Yannis Schumann
| Snapshot Date: 2025-12-04 13:45 -0500 (Thu, 04 Dec 2025) |
| 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 Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-08 12:00 -0500 (Mon, 08 Dec 2025).
| 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" | 4879 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4668 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 2025-12-04 21:37:35 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 21:39:04 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 89.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 24.758 1.821 18.036
* 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")
2025-12-04 21:38:27.645417 INFO::Formatting Data.
2025-12-04 21:38:27.646882 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:27.65952 INFO::Removing potential empty rows and columns
2025-12-04 21:38:27.915027 INFO::Found 0 missing values.
2025-12-04 21:38:27.919058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:27.919759 INFO::Done
2025-12-04 21:38:27.920399 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:27.933609 INFO::Starting hierarchical adjustment
2025-12-04 21:38:27.934532 INFO::Found 3 batches.
2025-12-04 21:38:27.935097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:27.936239 INFO::Using default BPPARAM
2025-12-04 21:38:27.936816 INFO::Processing subtree level 1
2025-12-04 21:38:28.095333 INFO::Adjusting the last 1 batches sequentially
2025-12-04 21:38:28.097287 INFO::Done
2025-12-04 21:38:28.09801 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:28.100804 INFO::ASW Batch was -0.0439998460482552 prior to batch effect correction and is now -0.0439998460482552 .
2025-12-04 21:38:28.101996 INFO::Total function execution time is 0.457328796386719 s and adjustment time is 0.162937641143799 s ( 35.63 )
2025-12-04 21:38:28.117325 INFO::Formatting Data.
2025-12-04 21:38:28.118342 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:28.11942 INFO::Removing potential empty rows and columns
2025-12-04 21:38:28.120718 INFO::Found 0 missing values.
2025-12-04 21:38:28.12173 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.
2025-12-04 21:38:28.133609 INFO::Formatting Data.
2025-12-04 21:38:28.134447 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:28.135375 INFO::Removing potential empty rows and columns
2025-12-04 21:38:28.136469 INFO::Found 0 missing values.
2025-12-04 21:38:28.137431 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.
2025-12-04 21:38:28.154493 INFO::Formatting Data.
2025-12-04 21:38:28.155344 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:28.156316 INFO::Removing potential empty rows and columns
2025-12-04 21:38:28.157403 INFO::Found 0 missing values.
2025-12-04 21:38:28.158378 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.
2025-12-04 21:38:28.163244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:28.163868 INFO::Done
2025-12-04 21:38:28.164427 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:28.166655 INFO::Starting hierarchical adjustment
2025-12-04 21:38:28.167385 INFO::Found 2 batches.
2025-12-04 21:38:28.167914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:28.168556 INFO::Using default BPPARAM
2025-12-04 21:38:28.169093 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:28.170058 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-04 21:38:28.192958 INFO::Done
2025-12-04 21:38:28.19379 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:28.196001 INFO::ASW Batch was -0.0444631748055698 prior to batch effect correction and is now -0.124969197285435 .
2025-12-04 21:38:28.196865 INFO::Total function execution time is 0.0424652099609375 s and adjustment time is 0.0256707668304443 s ( 60.45 )
2025-12-04 21:38:28.19986 INFO::Formatting Data.
2025-12-04 21:38:28.200547 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:28.20982 INFO::Formatting Data.
2025-12-04 21:38:28.210645 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:28.211601 INFO::Removing potential empty rows and columns
2025-12-04 21:38:28.212734 INFO::Found 0 missing values.
2025-12-04 21:38:28.215838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:28.216391 INFO::Done
2025-12-04 21:38:28.216953 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:28.219044 INFO::Starting hierarchical adjustment
2025-12-04 21:38:28.219813 INFO::Found 2 batches.
2025-12-04 21:38:28.220361 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:28.253022 INFO::Using default BPPARAM
2025-12-04 21:38:28.256048 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:28.257144 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-04 21:38:28.272114 INFO::Done
2025-12-04 21:38:28.272834 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:28.274904 INFO::ASW Batch was -0.00304236506718227 prior to batch effect correction and is now -0.0843877429418617 .
2025-12-04 21:38:28.275709 INFO::Total function execution time is 0.0659613609313965 s and adjustment time is 0.0524423122406006 s ( 79.5 )
2025-12-04 21:38:28.276778 INFO::Formatting Data.
2025-12-04 21:38:28.277362 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:28.27819 INFO::Removing potential empty rows and columns
2025-12-04 21:38:28.27918 INFO::Found 0 missing values.
2025-12-04 21:38:28.281932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:28.282448 INFO::Done
2025-12-04 21:38:28.282971 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:28.28501 INFO::Starting hierarchical adjustment
2025-12-04 21:38:28.285707 INFO::Found 2 batches.
2025-12-04 21:38:28.286218 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:28.286804 INFO::Using default BPPARAM
2025-12-04 21:38:28.287314 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:28.288208 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-04 21:38:28.303695 INFO::Done
2025-12-04 21:38:28.304458 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:28.306684 INFO::ASW Batch was -0.00304236506718227 prior to batch effect correction and is now -0.0843877429418617 .
2025-12-04 21:38:28.307487 INFO::Total function execution time is 0.0306942462921143 s and adjustment time is 0.0180938243865967 s ( 58.95 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-04 21:38:31.292313 INFO::Formatting Data.
2025-12-04 21:38:31.293001 INFO::Recognized SummarizedExperiment
2025-12-04 21:38:31.293453 INFO::Typecasting input to dataframe.
2025-12-04 21:38:31.321764 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:31.322998 INFO::Removing potential empty rows and columns
2025-12-04 21:38:31.326956 INFO::Found 0 missing values.
2025-12-04 21:38:31.334272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:31.334896 INFO::Done
2025-12-04 21:38:31.335426 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:31.338989 INFO::Starting hierarchical adjustment
2025-12-04 21:38:31.339702 INFO::Found 2 batches.
2025-12-04 21:38:31.340221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:31.341293 INFO::Using default BPPARAM
2025-12-04 21:38:31.341833 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:31.342777 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-04 21:38:31.398185 INFO::Done
2025-12-04 21:38:31.398903 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:31.402441 INFO::ASW Batch was -0.00299178961638042 prior to batch effect correction and is now -0.0872592221230387 .
2025-12-04 21:38:31.403307 INFO::Total function execution time is 0.111244201660156 s and adjustment time is 0.0586130619049072 s ( 52.69 )
Warning: stack imbalance in '{', 73 then 75
2025-12-04 21:38:31.422082 INFO::Formatting Data.
2025-12-04 21:38:31.422806 INFO::Recognized SummarizedExperiment
2025-12-04 21:38:31.423311 INFO::Typecasting input to dataframe.
2025-12-04 21:38:31.432532 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:31.433605 INFO::Removing potential empty rows and columns
2025-12-04 21:38:31.43724 INFO::Found 0 missing values.
2025-12-04 21:38:31.444212 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:31.444788 INFO::Done
2025-12-04 21:38:31.445299 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:31.448799 INFO::Starting hierarchical adjustment
2025-12-04 21:38:31.449491 INFO::Found 2 batches.
2025-12-04 21:38:31.450007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:31.45059 INFO::Using default BPPARAM
2025-12-04 21:38:31.451101 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:31.45205 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-04 21:38:31.477104 INFO::Done
2025-12-04 21:38:31.47785 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:31.481365 INFO::ASW Batch was -0.00146823759274049 prior to batch effect correction and is now -0.00146823759274049 .
2025-12-04 21:38:31.482211 INFO::Total function execution time is 0.0600957870483398 s and adjustment time is 0.0277197360992432 s ( 46.13 )
2025-12-04 21:38:31.499985 INFO::Formatting Data.
2025-12-04 21:38:31.500761 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:31.501644 INFO::Removing potential empty rows and columns
2025-12-04 21:38:31.502646 INFO::Found 0 missing values.
2025-12-04 21:38:31.505554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:31.506076 INFO::Done
2025-12-04 21:38:31.506592 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:31.50852 INFO::Starting hierarchical adjustment
2025-12-04 21:38:31.509207 INFO::Found 3 batches.
2025-12-04 21:38:31.509731 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:31.510312 INFO::Using default BPPARAM
2025-12-04 21:38:31.510834 INFO::Processing subtree level 1
2025-12-04 21:38:31.643853 INFO::Adjusting the last 1 batches sequentially
2025-12-04 21:38:31.645905 INFO::Done
2025-12-04 21:38:31.646574 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:31.649029 INFO::ASW Batch was -0.0362750263556404 prior to batch effect correction and is now -0.179374761543408 .
2025-12-04 21:38:31.649977 INFO::Total function execution time is 0.150001525878906 s and adjustment time is 0.136802911758423 s ( 91.2 )
2025-12-04 21:38:31.664049 INFO::Skipping initial DF formatting
2025-12-04 21:38:31.664727 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:31.668708 INFO::Starting hierarchical adjustment
2025-12-04 21:38:31.669462 INFO::Found 5 batches.
2025-12-04 21:38:31.670003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:31.670624 INFO::Using default BPPARAM
2025-12-04 21:38:31.671142 INFO::Processing subtree level 1
2025-12-04 21:38:31.932089 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:31.933832 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-04 21:38:31.953577 INFO::Done
2025-12-04 21:38:31.95432 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:31.958719 INFO::ASW Batch was 0.553425052095804 prior to batch effect correction and is now 0.553425052095804 .
2025-12-04 21:38:31.959374 INFO::ASW Label was 0.358673820623236 prior to batch effect correction and is now 0.358673820623236 .
2025-12-04 21:38:31.960243 INFO::Total function execution time is 0.29625391960144 s and adjustment time is 0.284236907958984 s ( 95.94 )
2025-12-04 21:38:32.034689 INFO::Formatting Data.
2025-12-04 21:38:32.03562 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.036702 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.03783 INFO::Found 0 missing values.
2025-12-04 21:38:32.042258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.042873 INFO::Done
2025-12-04 21:38:32.043405 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.046779 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.047541 INFO::Found 5 batches.
2025-12-04 21:38:32.048079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.048745 INFO::Using default BPPARAM
2025-12-04 21:38:32.049284 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.
2025-12-04 21:38:32.206848 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.208878 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-04 21:38:32.22859 INFO::Done
2025-12-04 21:38:32.229439 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:32.234174 INFO::ASW Batch was 0.203602381031252 prior to batch effect correction and is now -0.0800169405733455 .
2025-12-04 21:38:32.235077 INFO::ASW Label was 0.526248381159414 prior to batch effect correction and is now 0.84142111421654 .
2025-12-04 21:38:32.236035 INFO::Total function execution time is 0.201488733291626 s and adjustment time is 0.181186437606812 s ( 89.92 )
2025-12-04 21:38:32.23704 INFO::Formatting Data.
2025-12-04 21:38:32.237753 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.238892 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.240224 INFO::Found 0 missing values.
2025-12-04 21:38:32.245665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.246323 INFO::Done
2025-12-04 21:38:32.246924 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.250587 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.251454 INFO::Found 5 batches.
2025-12-04 21:38:32.252088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.252845 INFO::Using default BPPARAM
2025-12-04 21:38:32.253503 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.
2025-12-04 21:38:32.405229 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.40685 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-04 21:38:32.422323 INFO::Done
2025-12-04 21:38:32.422994 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:32.426119 INFO::ASW Batch was 0.203602381031252 prior to batch effect correction and is now -0.0800169405733455 .
2025-12-04 21:38:32.4267 INFO::ASW Label was 0.526248381159414 prior to batch effect correction and is now 0.84142111421654 .
2025-12-04 21:38:32.427464 INFO::Total function execution time is 0.190467596054077 s and adjustment time is 0.171092748641968 s ( 89.83 )
2025-12-04 21:38:32.440712 INFO::Formatting Data.
2025-12-04 21:38:32.441453 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.442314 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.443291 INFO::Found 0 missing values.
2025-12-04 21:38:32.447239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.447769 INFO::Done
2025-12-04 21:38:32.448259 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.451169 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.451846 INFO::Found 5 batches.
2025-12-04 21:38:32.45236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.452955 INFO::Using default BPPARAM
2025-12-04 21:38:32.453453 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.
2025-12-04 21:38:32.576617 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.578217 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-04 21:38:32.593945 INFO::Done
2025-12-04 21:38:32.594774 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:32.598151 INFO::ASW Batch was 0.264851547337279 prior to batch effect correction and is now -0.0816210729794703 .
2025-12-04 21:38:32.598789 INFO::ASW Label was 0.395029283375327 prior to batch effect correction and is now 0.904404972667495 .
2025-12-04 21:38:32.599602 INFO::Total function execution time is 0.158954381942749 s and adjustment time is 0.142190933227539 s ( 89.45 )
2025-12-04 21:38:32.600443 INFO::Formatting Data.
2025-12-04 21:38:32.601092 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.601994 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.60298 INFO::Found 0 missing values.
2025-12-04 21:38:32.607004 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.607578 INFO::Done
2025-12-04 21:38:32.608096 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.611014 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.611716 INFO::Found 5 batches.
2025-12-04 21:38:32.612239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.612837 INFO::Using default BPPARAM
2025-12-04 21:38:32.613364 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.
2025-12-04 21:38:32.74475 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.746423 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-04 21:38:32.762545 INFO::Done
2025-12-04 21:38:32.763363 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:32.767071 INFO::ASW Batch was 0.264851547337279 prior to batch effect correction and is now -0.0816210729794703 .
2025-12-04 21:38:32.767834 INFO::ASW Label was 0.395029283375327 prior to batch effect correction and is now 0.904404972667495 .
2025-12-04 21:38:32.768807 INFO::Total function execution time is 0.168344259262085 s and adjustment time is 0.15094256401062 s ( 89.66 )
2025-12-04 21:38:32.782823 INFO::Formatting Data.
2025-12-04 21:38:32.783576 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.784484 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.785491 INFO::Found 0 missing values.
2025-12-04 21:38:32.788216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.788758 INFO::Done
2025-12-04 21:38:32.789252 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.792211 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.792922 INFO::Found 2 batches.
2025-12-04 21:38:32.793431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.79405 INFO::Using default BPPARAM
2025-12-04 21:38:32.794585 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.795466 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-04 21:38:32.810233 INFO::Done
2025-12-04 21:38:32.81086 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:32.813768 INFO::ASW Batch was 0.635446918662788 prior to batch effect correction and is now -0.00587922250804379 .
2025-12-04 21:38:32.814333 INFO::ASW Label was 0.425959801282901 prior to batch effect correction and is now 0.905542710802779 .
2025-12-04 21:38:32.815087 INFO::Total function execution time is 0.0323326587677002 s and adjustment time is 0.0174565315246582 s ( 53.99 )
2025-12-04 21:38:32.815858 INFO::Formatting Data.
2025-12-04 21:38:32.816458 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.817316 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.818292 INFO::Found 0 missing values.
2025-12-04 21:38:32.830727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.83172 INFO::Done
2025-12-04 21:38:32.832254 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.835754 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.836524 INFO::Found 2 batches.
2025-12-04 21:38:32.837054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.837713 INFO::Using default BPPARAM
2025-12-04 21:38:32.838227 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.839198 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-04 21:38:32.856406 INFO::Done
2025-12-04 21:38:32.857088 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:32.860414 INFO::ASW Batch was 0.635446918662788 prior to batch effect correction and is now -0.00587922250804379 .
2025-12-04 21:38:32.861098 INFO::ASW Label was 0.425959801282901 prior to batch effect correction and is now 0.905542710802779 .
2025-12-04 21:38:32.861995 INFO::Total function execution time is 0.0461163520812988 s and adjustment time is 0.0200591087341309 s ( 43.5 )
2025-12-04 21:38:32.875926 INFO::Formatting Data.
2025-12-04 21:38:32.876738 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.877684 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.878658 INFO::Found 0 missing values.
2025-12-04 21:38:32.880863 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.881417 INFO::Done
2025-12-04 21:38:32.881952 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.884015 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.884743 INFO::Found 2 batches.
2025-12-04 21:38:32.885276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.885909 INFO::Using default BPPARAM
2025-12-04 21:38:32.886456 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.887398 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-04 21:38:32.919837 INFO::Done
2025-12-04 21:38:32.920553 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:32.9225 INFO::ASW Batch was 0.0582349697149549 prior to batch effect correction and is now -0.0569169230891547 .
2025-12-04 21:38:32.923311 INFO::Total function execution time is 0.0475003719329834 s and adjustment time is 0.0352396965026855 s ( 74.19 )
2025-12-04 21:38:32.935109 INFO::Formatting Data.
2025-12-04 21:38:32.935898 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.936816 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.93786 INFO::Found 0 missing values.
2025-12-04 21:38:32.939108 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.
2025-12-04 21:38:32.943906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.944483 INFO::Done
2025-12-04 21:38:32.94501 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.948247 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.949011 INFO::Found 2 batches.
2025-12-04 21:38:32.949566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.950193 INFO::Using default BPPARAM
2025-12-04 21:38:32.950716 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.951673 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-04 21:38:32.968315 INFO::Done
2025-12-04 21:38:32.96901 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:32.971985 INFO::ASW Batch was 0.648956596942118 prior to batch effect correction and is now -0.00940587515384538 .
2025-12-04 21:38:32.972595 INFO::ASW Label was 0.395499291760348 prior to batch effect correction and is now 0.920887007450527 .
2025-12-04 21:38:32.973385 INFO::Total function execution time is 0.0383541584014893 s and adjustment time is 0.0194485187530518 s ( 50.71 )
2025-12-04 21:38:32.97421 INFO::Formatting Data.
2025-12-04 21:38:32.974834 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:32.975754 INFO::Removing potential empty rows and columns
2025-12-04 21:38:32.976764 INFO::Found 0 missing values.
2025-12-04 21:38:32.977679 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.
2025-12-04 21:38:32.982134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:32.982692 INFO::Done
2025-12-04 21:38:32.983222 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:32.986341 INFO::Starting hierarchical adjustment
2025-12-04 21:38:32.987076 INFO::Found 2 batches.
2025-12-04 21:38:32.987615 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:32.988209 INFO::Using default BPPARAM
2025-12-04 21:38:32.988739 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:32.989662 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-04 21:38:33.006425 INFO::Done
2025-12-04 21:38:33.007093 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:33.010108 INFO::ASW Batch was 0.648956596942118 prior to batch effect correction and is now -0.00940587515384538 .
2025-12-04 21:38:33.010705 INFO::ASW Label was 0.395499291760348 prior to batch effect correction and is now 0.920887007450527 .
2025-12-04 21:38:33.011544 INFO::Total function execution time is 0.0373542308807373 s and adjustment time is 0.0194857120513916 s ( 52.16 )
2025-12-04 21:38:33.211655 INFO::Formatting Data.
2025-12-04 21:38:33.212525 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:33.213494 INFO::Removing potential empty rows and columns
2025-12-04 21:38:33.21457 INFO::Found 0 missing values.
2025-12-04 21:38:33.217574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:33.218118 INFO::Done
2025-12-04 21:38:33.218643 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:33.220682 INFO::Starting hierarchical adjustment
2025-12-04 21:38:33.221386 INFO::Found 3 batches.
2025-12-04 21:38:33.221912 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:33.222503 INFO::Using default BPPARAM
2025-12-04 21:38:33.223032 INFO::Processing subtree level 1
2025-12-04 21:38:33.312229 INFO::Adjusting the last 1 batches sequentially
2025-12-04 21:38:33.314085 INFO::Done
2025-12-04 21:38:33.314794 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:33.317353 INFO::ASW Batch was 0.0596474222088532 prior to batch effect correction and is now 0.0596474222088532 .
2025-12-04 21:38:33.318341 INFO::Total function execution time is 0.106782913208008 s and adjustment time is 0.0928211212158203 s ( 86.93 )
2025-12-04 21:38:33.319462 INFO::Formatting Data.
2025-12-04 21:38:33.32015 INFO::Typecasting input to dataframe.
2025-12-04 21:38:33.320937 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:33.321873 INFO::Removing potential empty rows and columns
2025-12-04 21:38:33.322972 INFO::Found 0 missing values.
2025-12-04 21:38:33.326086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:33.326673 INFO::Done
2025-12-04 21:38:33.327199 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:33.329283 INFO::Starting hierarchical adjustment
2025-12-04 21:38:33.330014 INFO::Found 3 batches.
2025-12-04 21:38:33.330547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:33.331201 INFO::Using default BPPARAM
2025-12-04 21:38:33.331742 INFO::Processing subtree level 1
2025-12-04 21:38:33.420451 INFO::Adjusting the last 1 batches sequentially
2025-12-04 21:38:33.422323 INFO::Done
2025-12-04 21:38:33.423039 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:33.425701 INFO::ASW Batch was 0.0596474222088532 prior to batch effect correction and is now 0.0596474222088532 .
2025-12-04 21:38:33.426703 INFO::Total function execution time is 0.107197523117065 s and adjustment time is 0.0924348831176758 s ( 86.23 )
2025-12-04 21:38:33.440429 INFO::Formatting Data.
2025-12-04 21:38:33.441318 INFO::Typecasting input to dataframe.
2025-12-04 21:38:33.442207 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:33.443252 INFO::Removing potential empty rows and columns
2025-12-04 21:38:33.444384 INFO::Found 0 missing values.
2025-12-04 21:38:33.447533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:33.448088 INFO::Done
2025-12-04 21:38:33.448628 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:33.450721 INFO::Starting hierarchical adjustment
2025-12-04 21:38:33.451444 INFO::Found 3 batches.
2025-12-04 21:38:33.451995 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:33.452647 INFO::Using default BPPARAM
2025-12-04 21:38:33.453187 INFO::Processing subtree level 1
2025-12-04 21:38:33.540761 INFO::Adjusting the last 1 batches sequentially
2025-12-04 21:38:33.542603 INFO::Done
2025-12-04 21:38:33.543295 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:33.545995 INFO::ASW Batch was -0.0822568708668133 prior to batch effect correction and is now -0.0822568708668133 .
2025-12-04 21:38:33.547027 INFO::Total function execution time is 0.106671094894409 s and adjustment time is 0.091285228729248 s ( 85.58 )
2025-12-04 21:38:33.68505 INFO::Formatting Data.
2025-12-04 21:38:33.685864 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:33.686973 INFO::Removing potential empty rows and columns
2025-12-04 21:38:33.689745 INFO::Found 1000 missing values.
2025-12-04 21:38:33.708776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:33.709586 INFO::Done
2025-12-04 21:38:33.710174 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:33.715956 INFO::Starting hierarchical adjustment
2025-12-04 21:38:33.716832 INFO::Found 10 batches.
2025-12-04 21:38:33.717397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:33.718047 INFO::Using default BPPARAM
2025-12-04 21:38:33.718582 INFO::Processing subtree level 1
2025-12-04 21:38:33.849264 INFO::Processing subtree level 2
2025-12-04 21:38:33.981883 INFO::Adjusting the last 1 batches sequentially
2025-12-04 21:38:33.98373 INFO::Done
2025-12-04 21:38:33.984357 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:33.989767 INFO::ASW Batch was 0.456632903760043 prior to batch effect correction and is now 0.456632903760043 .
2025-12-04 21:38:33.990408 INFO::ASW Label was 0.350638318684288 prior to batch effect correction and is now 0.350638318684288 .
2025-12-04 21:38:33.991339 INFO::Total function execution time is 0.306352376937866 s and adjustment time is 0.267077922821045 s ( 87.18 )
2025-12-04 21:38:33.992191 INFO::Formatting Data.
2025-12-04 21:38:33.992832 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:33.994031 INFO::Removing potential empty rows and columns
2025-12-04 21:38:33.996818 INFO::Found 1000 missing values.
2025-12-04 21:38:34.015647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:34.016357 INFO::Done
2025-12-04 21:38:34.016917 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:34.022376 INFO::Starting hierarchical adjustment
2025-12-04 21:38:34.023164 INFO::Found 10 batches.
2025-12-04 21:38:35.068056 INFO::Set up parallel execution backend with 2 workers
2025-12-04 21:38:35.075192 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-04 21:38:36.447844 INFO::Adjusting the last 2 batches sequentially
2025-12-04 21:38:36.449636 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-04 21:38:36.465808 INFO::Done
2025-12-04 21:38:36.466504 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:36.470973 INFO::ASW Batch was 0.456632903760043 prior to batch effect correction and is now 0.456632903760043 .
2025-12-04 21:38:36.471577 INFO::ASW Label was 0.350638318684288 prior to batch effect correction and is now 0.350638318684288 .
2025-12-04 21:38:36.472277 INFO::Total function execution time is 2.48012661933899 s and adjustment time is 2.44278621673584 s ( 98.49 )
2025-12-04 21:38:36.622075 INFO::Formatting Data.
2025-12-04 21:38:36.623079 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:36.624132 INFO::Removing potential empty rows and columns
2025-12-04 21:38:36.625266 INFO::Found 0 missing values.
2025-12-04 21:38:36.629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:36.629563 INFO::Done
2025-12-04 21:38:36.630086 INFO::Acquiring quality metrics before batch effect correction.
2025-12-04 21:38:36.633041 INFO::Starting hierarchical adjustment
2025-12-04 21:38:36.633785 INFO::Found 3 batches.
2025-12-04 21:38:36.63431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-04 21:38:36.634953 INFO::Using default BPPARAM
2025-12-04 21:38:36.635482 INFO::Processing subtree level 1
2025-12-04 21:38:36.745965 INFO::Adjusting the last 1 batches sequentially
2025-12-04 21:38:36.747938 INFO::Done
2025-12-04 21:38:36.748683 INFO::Acquiring quality metrics after batch effect correction.
2025-12-04 21:38:36.752181 INFO::ASW Batch was 0.15878616366253 prior to batch effect correction and is now -0.139133360365159 .
2025-12-04 21:38:36.752836 INFO::ASW Label was -0.199298773420129 prior to batch effect correction and is now -0.0784536810799733 .
2025-12-04 21:38:36.753793 INFO::Total function execution time is 0.131860733032227 s and adjustment time is 0.1142737865448 s ( 86.66 )
2025-12-04 21:38:36.933626 INFO::Formatting Data.
2025-12-04 21:38:36.934688 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:36.935719 INFO::Removing potential empty rows and columns
2025-12-04 21:38:36.936848 INFO::Found 2 missing values.
2025-12-04 21:38:36.939751 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:36.940298 INFO::Done
2025-12-04 21:38:36.967365 INFO::Found NA in Reference column
2025-12-04 21:38:36.976961 INFO::Require at least two references per batch.
2025-12-04 21:38:36.997154 INFO::Formatting Data.
2025-12-04 21:38:36.997905 INFO::Recognized SummarizedExperiment
2025-12-04 21:38:36.998413 INFO::Typecasting input to dataframe.
2025-12-04 21:38:37.007489 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.008619 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.011925 INFO::Found 0 missing values.
2025-12-04 21:38:37.018236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.018862 INFO::Done
2025-12-04 21:38:37.033843 INFO::Formatting Data.
2025-12-04 21:38:37.034576 INFO::Recognized SummarizedExperiment
2025-12-04 21:38:37.035079 INFO::Typecasting input to dataframe.
2025-12-04 21:38:37.051847 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.053027 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.056294 INFO::Found 0 missing values.
2025-12-04 21:38:37.066308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.066967 INFO::Done
2025-12-04 21:38:37.081623 INFO::Formatting Data.
2025-12-04 21:38:37.082359 INFO::Recognized SummarizedExperiment
2025-12-04 21:38:37.082864 INFO::Typecasting input to dataframe.
2025-12-04 21:38:37.09854 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.099555 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.100579 INFO::Found 0 missing values.
2025-12-04 21:38:37.101427 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.
2025-12-04 21:38:37.105459 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.105979 INFO::Done
2025-12-04 21:38:37.115374 INFO::Formatting Data.
2025-12-04 21:38:37.116214 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.117061 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.117998 INFO::Found 0 missing values.
2025-12-04 21:38:37.120661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.121163 INFO::Done
2025-12-04 21:38:37.132068 INFO::Formatting Data.
2025-12-04 21:38:37.132973 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.133804 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.134744 INFO::Found 0 missing values.
2025-12-04 21:38:37.137418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.137931 INFO::Done
2025-12-04 21:38:37.166127 INFO::Formatting Data.
2025-12-04 21:38:37.166974 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.16797 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.16907 INFO::Found 1 missing values.
2025-12-04 21:38:37.171685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.172188 INFO::Done
2025-12-04 21:38:37.190082 INFO::Formatting Data.
2025-12-04 21:38:37.190847 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.191691 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.192577 INFO::Found 2 missing values.
2025-12-04 21:38:37.193422 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.
2025-12-04 21:38:37.19552 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.196024 INFO::Done
2025-12-04 21:38:37.2054 INFO::Formatting Data.
2025-12-04 21:38:37.206168 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.206994 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.207857 INFO::Found 2 missing values.
2025-12-04 21:38:37.209338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.209867 INFO::Done
2025-12-04 21:38:37.219386 INFO::Formatting Data.
2025-12-04 21:38:37.220177 INFO::Typecasting input to dataframe.
2025-12-04 21:38:37.220927 INFO::Replacing NaNs with NAs.
2025-12-04 21:38:37.221735 INFO::Removing potential empty rows and columns
2025-12-04 21:38:37.222665 INFO::Found 0 missing values.
2025-12-04 21:38:37.225275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-04 21:38:37.22578 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.174 3.631 21.423
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.758 | 1.821 | 18.036 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |