Yannis Schumann
| Snapshot Date: 2026-02-27 13:45 -0500 (Fri, 27 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-28 11:57 -0500 (Sat, 28 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-02-27 21:30:45 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 21:32:13 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.125 1.655 18.167
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-27 21:31:36.797062 INFO::Formatting Data.
2026-02-27 21:31:36.798418 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:36.809196 INFO::Removing potential empty rows and columns
2026-02-27 21:31:37.050385 INFO::Found 0 missing values.
2026-02-27 21:31:37.053464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:37.054063 INFO::Done
2026-02-27 21:31:37.054573 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:37.06511 INFO::Starting hierarchical adjustment
2026-02-27 21:31:37.065907 INFO::Found 3 batches.
2026-02-27 21:31:37.066432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:37.067514 INFO::Using default BPPARAM
2026-02-27 21:31:37.06803 INFO::Processing subtree level 1
2026-02-27 21:31:37.163691 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:31:37.165323 INFO::Done
2026-02-27 21:31:37.165933 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:37.168288 INFO::ASW Batch was -0.0536087463066742 prior to batch effect correction and is now -0.0536087463066742 .
2026-02-27 21:31:37.169278 INFO::Total function execution time is 0.372969627380371 s and adjustment time is 0.0995752811431885 s ( 26.7 )
2026-02-27 21:31:37.182264 INFO::Formatting Data.
2026-02-27 21:31:37.182995 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:37.18391 INFO::Removing potential empty rows and columns
2026-02-27 21:31:37.185037 INFO::Found 0 missing values.
2026-02-27 21:31:37.185977 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.
2026-02-27 21:31:37.196491 INFO::Formatting Data.
2026-02-27 21:31:37.197228 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:37.198112 INFO::Removing potential empty rows and columns
2026-02-27 21:31:37.199152 INFO::Found 0 missing values.
2026-02-27 21:31:37.200076 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.
2026-02-27 21:31:37.21563 INFO::Formatting Data.
2026-02-27 21:31:37.21635 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:37.217238 INFO::Removing potential empty rows and columns
2026-02-27 21:31:37.218266 INFO::Found 0 missing values.
2026-02-27 21:31:37.219167 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.
2026-02-27 21:31:37.223463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:37.224007 INFO::Done
2026-02-27 21:31:37.224614 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:37.226503 INFO::Starting hierarchical adjustment
2026-02-27 21:31:37.227183 INFO::Found 2 batches.
2026-02-27 21:31:37.227707 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:37.228311 INFO::Using default BPPARAM
2026-02-27 21:31:37.228826 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:37.229716 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:31:37.250227 INFO::Done
2026-02-27 21:31:37.250918 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:37.253103 INFO::ASW Batch was 0.0658070221196873 prior to batch effect correction and is now -0.115024048797415 .
2026-02-27 21:31:37.253937 INFO::Total function execution time is 0.0383744239807129 s and adjustment time is 0.0231575965881348 s ( 60.35 )
2026-02-27 21:31:37.256787 INFO::Formatting Data.
2026-02-27 21:31:37.257439 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:37.266234 INFO::Formatting Data.
2026-02-27 21:31:37.266951 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:37.26785 INFO::Removing potential empty rows and columns
2026-02-27 21:31:37.268898 INFO::Found 0 missing values.
2026-02-27 21:31:37.271855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:37.272385 INFO::Done
2026-02-27 21:31:37.272918 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:37.30117 INFO::Starting hierarchical adjustment
2026-02-27 21:31:37.302363 INFO::Found 2 batches.
2026-02-27 21:31:37.302881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:37.3034 INFO::Using default BPPARAM
2026-02-27 21:31:37.303882 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:37.304712 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:31:37.318034 INFO::Done
2026-02-27 21:31:37.318612 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:37.320441 INFO::ASW Batch was 0.0174416443032624 prior to batch effect correction and is now -0.113306807141957 .
2026-02-27 21:31:37.321156 INFO::Total function execution time is 0.0549736022949219 s and adjustment time is 0.0158281326293945 s ( 28.79 )
2026-02-27 21:31:37.322118 INFO::Formatting Data.
2026-02-27 21:31:37.32268 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:37.323453 INFO::Removing potential empty rows and columns
2026-02-27 21:31:37.32438 INFO::Found 0 missing values.
2026-02-27 21:31:37.326888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:37.327368 INFO::Done
2026-02-27 21:31:37.327839 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:37.329654 INFO::Starting hierarchical adjustment
2026-02-27 21:31:37.330298 INFO::Found 2 batches.
2026-02-27 21:31:37.330783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:37.331334 INFO::Using default BPPARAM
2026-02-27 21:31:37.331817 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:37.332657 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:31:37.346265 INFO::Done
2026-02-27 21:31:37.346882 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:37.348727 INFO::ASW Batch was 0.0174416443032624 prior to batch effect correction and is now -0.113306807141957 .
2026-02-27 21:31:37.349462 INFO::Total function execution time is 0.0273385047912598 s and adjustment time is 0.016077995300293 s ( 58.81 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-27 21:31:40.124197 INFO::Formatting Data.
2026-02-27 21:31:40.124906 INFO::Recognized SummarizedExperiment
2026-02-27 21:31:40.125369 INFO::Typecasting input to dataframe.
2026-02-27 21:31:40.154379 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:40.155599 INFO::Removing potential empty rows and columns
2026-02-27 21:31:40.159331 INFO::Found 0 missing values.
2026-02-27 21:31:40.166386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:40.167028 INFO::Done
2026-02-27 21:31:40.167553 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:40.171107 INFO::Starting hierarchical adjustment
2026-02-27 21:31:40.171844 INFO::Found 2 batches.
2026-02-27 21:31:40.172361 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:40.173422 INFO::Using default BPPARAM
2026-02-27 21:31:40.173968 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:40.174937 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:31:40.230422 INFO::Done
2026-02-27 21:31:40.231092 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:40.234618 INFO::ASW Batch was -0.00109118118312622 prior to batch effect correction and is now -0.0911134555396762 .
2026-02-27 21:31:40.235419 INFO::Total function execution time is 0.111509561538696 s and adjustment time is 0.0587024688720703 s ( 52.64 )
Warning: stack imbalance in '{', 73 then 75
2026-02-27 21:31:40.253674 INFO::Formatting Data.
2026-02-27 21:31:40.254373 INFO::Recognized SummarizedExperiment
2026-02-27 21:31:40.254913 INFO::Typecasting input to dataframe.
2026-02-27 21:31:40.264068 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:40.265223 INFO::Removing potential empty rows and columns
2026-02-27 21:31:40.268874 INFO::Found 0 missing values.
2026-02-27 21:31:40.275934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:40.276586 INFO::Done
2026-02-27 21:31:40.277109 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:40.280591 INFO::Starting hierarchical adjustment
2026-02-27 21:31:40.28129 INFO::Found 2 batches.
2026-02-27 21:31:40.281816 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:40.282395 INFO::Using default BPPARAM
2026-02-27 21:31:40.282912 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:40.283863 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:31:40.308489 INFO::Done
2026-02-27 21:31:40.309177 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:40.312695 INFO::ASW Batch was 0.0227428935769421 prior to batch effect correction and is now 0.0227428935769421 .
2026-02-27 21:31:40.313534 INFO::Total function execution time is 0.059840202331543 s and adjustment time is 0.0273048877716064 s ( 45.63 )
2026-02-27 21:31:40.33133 INFO::Formatting Data.
2026-02-27 21:31:40.332091 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:40.333091 INFO::Removing potential empty rows and columns
2026-02-27 21:31:40.334097 INFO::Found 0 missing values.
2026-02-27 21:31:40.336969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:40.337495 INFO::Done
2026-02-27 21:31:40.338015 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:40.339928 INFO::Starting hierarchical adjustment
2026-02-27 21:31:40.340618 INFO::Found 3 batches.
2026-02-27 21:31:40.341125 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:40.341712 INFO::Using default BPPARAM
2026-02-27 21:31:40.342223 INFO::Processing subtree level 1
2026-02-27 21:31:40.47538 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:31:40.477124 INFO::Done
2026-02-27 21:31:40.477762 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:40.480157 INFO::ASW Batch was -0.108317804350155 prior to batch effect correction and is now -0.165881654880442 .
2026-02-27 21:31:40.48103 INFO::Total function execution time is 0.149756193161011 s and adjustment time is 0.136636257171631 s ( 91.24 )
2026-02-27 21:31:40.494985 INFO::Skipping initial DF formatting
2026-02-27 21:31:40.495668 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:40.499606 INFO::Starting hierarchical adjustment
2026-02-27 21:31:40.500388 INFO::Found 5 batches.
2026-02-27 21:31:40.500932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:40.501549 INFO::Using default BPPARAM
2026-02-27 21:31:40.502077 INFO::Processing subtree level 1
2026-02-27 21:31:40.736629 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:40.738451 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:31:40.758898 INFO::Done
2026-02-27 21:31:40.75977 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:40.764442 INFO::ASW Batch was 0.532147681925422 prior to batch effect correction and is now 0.532147681925422 .
2026-02-27 21:31:40.765339 INFO::ASW Label was 0.338818659553049 prior to batch effect correction and is now 0.338818659553049 .
2026-02-27 21:31:40.767305 INFO::Total function execution time is 0.272279500961304 s and adjustment time is 0.258626222610474 s ( 94.99 )
2026-02-27 21:31:40.837201 INFO::Formatting Data.
2026-02-27 21:31:40.838015 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:40.83894 INFO::Removing potential empty rows and columns
2026-02-27 21:31:40.839941 INFO::Found 0 missing values.
2026-02-27 21:31:40.843875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:40.844398 INFO::Done
2026-02-27 21:31:40.844914 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:40.847816 INFO::Starting hierarchical adjustment
2026-02-27 21:31:40.848521 INFO::Found 5 batches.
2026-02-27 21:31:40.849019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:40.849622 INFO::Using default BPPARAM
2026-02-27 21:31:40.850126 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.
2026-02-27 21:31:40.981098 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:40.982681 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:31:40.999313 INFO::Done
2026-02-27 21:31:41.000043 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.003488 INFO::ASW Batch was 0.294942375202933 prior to batch effect correction and is now -0.0942782916506454 .
2026-02-27 21:31:41.004144 INFO::ASW Label was 0.406711376676656 prior to batch effect correction and is now 0.926167541027597 .
2026-02-27 21:31:41.005003 INFO::Total function execution time is 0.167900085449219 s and adjustment time is 0.150917053222656 s ( 89.89 )
2026-02-27 21:31:41.005841 INFO::Formatting Data.
2026-02-27 21:31:41.006476 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.007375 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.008427 INFO::Found 0 missing values.
2026-02-27 21:31:41.012951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.013545 INFO::Done
2026-02-27 21:31:41.014066 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.017146 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.017873 INFO::Found 5 batches.
2026-02-27 21:31:41.018415 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.019049 INFO::Using default BPPARAM
2026-02-27 21:31:41.019592 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.
2026-02-27 21:31:41.147817 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:41.149445 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:31:41.167074 INFO::Done
2026-02-27 21:31:41.167959 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.171705 INFO::ASW Batch was 0.294942375202933 prior to batch effect correction and is now -0.0942782916506454 .
2026-02-27 21:31:41.172439 INFO::ASW Label was 0.406711376676656 prior to batch effect correction and is now 0.926167541027597 .
2026-02-27 21:31:41.173352 INFO::Total function execution time is 0.167498350143433 s and adjustment time is 0.149292230606079 s ( 89.13 )
2026-02-27 21:31:41.188125 INFO::Formatting Data.
2026-02-27 21:31:41.188925 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.189944 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.190946 INFO::Found 0 missing values.
2026-02-27 21:31:41.194891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.195415 INFO::Done
2026-02-27 21:31:41.19592 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.198934 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.199662 INFO::Found 5 batches.
2026-02-27 21:31:41.200174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.20079 INFO::Using default BPPARAM
2026-02-27 21:31:41.201301 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.
2026-02-27 21:31:41.322902 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:41.324434 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:31:41.339652 INFO::Done
2026-02-27 21:31:41.34035 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.343545 INFO::ASW Batch was 0.40201939501073 prior to batch effect correction and is now -0.0259781042568454 .
2026-02-27 21:31:41.344135 INFO::ASW Label was 0.361578496942654 prior to batch effect correction and is now 0.78485656676049 .
2026-02-27 21:31:41.344918 INFO::Total function execution time is 0.156869411468506 s and adjustment time is 0.140142679214478 s ( 89.34 )
2026-02-27 21:31:41.345709 INFO::Formatting Data.
2026-02-27 21:31:41.346319 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.347159 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.348127 INFO::Found 0 missing values.
2026-02-27 21:31:41.352017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.352544 INFO::Done
2026-02-27 21:31:41.353052 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.355917 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.356624 INFO::Found 5 batches.
2026-02-27 21:31:41.357131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.357731 INFO::Using default BPPARAM
2026-02-27 21:31:41.358262 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.
2026-02-27 21:31:41.47762 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:41.479199 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:31:41.495424 INFO::Done
2026-02-27 21:31:41.496171 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.499931 INFO::ASW Batch was 0.40201939501073 prior to batch effect correction and is now -0.0259781042568454 .
2026-02-27 21:31:41.500576 INFO::ASW Label was 0.361578496942654 prior to batch effect correction and is now 0.78485656676049 .
2026-02-27 21:31:41.50136 INFO::Total function execution time is 0.155645608901978 s and adjustment time is 0.138884544372559 s ( 89.23 )
2026-02-27 21:31:41.514566 INFO::Formatting Data.
2026-02-27 21:31:41.515321 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.516222 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.517225 INFO::Found 0 missing values.
2026-02-27 21:31:41.519862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.520397 INFO::Done
2026-02-27 21:31:41.520931 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.523899 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.524607 INFO::Found 2 batches.
2026-02-27 21:31:41.525124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.525744 INFO::Using default BPPARAM
2026-02-27 21:31:41.526258 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:41.527145 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:31:41.541459 INFO::Done
2026-02-27 21:31:41.542086 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.545004 INFO::ASW Batch was 0.593166109870879 prior to batch effect correction and is now 0.0252604068987753 .
2026-02-27 21:31:41.545597 INFO::ASW Label was 0.45681468405745 prior to batch effect correction and is now 0.88902742899212 .
2026-02-27 21:31:41.546345 INFO::Total function execution time is 0.0318894386291504 s and adjustment time is 0.0170044898986816 s ( 53.32 )
2026-02-27 21:31:41.547132 INFO::Formatting Data.
2026-02-27 21:31:41.547763 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.54862 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.549567 INFO::Found 0 missing values.
2026-02-27 21:31:41.552152 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.552694 INFO::Done
2026-02-27 21:31:41.55319 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.556067 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.556749 INFO::Found 2 batches.
2026-02-27 21:31:41.557248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.557836 INFO::Using default BPPARAM
2026-02-27 21:31:41.558348 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:41.55923 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 21:31:41.573545 INFO::Done
2026-02-27 21:31:41.574167 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.577167 INFO::ASW Batch was 0.593166109870879 prior to batch effect correction and is now 0.0252604068987753 .
2026-02-27 21:31:41.577777 INFO::ASW Label was 0.45681468405745 prior to batch effect correction and is now 0.88902742899212 .
2026-02-27 21:31:41.578555 INFO::Total function execution time is 0.0314168930053711 s and adjustment time is 0.0169267654418945 s ( 53.88 )
2026-02-27 21:31:41.589702 INFO::Formatting Data.
2026-02-27 21:31:41.590453 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.591354 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.592268 INFO::Found 0 missing values.
2026-02-27 21:31:41.594301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.594838 INFO::Done
2026-02-27 21:31:41.595364 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.597209 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.597914 INFO::Found 2 batches.
2026-02-27 21:31:41.598438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.599043 INFO::Using default BPPARAM
2026-02-27 21:31:41.599598 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:41.600491 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:31:41.630402 INFO::Done
2026-02-27 21:31:41.631061 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.632894 INFO::ASW Batch was 0.0785053592379424 prior to batch effect correction and is now -0.178356187040837 .
2026-02-27 21:31:41.63368 INFO::Total function execution time is 0.0441486835479736 s and adjustment time is 0.0326201915740967 s ( 73.89 )
2026-02-27 21:31:41.644795 INFO::Formatting Data.
2026-02-27 21:31:41.64548 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.646307 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.647243 INFO::Found 0 missing values.
2026-02-27 21:31:41.648425 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.
2026-02-27 21:31:41.652817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.653347 INFO::Done
2026-02-27 21:31:41.653861 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.65666 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.657319 INFO::Found 2 batches.
2026-02-27 21:31:41.657832 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.658394 INFO::Using default BPPARAM
2026-02-27 21:31:41.658894 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:41.65976 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:31:41.67515 INFO::Done
2026-02-27 21:31:41.675793 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.678555 INFO::ASW Batch was 0.469221072262303 prior to batch effect correction and is now -0.0264752339186674 .
2026-02-27 21:31:41.679111 INFO::ASW Label was 0.61175737172732 prior to batch effect correction and is now 0.933911623056115 .
2026-02-27 21:31:41.679868 INFO::Total function execution time is 0.0351357460021973 s and adjustment time is 0.0179557800292969 s ( 51.1 )
2026-02-27 21:31:41.680637 INFO::Formatting Data.
2026-02-27 21:31:41.681228 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.68211 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.683036 INFO::Found 0 missing values.
2026-02-27 21:31:41.683891 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.
2026-02-27 21:31:41.6881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.688629 INFO::Done
2026-02-27 21:31:41.689111 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.691889 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.692567 INFO::Found 2 batches.
2026-02-27 21:31:41.693084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.69368 INFO::Using default BPPARAM
2026-02-27 21:31:41.694186 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:41.695064 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:31:41.710723 INFO::Done
2026-02-27 21:31:41.711369 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:41.714171 INFO::ASW Batch was 0.469221072262303 prior to batch effect correction and is now -0.0264752339186674 .
2026-02-27 21:31:41.714749 INFO::ASW Label was 0.61175737172732 prior to batch effect correction and is now 0.933911623056115 .
2026-02-27 21:31:41.715569 INFO::Total function execution time is 0.0349252223968506 s and adjustment time is 0.0182943344116211 s ( 52.38 )
2026-02-27 21:31:41.917881 INFO::Formatting Data.
2026-02-27 21:31:41.918679 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:41.919577 INFO::Removing potential empty rows and columns
2026-02-27 21:31:41.920683 INFO::Found 0 missing values.
2026-02-27 21:31:41.923679 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:41.924208 INFO::Done
2026-02-27 21:31:41.924726 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:41.926677 INFO::Starting hierarchical adjustment
2026-02-27 21:31:41.927363 INFO::Found 3 batches.
2026-02-27 21:31:41.927894 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:41.928478 INFO::Using default BPPARAM
2026-02-27 21:31:41.929022 INFO::Processing subtree level 1
2026-02-27 21:31:42.012563 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:31:42.014307 INFO::Done
2026-02-27 21:31:42.014971 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:42.01741 INFO::ASW Batch was -0.0374484454354981 prior to batch effect correction and is now -0.0374484454354981 .
2026-02-27 21:31:42.018341 INFO::Total function execution time is 0.100496292114258 s and adjustment time is 0.0870571136474609 s ( 86.63 )
2026-02-27 21:31:42.019383 INFO::Formatting Data.
2026-02-27 21:31:42.020046 INFO::Typecasting input to dataframe.
2026-02-27 21:31:42.020807 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:42.021745 INFO::Removing potential empty rows and columns
2026-02-27 21:31:42.022822 INFO::Found 0 missing values.
2026-02-27 21:31:42.025882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:42.026423 INFO::Done
2026-02-27 21:31:42.026961 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:42.028984 INFO::Starting hierarchical adjustment
2026-02-27 21:31:42.029733 INFO::Found 3 batches.
2026-02-27 21:31:42.030278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:42.030906 INFO::Using default BPPARAM
2026-02-27 21:31:42.031425 INFO::Processing subtree level 1
2026-02-27 21:31:42.114628 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:31:42.116379 INFO::Done
2026-02-27 21:31:42.117086 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:42.119696 INFO::ASW Batch was -0.0374484454354981 prior to batch effect correction and is now -0.0374484454354981 .
2026-02-27 21:31:42.120674 INFO::Total function execution time is 0.101245641708374 s and adjustment time is 0.086775541305542 s ( 85.71 )
2026-02-27 21:31:42.139833 INFO::Formatting Data.
2026-02-27 21:31:42.140759 INFO::Typecasting input to dataframe.
2026-02-27 21:31:42.141656 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:42.142611 INFO::Removing potential empty rows and columns
2026-02-27 21:31:42.143707 INFO::Found 0 missing values.
2026-02-27 21:31:42.146791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:42.147342 INFO::Done
2026-02-27 21:31:42.147893 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:42.149925 INFO::Starting hierarchical adjustment
2026-02-27 21:31:42.150651 INFO::Found 3 batches.
2026-02-27 21:31:42.15117 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:42.151812 INFO::Using default BPPARAM
2026-02-27 21:31:42.152353 INFO::Processing subtree level 1
2026-02-27 21:31:42.236281 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:31:42.238067 INFO::Done
2026-02-27 21:31:42.238707 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:42.241158 INFO::ASW Batch was -0.00201294338633154 prior to batch effect correction and is now -0.00201294338633154 .
2026-02-27 21:31:42.242107 INFO::Total function execution time is 0.102358818054199 s and adjustment time is 0.0875554084777832 s ( 85.54 )
2026-02-27 21:31:42.377575 INFO::Formatting Data.
2026-02-27 21:31:42.378379 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:42.37955 INFO::Removing potential empty rows and columns
2026-02-27 21:31:42.382349 INFO::Found 1000 missing values.
2026-02-27 21:31:42.401729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:42.402477 INFO::Done
2026-02-27 21:31:42.40304 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:42.408551 INFO::Starting hierarchical adjustment
2026-02-27 21:31:42.409553 INFO::Found 10 batches.
2026-02-27 21:31:42.41011 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:42.410738 INFO::Using default BPPARAM
2026-02-27 21:31:42.411276 INFO::Processing subtree level 1
2026-02-27 21:31:42.545009 INFO::Processing subtree level 2
2026-02-27 21:31:42.681106 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:31:42.682966 INFO::Done
2026-02-27 21:31:42.683606 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:42.689045 INFO::ASW Batch was 0.489215104428732 prior to batch effect correction and is now 0.489215104428732 .
2026-02-27 21:31:42.689666 INFO::ASW Label was 0.358773297691514 prior to batch effect correction and is now 0.358773297691513 .
2026-02-27 21:31:42.690562 INFO::Total function execution time is 0.313046216964722 s and adjustment time is 0.273788928985596 s ( 87.46 )
2026-02-27 21:31:42.691479 INFO::Formatting Data.
2026-02-27 21:31:42.692133 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:42.693338 INFO::Removing potential empty rows and columns
2026-02-27 21:31:42.696088 INFO::Found 1000 missing values.
2026-02-27 21:31:42.715077 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:42.7158 INFO::Done
2026-02-27 21:31:42.716352 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:42.721806 INFO::Starting hierarchical adjustment
2026-02-27 21:31:42.72257 INFO::Found 10 batches.
2026-02-27 21:31:43.791931 INFO::Set up parallel execution backend with 2 workers
2026-02-27 21:31:43.794243 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-27 21:31:44.878781 INFO::Adjusting the last 2 batches sequentially
2026-02-27 21:31:44.880393 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 21:31:44.895921 INFO::Done
2026-02-27 21:31:44.896539 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:44.900849 INFO::ASW Batch was 0.489215104428732 prior to batch effect correction and is now 0.489215104428732 .
2026-02-27 21:31:44.901371 INFO::ASW Label was 0.358773297691514 prior to batch effect correction and is now 0.358773297691513 .
2026-02-27 21:31:44.902066 INFO::Total function execution time is 2.21062231063843 s and adjustment time is 2.17349338531494 s ( 98.32 )
2026-02-27 21:31:45.042885 INFO::Formatting Data.
2026-02-27 21:31:45.043645 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.044502 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.045527 INFO::Found 0 missing values.
2026-02-27 21:31:45.048944 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.049449 INFO::Done
2026-02-27 21:31:45.049964 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 21:31:45.052542 INFO::Starting hierarchical adjustment
2026-02-27 21:31:45.05319 INFO::Found 3 batches.
2026-02-27 21:31:45.053694 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 21:31:45.054267 INFO::Using default BPPARAM
2026-02-27 21:31:45.054769 INFO::Processing subtree level 1
2026-02-27 21:31:45.156168 INFO::Adjusting the last 1 batches sequentially
2026-02-27 21:31:45.157969 INFO::Done
2026-02-27 21:31:45.158614 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 21:31:45.161773 INFO::ASW Batch was 0.275617593455408 prior to batch effect correction and is now -0.12602288854965 .
2026-02-27 21:31:45.162377 INFO::ASW Label was -0.205581861288908 prior to batch effect correction and is now -0.0666697039305911 .
2026-02-27 21:31:45.163252 INFO::Total function execution time is 0.120410919189453 s and adjustment time is 0.104887962341309 s ( 87.11 )
2026-02-27 21:31:45.279252 INFO::Formatting Data.
2026-02-27 21:31:45.28007 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.281006 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.28204 INFO::Found 2 missing values.
2026-02-27 21:31:45.284718 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.285225 INFO::Done
2026-02-27 21:31:45.321877 INFO::Found NA in Reference column
2026-02-27 21:31:45.331574 INFO::Require at least two references per batch.
2026-02-27 21:31:45.352682 INFO::Formatting Data.
2026-02-27 21:31:45.353396 INFO::Recognized SummarizedExperiment
2026-02-27 21:31:45.353934 INFO::Typecasting input to dataframe.
2026-02-27 21:31:45.363664 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.36482 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.36846 INFO::Found 0 missing values.
2026-02-27 21:31:45.37541 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.376047 INFO::Done
2026-02-27 21:31:45.392199 INFO::Formatting Data.
2026-02-27 21:31:45.392945 INFO::Recognized SummarizedExperiment
2026-02-27 21:31:45.393491 INFO::Typecasting input to dataframe.
2026-02-27 21:31:45.411397 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.412631 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.416243 INFO::Found 0 missing values.
2026-02-27 21:31:45.427358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.427988 INFO::Done
2026-02-27 21:31:45.443861 INFO::Formatting Data.
2026-02-27 21:31:45.444602 INFO::Recognized SummarizedExperiment
2026-02-27 21:31:45.445141 INFO::Typecasting input to dataframe.
2026-02-27 21:31:45.462096 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.463126 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.464197 INFO::Found 0 missing values.
2026-02-27 21:31:45.465102 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.
2026-02-27 21:31:45.46956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.470101 INFO::Done
2026-02-27 21:31:45.480416 INFO::Formatting Data.
2026-02-27 21:31:45.481252 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.48213 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.483135 INFO::Found 0 missing values.
2026-02-27 21:31:45.486067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.486619 INFO::Done
2026-02-27 21:31:45.498098 INFO::Formatting Data.
2026-02-27 21:31:45.498937 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.499936 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.500968 INFO::Found 0 missing values.
2026-02-27 21:31:45.503774 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.504303 INFO::Done
2026-02-27 21:31:45.533651 INFO::Formatting Data.
2026-02-27 21:31:45.534465 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.535493 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.53666 INFO::Found 1 missing values.
2026-02-27 21:31:45.539268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.539799 INFO::Done
2026-02-27 21:31:45.558864 INFO::Formatting Data.
2026-02-27 21:31:45.559644 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.560519 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.561486 INFO::Found 2 missing values.
2026-02-27 21:31:45.562397 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.
2026-02-27 21:31:45.564653 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.565181 INFO::Done
2026-02-27 21:31:45.574724 INFO::Formatting Data.
2026-02-27 21:31:45.575423 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.57625 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.577146 INFO::Found 2 missing values.
2026-02-27 21:31:45.578748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.579261 INFO::Done
2026-02-27 21:31:45.589751 INFO::Formatting Data.
2026-02-27 21:31:45.590464 INFO::Typecasting input to dataframe.
2026-02-27 21:31:45.591339 INFO::Replacing NaNs with NAs.
2026-02-27 21:31:45.592175 INFO::Removing potential empty rows and columns
2026-02-27 21:31:45.593144 INFO::Found 0 missing values.
2026-02-27 21:31:45.595983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 21:31:45.596496 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.418 3.157 19.334
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.125 | 1.655 | 18.167 | |
| compute_asw | 0.025 | 0.000 | 0.025 | |
| count_existing | 0.010 | 0.004 | 0.015 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |