 0.124154567718506 s and adjustment time is 0.108267545700073 s ( 87.2 )
2026-02-23 21:34:11.328195 INFO::Formatting Data.
2026-02-23 21:34:11.329036 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.329943 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.330976 INFO::Found 2 missing values.
2026-02-23 21:34:11.333743 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.334285 INFO::Done
2026-02-23 21:34:11.360647 INFO::Found NA in Reference column
2026-02-23 21:34:11.369625 INFO::Require at least two references per batch.
2026-02-23 21:34:11.389026 INFO::Formatting Data.
2026-02-23 21:34:11.389798 INFO::Recognized SummarizedExperiment
2026-02-23 21:34:11.390344 INFO::Typecasting input to dataframe.
2026-02-23 21:34:11.39973 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.400936 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.404477 INFO::Found 0 missing values.
2026-02-23 21:34:11.411183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.411794 INFO::Done
2026-02-23 21:34:11.426545 INFO::Formatting Data.
2026-02-23 21:34:11.427246 INFO::Recognized SummarizedExperiment
2026-02-23 21:34:11.427771 INFO::Typecasting input to dataframe.
2026-02-23 21:34:11.44386 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.44508 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.448649 INFO::Found 0 missing values.
2026-02-23 21:34:11.459411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.460097 INFO::Done
2026-02-23 21:34:11.474904 INFO::Formatting Data.
2026-02-23 21:34:11.475675 INFO::Recognized SummarizedExperiment
2026-02-23 21:34:11.476194 INFO::Typecasting input to dataframe.
2026-02-23 21:34:11.491913 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.492996 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.49406 INFO::Found 0 missing values.
2026-02-23 21:34:11.494959 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.
2026-02-23 21:34:11.499153 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.499718 INFO::Done
2026-02-23 21:34:11.5094 INFO::Formatting Data.
2026-02-23 21:34:11.510147 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.510999 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.511984 INFO::Found 0 missing values.
2026-02-23 21:34:11.514777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.515293 INFO::Done
2026-02-23 21:34:11.526877 INFO::Formatting Data.
2026-02-23 21:34:11.527702 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.528617 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.529642 INFO::Found 0 missing values.
2026-02-23 21:34:11.532555 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.533073 INFO::Done
2026-02-23 21:34:11.563542 INFO::Formatting Data.
2026-02-23 21:34:11.564399 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.565416 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.566548 INFO::Found 1 missing values.
2026-02-23 21:34:11.569069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.569624 INFO::Done
2026-02-23 21:34:11.588322 INFO::Formatting Data.
2026-02-23 21:34:11.589147 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.590055 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.590995 INFO::Found 2 missing values.
2026-02-23 21:34:11.59192 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.
2026-02-23 21:34:11.594329 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.594875 INFO::Done
2026-02-23 21:34:11.604709 INFO::Formatting Data.
2026-02-23 21:34:11.605509 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.606381 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.607263 INFO::Found 2 missing values.
2026-02-23 21:34:11.608792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.609334 INFO::Done
2026-02-23 21:34:11.619421 INFO::Formatting Data.
2026-02-23 21:34:11.620187 INFO::Typecasting input to dataframe.
2026-02-23 21:34:11.620982 INFO::Replacing NaNs with NAs.
2026-02-23 21:34:11.62183 INFO::Removing potential empty rows and columns
2026-02-23 21:34:11.622806 INFO::Found 0 missing values.
2026-02-23 21:34:11.625651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-23 21:34:11.626211 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.990 4.524 21.196
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.451 | 1.161 | 16.888 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |