Yannis Schumann
| Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-20 12:04 -0400 (Mon, 20 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 165/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | 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: 1.5.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-10-19 20:31:04 -0400 (Sun, 19 Oct 2025) |
| EndedAt: 2025-10-19 20:32:37 -0400 (Sun, 19 Oct 2025) |
| EllapsedTime: 92.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* 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 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 27.981 1.676 20.139
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
2025-10-19 20:32:10.641794 INFO::Formatting Data.
2025-10-19 20:32:10.646058 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:10.662263 INFO::Removing potential empty rows and columns
2025-10-19 20:32:10.950238 INFO::Found 0 missing values.
2025-10-19 20:32:10.954639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:10.955745 INFO::Done
2025-10-19 20:32:10.956726 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:10.972092 INFO::Starting hierarchical adjustment
2025-10-19 20:32:10.973096 INFO::Found 3 batches.
2025-10-19 20:32:10.974134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:10.975866 INFO::Using default BPPARAM
2025-10-19 20:32:10.976711 INFO::Processing subtree level 1
2025-10-19 20:32:11.139921 INFO::Adjusting the last 1 batches sequentially
2025-10-19 20:32:11.147021 INFO::Done
2025-10-19 20:32:11.147864 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:11.156089 INFO::ASW Batch was -0.073781880257147 prior to batch effect correction and is now -0.073781880257147 .
2025-10-19 20:32:11.159071 INFO::Total function execution time is 0.517103910446167 s and adjustment time is 0.174100875854492 s ( 33.67 )
2025-10-19 20:32:11.180207 INFO::Formatting Data.
2025-10-19 20:32:11.181003 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:11.181916 INFO::Removing potential empty rows and columns
2025-10-19 20:32:11.182998 INFO::Found 0 missing values.
2025-10-19 20:32:11.184484 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.
2025-10-19 20:32:11.198784 INFO::Formatting Data.
2025-10-19 20:32:11.199608 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:11.20058 INFO::Removing potential empty rows and columns
2025-10-19 20:32:11.202144 INFO::Found 0 missing values.
2025-10-19 20:32:11.203599 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.
2025-10-19 20:32:11.225024 INFO::Formatting Data.
2025-10-19 20:32:11.225937 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:11.226837 INFO::Removing potential empty rows and columns
2025-10-19 20:32:11.228014 INFO::Found 0 missing values.
2025-10-19 20:32:11.229057 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.
2025-10-19 20:32:11.233437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:11.234193 INFO::Done
2025-10-19 20:32:11.235365 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:11.237248 INFO::Starting hierarchical adjustment
2025-10-19 20:32:11.237925 INFO::Found 2 batches.
2025-10-19 20:32:11.238424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:11.239195 INFO::Using default BPPARAM
2025-10-19 20:32:11.239987 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:11.240924 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-19 20:32:11.267216 INFO::Done
2025-10-19 20:32:11.26795 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:11.270219 INFO::ASW Batch was 0.0233918397568377 prior to batch effect correction and is now -0.123563593467578 .
2025-10-19 20:32:11.271103 INFO::Total function execution time is 0.0461809635162354 s and adjustment time is 0.0293879508972168 s ( 63.64 )
2025-10-19 20:32:11.274592 INFO::Formatting Data.
2025-10-19 20:32:11.275548 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:11.287206 INFO::Formatting Data.
2025-10-19 20:32:11.28814 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:11.289216 INFO::Removing potential empty rows and columns
2025-10-19 20:32:11.290625 INFO::Found 0 missing values.
2025-10-19 20:32:11.294317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:11.295021 INFO::Done
2025-10-19 20:32:11.295903 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:11.298492 INFO::Starting hierarchical adjustment
2025-10-19 20:32:11.299163 INFO::Found 2 batches.
2025-10-19 20:32:11.299791 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:11.300664 INFO::Using default BPPARAM
2025-10-19 20:32:11.30143 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:11.302369 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-19 20:32:11.354096 INFO::Done
2025-10-19 20:32:11.355055 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:11.357286 INFO::ASW Batch was 0.104087621934284 prior to batch effect correction and is now -0.0881246007864126 .
2025-10-19 20:32:11.358535 INFO::Total function execution time is 0.0714080333709717 s and adjustment time is 0.0549180507659912 s ( 76.91 )
2025-10-19 20:32:11.360089 INFO::Formatting Data.
2025-10-19 20:32:11.360957 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:11.362116 INFO::Removing potential empty rows and columns
2025-10-19 20:32:11.363447 INFO::Found 0 missing values.
2025-10-19 20:32:11.367128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:11.367881 INFO::Done
2025-10-19 20:32:11.368657 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:11.371294 INFO::Starting hierarchical adjustment
2025-10-19 20:32:11.372259 INFO::Found 2 batches.
2025-10-19 20:32:11.372964 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:11.373761 INFO::Using default BPPARAM
2025-10-19 20:32:11.37446 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:11.375681 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-19 20:32:11.392299 INFO::Done
2025-10-19 20:32:11.392968 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:11.394859 INFO::ASW Batch was 0.104087621934284 prior to batch effect correction and is now -0.0881246007864126 .
2025-10-19 20:32:11.39564 INFO::Total function execution time is 0.0356271266937256 s and adjustment time is 0.0202269554138184 s ( 56.77 )
2025-10-19 20:32:14.685675 INFO::Formatting Data.
2025-10-19 20:32:14.686592 INFO::Recognized SummarizedExperiment
2025-10-19 20:32:14.687305 INFO::Typecasting input to dataframe.
2025-10-19 20:32:14.720602 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:14.721867 INFO::Removing potential empty rows and columns
2025-10-19 20:32:14.726404 INFO::Found 0 missing values.
2025-10-19 20:32:14.735939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:14.736903 INFO::Done
2025-10-19 20:32:14.737812 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:14.741556 INFO::Starting hierarchical adjustment
2025-10-19 20:32:14.742306 INFO::Found 2 batches.
2025-10-19 20:32:14.742787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:14.744269 INFO::Using default BPPARAM
2025-10-19 20:32:14.744969 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:14.746316 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-19 20:32:14.809652 INFO::Done
2025-10-19 20:32:14.810332 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:14.813894 INFO::ASW Batch was -0.00597411950959353 prior to batch effect correction and is now -0.0911829482097987 .
2025-10-19 20:32:14.814725 INFO::Total function execution time is 0.129478931427002 s and adjustment time is 0.0674731731414795 s ( 52.11 )
2025-10-19 20:32:14.839402 INFO::Formatting Data.
2025-10-19 20:32:14.840218 INFO::Recognized SummarizedExperiment
2025-10-19 20:32:14.840992 INFO::Typecasting input to dataframe.
2025-10-19 20:32:14.850614 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:14.851839 INFO::Removing potential empty rows and columns
2025-10-19 20:32:14.855926 INFO::Found 0 missing values.
2025-10-19 20:32:14.864797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:14.865603 INFO::Done
2025-10-19 20:32:14.866166 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:14.871507 INFO::Starting hierarchical adjustment
2025-10-19 20:32:14.872503 INFO::Found 2 batches.
2025-10-19 20:32:14.873378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:14.874184 INFO::Using default BPPARAM
2025-10-19 20:32:14.874809 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:14.876224 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-19 20:32:14.903604 INFO::Done
2025-10-19 20:32:14.904464 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:14.908564 INFO::ASW Batch was -0.00867463814572049 prior to batch effect correction and is now -0.00867463814572049 .
2025-10-19 20:32:14.909735 INFO::Total function execution time is 0.0702180862426758 s and adjustment time is 0.0312421321868896 s ( 44.49 )
2025-10-19 20:32:14.9366 INFO::Formatting Data.
2025-10-19 20:32:14.937746 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:14.93923 INFO::Removing potential empty rows and columns
2025-10-19 20:32:14.940323 INFO::Found 0 missing values.
2025-10-19 20:32:14.944186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:14.945148 INFO::Done
2025-10-19 20:32:14.945863 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:14.947855 INFO::Starting hierarchical adjustment
2025-10-19 20:32:14.948636 INFO::Found 3 batches.
2025-10-19 20:32:14.949183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:14.94977 INFO::Using default BPPARAM
2025-10-19 20:32:14.950254 INFO::Processing subtree level 1
2025-10-19 20:32:15.176194 INFO::Adjusting the last 1 batches sequentially
2025-10-19 20:32:15.191522 INFO::Done
2025-10-19 20:32:15.195157 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:15.208465 INFO::ASW Batch was 0.0210133040737898 prior to batch effect correction and is now -0.146527795985322 .
2025-10-19 20:32:15.210515 INFO::Total function execution time is 0.273911952972412 s and adjustment time is 0.243005037307739 s ( 88.72 )
2025-10-19 20:32:15.238162 INFO::Skipping initial DF formatting
2025-10-19 20:32:15.239107 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:15.244278 INFO::Starting hierarchical adjustment
2025-10-19 20:32:15.24562 INFO::Found 5 batches.
2025-10-19 20:32:15.246653 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:15.247817 INFO::Using default BPPARAM
2025-10-19 20:32:15.248876 INFO::Processing subtree level 1
2025-10-19 20:32:15.657351 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:15.66119 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-19 20:32:15.730147 INFO::Done
2025-10-19 20:32:15.731665 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:15.747193 INFO::ASW Batch was 0.578466226645029 prior to batch effect correction and is now 0.578466226645029 .
2025-10-19 20:32:15.748607 INFO::ASW Label was 0.306348139252361 prior to batch effect correction and is now 0.306348139252361 .
2025-10-19 20:32:15.751916 INFO::Total function execution time is 0.513833045959473 s and adjustment time is 0.484822988510132 s ( 94.35 )
2025-10-19 20:32:15.86537 INFO::Formatting Data.
2025-10-19 20:32:15.866616 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:15.868163 INFO::Removing potential empty rows and columns
2025-10-19 20:32:15.869797 INFO::Found 0 missing values.
2025-10-19 20:32:15.876193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:15.877199 INFO::Done
2025-10-19 20:32:15.878122 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:15.882936 INFO::Starting hierarchical adjustment
2025-10-19 20:32:15.884158 INFO::Found 5 batches.
2025-10-19 20:32:15.88499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:15.885924 INFO::Using default BPPARAM
2025-10-19 20:32:15.886703 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.
2025-10-19 20:32:16.131538 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:16.14751 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-19 20:32:16.1909 INFO::Done
2025-10-19 20:32:16.192357 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:16.198234 INFO::ASW Batch was 0.483695798326527 prior to batch effect correction and is now -0.00640516812222011 .
2025-10-19 20:32:16.199309 INFO::ASW Label was 0.315138224935287 prior to batch effect correction and is now 0.658895094565393 .
2025-10-19 20:32:16.200538 INFO::Total function execution time is 0.335270881652832 s and adjustment time is 0.306998014450073 s ( 91.57 )
2025-10-19 20:32:16.201782 INFO::Formatting Data.
2025-10-19 20:32:16.202687 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:16.204462 INFO::Removing potential empty rows and columns
2025-10-19 20:32:16.205828 INFO::Found 0 missing values.
2025-10-19 20:32:16.212477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:16.213425 INFO::Done
2025-10-19 20:32:16.214271 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:16.218818 INFO::Starting hierarchical adjustment
2025-10-19 20:32:16.220232 INFO::Found 5 batches.
2025-10-19 20:32:16.221054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:16.221964 INFO::Using default BPPARAM
2025-10-19 20:32:16.222592 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.
2025-10-19 20:32:16.448887 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:16.457271 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-19 20:32:16.489319 INFO::Done
2025-10-19 20:32:16.490508 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:16.494903 INFO::ASW Batch was 0.483695798326527 prior to batch effect correction and is now -0.00640516812222011 .
2025-10-19 20:32:16.496176 INFO::ASW Label was 0.315138224935287 prior to batch effect correction and is now 0.658895094565393 .
2025-10-19 20:32:16.497435 INFO::Total function execution time is 0.29565691947937 s and adjustment time is 0.269620895385742 s ( 91.19 )
2025-10-19 20:32:16.519244 INFO::Formatting Data.
2025-10-19 20:32:16.520082 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:16.521643 INFO::Removing potential empty rows and columns
2025-10-19 20:32:16.523302 INFO::Found 0 missing values.
2025-10-19 20:32:16.529534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:16.530561 INFO::Done
2025-10-19 20:32:16.531562 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:16.535772 INFO::Starting hierarchical adjustment
2025-10-19 20:32:16.536985 INFO::Found 5 batches.
2025-10-19 20:32:16.537833 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:16.538715 INFO::Using default BPPARAM
2025-10-19 20:32:16.539296 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.
2025-10-19 20:32:16.779065 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:16.787941 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-19 20:32:16.82638 INFO::Done
2025-10-19 20:32:16.827675 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:16.833693 INFO::ASW Batch was 0.162211559604974 prior to batch effect correction and is now -0.0933646293010739 .
2025-10-19 20:32:16.834494 INFO::ASW Label was 0.565474391598705 prior to batch effect correction and is now 0.897001376305448 .
2025-10-19 20:32:16.835616 INFO::Total function execution time is 0.316360950469971 s and adjustment time is 0.289572954177856 s ( 91.53 )
2025-10-19 20:32:16.836662 INFO::Formatting Data.
2025-10-19 20:32:16.838071 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:16.840516 INFO::Removing potential empty rows and columns
2025-10-19 20:32:16.841575 INFO::Found 0 missing values.
2025-10-19 20:32:16.846775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:16.84769 INFO::Done
2025-10-19 20:32:16.848431 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:16.852176 INFO::Starting hierarchical adjustment
2025-10-19 20:32:16.853269 INFO::Found 5 batches.
2025-10-19 20:32:16.854107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:16.855039 INFO::Using default BPPARAM
2025-10-19 20:32:16.855833 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.
2025-10-19 20:32:17.053996 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:17.072706 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-19 20:32:17.116582 INFO::Done
2025-10-19 20:32:17.117698 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:17.122862 INFO::ASW Batch was 0.162211559604974 prior to batch effect correction and is now -0.0933646293010739 .
2025-10-19 20:32:17.12457 INFO::ASW Label was 0.565474391598705 prior to batch effect correction and is now 0.897001376305448 .
2025-10-19 20:32:17.126189 INFO::Total function execution time is 0.289402961730957 s and adjustment time is 0.263477087020874 s ( 91.04 )
2025-10-19 20:32:17.147547 INFO::Formatting Data.
2025-10-19 20:32:17.148638 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:17.151177 INFO::Removing potential empty rows and columns
2025-10-19 20:32:17.15277 INFO::Found 0 missing values.
2025-10-19 20:32:17.156792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:17.157636 INFO::Done
2025-10-19 20:32:17.158383 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:17.162481 INFO::Starting hierarchical adjustment
2025-10-19 20:32:17.163537 INFO::Found 2 batches.
2025-10-19 20:32:17.164359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:17.165196 INFO::Using default BPPARAM
2025-10-19 20:32:17.165868 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:17.166749 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-19 20:32:17.185534 INFO::Done
2025-10-19 20:32:17.18645 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:17.190069 INFO::ASW Batch was 0.603702645205774 prior to batch effect correction and is now -0.024237749281684 .
2025-10-19 20:32:17.190952 INFO::ASW Label was 0.480151335316086 prior to batch effect correction and is now 0.916905887640747 .
2025-10-19 20:32:17.192027 INFO::Total function execution time is 0.0445880889892578 s and adjustment time is 0.0221719741821289 s ( 49.73 )
2025-10-19 20:32:17.193137 INFO::Formatting Data.
2025-10-19 20:32:17.194007 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:17.195224 INFO::Removing potential empty rows and columns
2025-10-19 20:32:17.196577 INFO::Found 0 missing values.
2025-10-19 20:32:17.199451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:17.200134 INFO::Done
2025-10-19 20:32:17.200848 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:17.204776 INFO::Starting hierarchical adjustment
2025-10-19 20:32:17.205794 INFO::Found 2 batches.
2025-10-19 20:32:17.206537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:17.207447 INFO::Using default BPPARAM
2025-10-19 20:32:17.208084 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:17.209598 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-19 20:32:17.230118 INFO::Done
2025-10-19 20:32:17.23083 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:17.233795 INFO::ASW Batch was 0.603702645205774 prior to batch effect correction and is now -0.024237749281684 .
2025-10-19 20:32:17.234398 INFO::ASW Label was 0.480151335316086 prior to batch effect correction and is now 0.916905887640747 .
2025-10-19 20:32:17.235135 INFO::Total function execution time is 0.0421030521392822 s and adjustment time is 0.0245130062103271 s ( 58.22 )
2025-10-19 20:32:17.254022 INFO::Formatting Data.
2025-10-19 20:32:17.255446 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:17.257057 INFO::Removing potential empty rows and columns
2025-10-19 20:32:17.258894 INFO::Found 0 missing values.
2025-10-19 20:32:17.261315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:17.2619 INFO::Done
2025-10-19 20:32:17.262414 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:17.264287 INFO::Starting hierarchical adjustment
2025-10-19 20:32:17.264991 INFO::Found 2 batches.
2025-10-19 20:32:17.265503 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:17.266083 INFO::Using default BPPARAM
2025-10-19 20:32:17.266586 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:17.267449 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-19 20:32:17.307102 INFO::Done
2025-10-19 20:32:17.308074 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:17.31072 INFO::ASW Batch was -0.127614292344952 prior to batch effect correction and is now -0.189348733411543 .
2025-10-19 20:32:17.311834 INFO::Total function execution time is 0.0580170154571533 s and adjustment time is 0.0421950817108154 s ( 72.73 )
2025-10-19 20:32:17.330072 INFO::Formatting Data.
2025-10-19 20:32:17.330833 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:17.331935 INFO::Removing potential empty rows and columns
2025-10-19 20:32:17.333294 INFO::Found 0 missing values.
2025-10-19 20:32:17.33442 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.
2025-10-19 20:32:17.339469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:17.340089 INFO::Done
2025-10-19 20:32:17.340597 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:17.344279 INFO::Starting hierarchical adjustment
2025-10-19 20:32:17.345468 INFO::Found 2 batches.
2025-10-19 20:32:17.346231 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:17.347071 INFO::Using default BPPARAM
2025-10-19 20:32:17.347805 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:17.349187 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-19 20:32:17.369668 INFO::Done
2025-10-19 20:32:17.37036 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:17.373827 INFO::ASW Batch was 0.668807153415772 prior to batch effect correction and is now -0.0221168163620683 .
2025-10-19 20:32:17.37448 INFO::ASW Label was 0.390741505858774 prior to batch effect correction and is now 0.910533859372813 .
2025-10-19 20:32:17.375586 INFO::Total function execution time is 0.0455420017242432 s and adjustment time is 0.0244100093841553 s ( 53.6 )
2025-10-19 20:32:17.376706 INFO::Formatting Data.
2025-10-19 20:32:17.377578 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:17.378871 INFO::Removing potential empty rows and columns
2025-10-19 20:32:17.380289 INFO::Found 0 missing values.
2025-10-19 20:32:17.38132 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.
2025-10-19 20:32:17.385419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:17.386716 INFO::Done
2025-10-19 20:32:17.387416 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:17.391646 INFO::Starting hierarchical adjustment
2025-10-19 20:32:17.392782 INFO::Found 2 batches.
2025-10-19 20:32:17.393593 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:17.394477 INFO::Using default BPPARAM
2025-10-19 20:32:17.395248 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:17.39664 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-19 20:32:17.417778 INFO::Done
2025-10-19 20:32:17.418708 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:17.423148 INFO::ASW Batch was 0.668807153415772 prior to batch effect correction and is now -0.0221168163620683 .
2025-10-19 20:32:17.424141 INFO::ASW Label was 0.390741505858774 prior to batch effect correction and is now 0.910533859372813 .
2025-10-19 20:32:17.425425 INFO::Total function execution time is 0.04874587059021 s and adjustment time is 0.0251970291137695 s ( 51.69 )
2025-10-19 20:32:17.714236 INFO::Formatting Data.
2025-10-19 20:32:17.715262 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:17.716533 INFO::Removing potential empty rows and columns
2025-10-19 20:32:17.717902 INFO::Found 0 missing values.
2025-10-19 20:32:17.722563 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:17.723533 INFO::Done
2025-10-19 20:32:17.724351 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:17.727214 INFO::Starting hierarchical adjustment
2025-10-19 20:32:17.728233 INFO::Found 3 batches.
2025-10-19 20:32:17.728984 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:17.729793 INFO::Using default BPPARAM
2025-10-19 20:32:17.730538 INFO::Processing subtree level 1
2025-10-19 20:32:17.87401 INFO::Adjusting the last 1 batches sequentially
2025-10-19 20:32:17.893375 INFO::Done
2025-10-19 20:32:17.895566 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:17.90937 INFO::ASW Batch was -0.078031675279326 prior to batch effect correction and is now -0.078031675279326 .
2025-10-19 20:32:17.914322 INFO::Total function execution time is 0.199557065963745 s and adjustment time is 0.165274143218994 s ( 82.82 )
2025-10-19 20:32:17.916689 INFO::Formatting Data.
2025-10-19 20:32:17.918014 INFO::Typecasting input to dataframe.
2025-10-19 20:32:17.920237 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:17.925901 INFO::Removing potential empty rows and columns
2025-10-19 20:32:17.928624 INFO::Found 0 missing values.
2025-10-19 20:32:17.933375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:17.934336 INFO::Done
2025-10-19 20:32:17.935168 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:17.937442 INFO::Starting hierarchical adjustment
2025-10-19 20:32:17.938759 INFO::Found 3 batches.
2025-10-19 20:32:17.939445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:17.94032 INFO::Using default BPPARAM
2025-10-19 20:32:17.941245 INFO::Processing subtree level 1
2025-10-19 20:32:18.09407 INFO::Adjusting the last 1 batches sequentially
2025-10-19 20:32:18.112691 INFO::Done
2025-10-19 20:32:18.116886 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:18.132266 INFO::ASW Batch was -0.078031675279326 prior to batch effect correction and is now -0.078031675279326 .
2025-10-19 20:32:18.135385 INFO::Total function execution time is 0.218695878982544 s and adjustment time is 0.174522161483765 s ( 79.8 )
2025-10-19 20:32:18.195727 INFO::Formatting Data.
2025-10-19 20:32:18.196968 INFO::Typecasting input to dataframe.
2025-10-19 20:32:18.198296 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:18.206874 INFO::Removing potential empty rows and columns
2025-10-19 20:32:18.208724 INFO::Found 0 missing values.
2025-10-19 20:32:18.214178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:18.215291 INFO::Done
2025-10-19 20:32:18.216259 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:18.219466 INFO::Starting hierarchical adjustment
2025-10-19 20:32:18.220401 INFO::Found 3 batches.
2025-10-19 20:32:18.221194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:18.222081 INFO::Using default BPPARAM
2025-10-19 20:32:18.222859 INFO::Processing subtree level 1
2025-10-19 20:32:18.378325 INFO::Adjusting the last 1 batches sequentially
2025-10-19 20:32:18.396507 INFO::Done
2025-10-19 20:32:18.397874 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:18.409154 INFO::ASW Batch was -0.058687452906065 prior to batch effect correction and is now -0.058687452906065 .
2025-10-19 20:32:18.411656 INFO::Total function execution time is 0.215940952301025 s and adjustment time is 0.176257133483887 s ( 81.62 )
2025-10-19 20:32:18.685422 INFO::Formatting Data.
2025-10-19 20:32:18.686652 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:18.690427 INFO::Removing potential empty rows and columns
2025-10-19 20:32:18.694174 INFO::Found 1000 missing values.
2025-10-19 20:32:18.720045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:18.721204 INFO::Done
2025-10-19 20:32:18.722252 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:18.732437 INFO::Starting hierarchical adjustment
2025-10-19 20:32:18.733512 INFO::Found 10 batches.
2025-10-19 20:32:18.734318 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:18.735213 INFO::Using default BPPARAM
2025-10-19 20:32:18.735942 INFO::Processing subtree level 1
2025-10-19 20:32:18.978318 INFO::Processing subtree level 2
2025-10-19 20:32:19.275324 INFO::Adjusting the last 1 batches sequentially
2025-10-19 20:32:19.295765 INFO::Done
2025-10-19 20:32:19.301483 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:19.325942 INFO::ASW Batch was 0.493731289215826 prior to batch effect correction and is now 0.493731289215826 .
2025-10-19 20:32:19.328097 INFO::ASW Label was 0.358493813564992 prior to batch effect correction and is now 0.358493813564992 .
2025-10-19 20:32:19.331779 INFO::Total function execution time is 0.646167993545532 s and adjustment time is 0.562376976013184 s ( 87.03 )
2025-10-19 20:32:19.334155 INFO::Formatting Data.
2025-10-19 20:32:19.33494 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:19.337092 INFO::Removing potential empty rows and columns
2025-10-19 20:32:19.342223 INFO::Found 1000 missing values.
2025-10-19 20:32:19.373377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:19.374434 INFO::Done
2025-10-19 20:32:19.37533 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:19.384926 INFO::Starting hierarchical adjustment
2025-10-19 20:32:19.386358 INFO::Found 10 batches.
2025-10-19 20:32:20.507092 INFO::Set up parallel execution backend with 2 workers
2025-10-19 20:32:20.507749 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-19 20:32:21.853092 INFO::Adjusting the last 2 batches sequentially
2025-10-19 20:32:21.855395 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-19 20:32:21.877226 INFO::Done
2025-10-19 20:32:21.878135 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:21.883953 INFO::ASW Batch was 0.493731289215826 prior to batch effect correction and is now 0.493731289215826 .
2025-10-19 20:32:21.884866 INFO::ASW Label was 0.358493813564992 prior to batch effect correction and is now 0.358493813564992 .
2025-10-19 20:32:21.885968 INFO::Total function execution time is 2.55200004577637 s and adjustment time is 2.49124598503113 s ( 97.62 )
2025-10-19 20:32:22.146409 INFO::Formatting Data.
2025-10-19 20:32:22.147421 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.149752 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.151333 INFO::Found 0 missing values.
2025-10-19 20:32:22.155987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.156941 INFO::Done
2025-10-19 20:32:22.157894 INFO::Acquiring quality metrics before batch effect correction.
2025-10-19 20:32:22.161277 INFO::Starting hierarchical adjustment
2025-10-19 20:32:22.162456 INFO::Found 3 batches.
2025-10-19 20:32:22.163152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-19 20:32:22.163765 INFO::Using default BPPARAM
2025-10-19 20:32:22.164264 INFO::Processing subtree level 1
2025-10-19 20:32:22.350969 INFO::Adjusting the last 1 batches sequentially
2025-10-19 20:32:22.369667 INFO::Done
2025-10-19 20:32:22.370882 INFO::Acquiring quality metrics after batch effect correction.
2025-10-19 20:32:22.385194 INFO::ASW Batch was 0.1427909345905 prior to batch effect correction and is now -0.156340158551109 .
2025-10-19 20:32:22.386267 INFO::ASW Label was -0.176249849532889 prior to batch effect correction and is now -0.00119509169583459 .
2025-10-19 20:32:22.388732 INFO::Total function execution time is 0.242195129394531 s and adjustment time is 0.207587957382202 s ( 85.71 )
2025-10-19 20:32:22.580508 INFO::Formatting Data.
2025-10-19 20:32:22.581326 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.582945 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.584642 INFO::Found 2 missing values.
2025-10-19 20:32:22.588658 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.589251 INFO::Done
2025-10-19 20:32:22.628643 INFO::Found NA in Reference column
2025-10-19 20:32:22.642327 INFO::Require at least two references per batch.
2025-10-19 20:32:22.671097 INFO::Formatting Data.
2025-10-19 20:32:22.672131 INFO::Recognized SummarizedExperiment
2025-10-19 20:32:22.672971 INFO::Typecasting input to dataframe.
2025-10-19 20:32:22.685472 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.687189 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.691264 INFO::Found 0 missing values.
2025-10-19 20:32:22.700869 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.701808 INFO::Done
2025-10-19 20:32:22.721281 INFO::Formatting Data.
2025-10-19 20:32:22.722025 INFO::Recognized SummarizedExperiment
2025-10-19 20:32:22.72256 INFO::Typecasting input to dataframe.
2025-10-19 20:32:22.742021 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.743205 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.746911 INFO::Found 0 missing values.
2025-10-19 20:32:22.760532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.76151 INFO::Done
2025-10-19 20:32:22.780671 INFO::Formatting Data.
2025-10-19 20:32:22.781701 INFO::Recognized SummarizedExperiment
2025-10-19 20:32:22.782512 INFO::Typecasting input to dataframe.
2025-10-19 20:32:22.801762 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.803134 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.804571 INFO::Found 0 missing values.
2025-10-19 20:32:22.805789 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.
2025-10-19 20:32:22.812354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.813303 INFO::Done
2025-10-19 20:32:22.831741 INFO::Formatting Data.
2025-10-19 20:32:22.832886 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.834521 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.835888 INFO::Found 0 missing values.
2025-10-19 20:32:22.839813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.840741 INFO::Done
2025-10-19 20:32:22.856679 INFO::Formatting Data.
2025-10-19 20:32:22.857555 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.85845 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.859906 INFO::Found 0 missing values.
2025-10-19 20:32:22.86289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.863419 INFO::Done
2025-10-19 20:32:22.9114 INFO::Formatting Data.
2025-10-19 20:32:22.912555 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.913771 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.914941 INFO::Found 1 missing values.
2025-10-19 20:32:22.918113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.918963 INFO::Done
2025-10-19 20:32:22.948193 INFO::Formatting Data.
2025-10-19 20:32:22.949004 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.950148 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.951362 INFO::Found 2 missing values.
2025-10-19 20:32:22.952288 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.
2025-10-19 20:32:22.954343 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.95489 INFO::Done
2025-10-19 20:32:22.971804 INFO::Formatting Data.
2025-10-19 20:32:22.97296 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.974144 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.975241 INFO::Found 2 missing values.
2025-10-19 20:32:22.977463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:22.9782 INFO::Done
2025-10-19 20:32:22.993696 INFO::Formatting Data.
2025-10-19 20:32:22.99446 INFO::Typecasting input to dataframe.
2025-10-19 20:32:22.995588 INFO::Replacing NaNs with NAs.
2025-10-19 20:32:22.996859 INFO::Removing potential empty rows and columns
2025-10-19 20:32:22.998368 INFO::Found 0 missing values.
2025-10-19 20:32:23.001434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-19 20:32:23.002113 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.705 4.834 25.818
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.981 | 1.676 | 20.139 | |
| compute_asw | 0.027 | 0.001 | 0.029 | |
| count_existing | 0.012 | 0.001 | 0.014 | |
| generate_data_covariables | 0.015 | 0.002 | 0.016 | |
| generate_dataset | 0.014 | 0.002 | 0.014 | |