Yannis Schumann
| Snapshot Date: 2025-11-26 13:40 -0500 (Wed, 26 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-27 11:38 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4865 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4614 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4571 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 167/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2025-11-26 19:35:23 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 19:36:52 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 89.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 28.308 1.616 20.121
* 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/4.6-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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")
2025-11-26 19:36:29.812177 INFO::Formatting Data.
2025-11-26 19:36:29.816248 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:29.831428 INFO::Removing potential empty rows and columns
2025-11-26 19:36:30.140838 INFO::Found 0 missing values.
2025-11-26 19:36:30.145128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:30.145883 INFO::Done
2025-11-26 19:36:30.146824 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:30.162285 INFO::Starting hierarchical adjustment
2025-11-26 19:36:30.163206 INFO::Found 3 batches.
2025-11-26 19:36:30.164045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:30.165347 INFO::Using default BPPARAM
2025-11-26 19:36:30.166047 INFO::Processing subtree level 1
2025-11-26 19:36:30.35379 INFO::Adjusting the last 1 batches sequentially
2025-11-26 19:36:30.35854 INFO::Done
2025-11-26 19:36:30.359517 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:30.364835 INFO::ASW Batch was 0.0243861508572988 prior to batch effect correction and is now 0.0243861508572988 .
2025-11-26 19:36:30.366477 INFO::Total function execution time is 0.555010080337524 s and adjustment time is 0.195462942123413 s ( 35.22 )
2025-11-26 19:36:30.391279 INFO::Formatting Data.
2025-11-26 19:36:30.392453 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:30.39373 INFO::Removing potential empty rows and columns
2025-11-26 19:36:30.395154 INFO::Found 0 missing values.
2025-11-26 19:36:30.396577 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.
2025-11-26 19:36:30.410638 INFO::Formatting Data.
2025-11-26 19:36:30.41261 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:30.415056 INFO::Removing potential empty rows and columns
2025-11-26 19:36:30.4167 INFO::Found 0 missing values.
2025-11-26 19:36:30.418172 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.
2025-11-26 19:36:30.446499 INFO::Formatting Data.
2025-11-26 19:36:30.447647 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:30.449016 INFO::Removing potential empty rows and columns
2025-11-26 19:36:30.450689 INFO::Found 0 missing values.
2025-11-26 19:36:30.452264 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.
2025-11-26 19:36:30.45927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:30.460261 INFO::Done
2025-11-26 19:36:30.461265 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:30.464473 INFO::Starting hierarchical adjustment
2025-11-26 19:36:30.46564 INFO::Found 2 batches.
2025-11-26 19:36:30.466577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:30.467568 INFO::Using default BPPARAM
2025-11-26 19:36:30.468369 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:30.469906 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 19:36:30.501593 INFO::Done
2025-11-26 19:36:30.502617 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:30.505752 INFO::ASW Batch was 0.0270211699743867 prior to batch effect correction and is now -0.120029895375494 .
2025-11-26 19:36:30.507114 INFO::Total function execution time is 0.0606389045715332 s and adjustment time is 0.0361549854278564 s ( 59.62 )
2025-11-26 19:36:30.51149 INFO::Formatting Data.
2025-11-26 19:36:30.512628 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:30.526609 INFO::Formatting Data.
2025-11-26 19:36:30.527797 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:30.529197 INFO::Removing potential empty rows and columns
2025-11-26 19:36:30.530726 INFO::Found 0 missing values.
2025-11-26 19:36:30.535225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:30.536146 INFO::Done
2025-11-26 19:36:30.536933 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:30.539897 INFO::Starting hierarchical adjustment
2025-11-26 19:36:30.541008 INFO::Found 2 batches.
2025-11-26 19:36:30.54198 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:30.542922 INFO::Using default BPPARAM
2025-11-26 19:36:30.544099 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:30.545602 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 19:36:30.608671 INFO::Done
2025-11-26 19:36:30.609637 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:30.612807 INFO::ASW Batch was -0.0262044554528654 prior to batch effect correction and is now -0.131514516558884 .
2025-11-26 19:36:30.613929 INFO::Total function execution time is 0.0874180793762207 s and adjustment time is 0.0678560733795166 s ( 77.62 )
2025-11-26 19:36:30.615322 INFO::Formatting Data.
2025-11-26 19:36:30.616119 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:30.617122 INFO::Removing potential empty rows and columns
2025-11-26 19:36:30.618412 INFO::Found 0 missing values.
2025-11-26 19:36:30.622664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:30.623537 INFO::Done
2025-11-26 19:36:30.624415 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:30.627262 INFO::Starting hierarchical adjustment
2025-11-26 19:36:30.62833 INFO::Found 2 batches.
2025-11-26 19:36:30.629092 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:30.629899 INFO::Using default BPPARAM
2025-11-26 19:36:30.630638 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:30.631906 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 19:36:30.653809 INFO::Done
2025-11-26 19:36:30.654808 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:30.657715 INFO::ASW Batch was -0.0262044554528654 prior to batch effect correction and is now -0.131514516558884 .
2025-11-26 19:36:30.658876 INFO::Total function execution time is 0.0435059070587158 s and adjustment time is 0.0256500244140625 s ( 58.96 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-26 19:36:34.422685 INFO::Formatting Data.
2025-11-26 19:36:34.423643 INFO::Recognized SummarizedExperiment
2025-11-26 19:36:34.424434 INFO::Typecasting input to dataframe.
2025-11-26 19:36:34.467625 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:34.469343 INFO::Removing potential empty rows and columns
2025-11-26 19:36:34.474865 INFO::Found 0 missing values.
2025-11-26 19:36:34.485757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:34.486783 INFO::Done
2025-11-26 19:36:34.487758 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:34.493409 INFO::Starting hierarchical adjustment
2025-11-26 19:36:34.494695 INFO::Found 2 batches.
2025-11-26 19:36:34.49557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:34.497205 INFO::Using default BPPARAM
2025-11-26 19:36:34.497991 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:34.499586 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 19:36:34.583317 INFO::Done
2025-11-26 19:36:34.584486 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:34.590029 INFO::ASW Batch was 0.0134460915858883 prior to batch effect correction and is now -0.0898947598740894 .
2025-11-26 19:36:34.591496 INFO::Total function execution time is 0.169204950332642 s and adjustment time is 0.088886022567749 s ( 52.53 )
Warning: stack imbalance in '{', 73 then 75
2025-11-26 19:36:34.622345 INFO::Formatting Data.
2025-11-26 19:36:34.623297 INFO::Recognized SummarizedExperiment
2025-11-26 19:36:34.624168 INFO::Typecasting input to dataframe.
2025-11-26 19:36:34.63796 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:34.639813 INFO::Removing potential empty rows and columns
2025-11-26 19:36:34.645517 INFO::Found 0 missing values.
2025-11-26 19:36:34.656642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:34.657747 INFO::Done
2025-11-26 19:36:34.658736 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:34.664417 INFO::Starting hierarchical adjustment
2025-11-26 19:36:34.665674 INFO::Found 2 batches.
2025-11-26 19:36:34.666537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:34.667464 INFO::Using default BPPARAM
2025-11-26 19:36:34.668244 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:34.669843 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 19:36:34.708367 INFO::Done
2025-11-26 19:36:34.709454 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:34.71508 INFO::ASW Batch was 0.0077049656191565 prior to batch effect correction and is now 0.0077049656191565 .
2025-11-26 19:36:34.71655 INFO::Total function execution time is 0.0940749645233154 s and adjustment time is 0.0429201126098633 s ( 45.62 )
2025-11-26 19:36:34.748325 INFO::Formatting Data.
2025-11-26 19:36:34.749553 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:34.751007 INFO::Removing potential empty rows and columns
2025-11-26 19:36:34.75268 INFO::Found 0 missing values.
2025-11-26 19:36:34.756744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:34.757578 INFO::Done
2025-11-26 19:36:34.758336 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:34.761257 INFO::Starting hierarchical adjustment
2025-11-26 19:36:34.762307 INFO::Found 3 batches.
2025-11-26 19:36:34.763077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:34.764135 INFO::Using default BPPARAM
2025-11-26 19:36:34.764919 INFO::Processing subtree level 1
2025-11-26 19:36:35.060951 INFO::Adjusting the last 1 batches sequentially
2025-11-26 19:36:35.089037 INFO::Done
2025-11-26 19:36:35.09012 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:35.10211 INFO::ASW Batch was 0.0440641570250174 prior to batch effect correction and is now -0.127716326847073 .
2025-11-26 19:36:35.104455 INFO::Total function execution time is 0.356119871139526 s and adjustment time is 0.32689094543457 s ( 91.79 )
2025-11-26 19:36:35.134191 INFO::Skipping initial DF formatting
2025-11-26 19:36:35.135298 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:35.141978 INFO::Starting hierarchical adjustment
2025-11-26 19:36:35.143359 INFO::Found 5 batches.
2025-11-26 19:36:35.144382 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:35.14565 INFO::Using default BPPARAM
2025-11-26 19:36:35.146661 INFO::Processing subtree level 1
2025-11-26 19:36:35.600677 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:35.604471 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 19:36:35.671798 INFO::Done
2025-11-26 19:36:35.673557 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:35.687565 INFO::ASW Batch was 0.521295148072045 prior to batch effect correction and is now 0.521295148072045 .
2025-11-26 19:36:35.688898 INFO::ASW Label was 0.338822729724374 prior to batch effect correction and is now 0.338822729724374 .
2025-11-26 19:36:35.691897 INFO::Total function execution time is 0.556833028793335 s and adjustment time is 0.528688192367554 s ( 94.95 )
2025-11-26 19:36:35.800542 INFO::Formatting Data.
2025-11-26 19:36:35.801591 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:35.802941 INFO::Removing potential empty rows and columns
2025-11-26 19:36:35.804224 INFO::Found 0 missing values.
2025-11-26 19:36:35.810389 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:35.811486 INFO::Done
2025-11-26 19:36:35.812442 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:35.8166 INFO::Starting hierarchical adjustment
2025-11-26 19:36:35.817771 INFO::Found 5 batches.
2025-11-26 19:36:35.818705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:35.819517 INFO::Using default BPPARAM
2025-11-26 19:36:35.820441 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.
2025-11-26 19:36:36.052621 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:36.063699 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 19:36:36.101911 INFO::Done
2025-11-26 19:36:36.102979 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:36.109295 INFO::ASW Batch was 0.323327294686242 prior to batch effect correction and is now -0.115360477744262 .
2025-11-26 19:36:36.110413 INFO::ASW Label was 0.527604880577311 prior to batch effect correction and is now 0.880212527639986 .
2025-11-26 19:36:36.11176 INFO::Total function execution time is 0.311291933059692 s and adjustment time is 0.284339904785156 s ( 91.34 )
2025-11-26 19:36:36.113294 INFO::Formatting Data.
2025-11-26 19:36:36.11434 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:36.115728 INFO::Removing potential empty rows and columns
2025-11-26 19:36:36.117245 INFO::Found 0 missing values.
2025-11-26 19:36:36.124395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:36.125557 INFO::Done
2025-11-26 19:36:36.126628 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:36.132026 INFO::Starting hierarchical adjustment
2025-11-26 19:36:36.1333 INFO::Found 5 batches.
2025-11-26 19:36:36.134262 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:36.135007 INFO::Using default BPPARAM
2025-11-26 19:36:36.135715 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.
2025-11-26 19:36:36.357545 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:36.368318 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 19:36:36.403242 INFO::Done
2025-11-26 19:36:36.404306 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:36.41009 INFO::ASW Batch was 0.323327294686242 prior to batch effect correction and is now -0.115360477744262 .
2025-11-26 19:36:36.411102 INFO::ASW Label was 0.527604880577311 prior to batch effect correction and is now 0.880212527639986 .
2025-11-26 19:36:36.41316 INFO::Total function execution time is 0.299812078475952 s and adjustment time is 0.270148992538452 s ( 90.11 )
2025-11-26 19:36:36.438056 INFO::Formatting Data.
2025-11-26 19:36:36.439236 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:36.440776 INFO::Removing potential empty rows and columns
2025-11-26 19:36:36.442447 INFO::Found 0 missing values.
2025-11-26 19:36:36.451373 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:36.452438 INFO::Done
2025-11-26 19:36:36.453629 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:36.458755 INFO::Starting hierarchical adjustment
2025-11-26 19:36:36.459797 INFO::Found 5 batches.
2025-11-26 19:36:36.460419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:36.461305 INFO::Using default BPPARAM
2025-11-26 19:36:36.462099 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.
2025-11-26 19:36:36.694964 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:36.706361 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 19:36:36.744007 INFO::Done
2025-11-26 19:36:36.745094 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:36.751548 INFO::ASW Batch was 0.586645219075203 prior to batch effect correction and is now -0.0994324772134358 .
2025-11-26 19:36:36.75277 INFO::ASW Label was 0.177126913584443 prior to batch effect correction and is now 0.851384032892608 .
2025-11-26 19:36:36.754193 INFO::Total function execution time is 0.316097021102905 s and adjustment time is 0.284358024597168 s ( 89.96 )
2025-11-26 19:36:36.755573 INFO::Formatting Data.
2025-11-26 19:36:36.756602 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:36.758508 INFO::Removing potential empty rows and columns
2025-11-26 19:36:36.760362 INFO::Found 0 missing values.
2025-11-26 19:36:36.766958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:36.768085 INFO::Done
2025-11-26 19:36:36.769051 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:36.773937 INFO::Starting hierarchical adjustment
2025-11-26 19:36:36.775186 INFO::Found 5 batches.
2025-11-26 19:36:36.776205 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:36.777205 INFO::Using default BPPARAM
2025-11-26 19:36:36.778143 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.
2025-11-26 19:36:36.992778 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:37.001215 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 19:36:37.038328 INFO::Done
2025-11-26 19:36:37.039637 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:37.046012 INFO::ASW Batch was 0.586645219075203 prior to batch effect correction and is now -0.0994324772134358 .
2025-11-26 19:36:37.047253 INFO::ASW Label was 0.177126913584443 prior to batch effect correction and is now 0.851384032892608 .
2025-11-26 19:36:37.049513 INFO::Total function execution time is 0.293840885162354 s and adjustment time is 0.263413906097412 s ( 89.65 )
2025-11-26 19:36:37.07453 INFO::Formatting Data.
2025-11-26 19:36:37.076079 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:37.077883 INFO::Removing potential empty rows and columns
2025-11-26 19:36:37.079021 INFO::Found 0 missing values.
2025-11-26 19:36:37.081696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:37.082266 INFO::Done
2025-11-26 19:36:37.082793 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:37.087053 INFO::Starting hierarchical adjustment
2025-11-26 19:36:37.088225 INFO::Found 2 batches.
2025-11-26 19:36:37.089047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:37.089962 INFO::Using default BPPARAM
2025-11-26 19:36:37.090746 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:37.092142 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 19:36:37.114225 INFO::Done
2025-11-26 19:36:37.115082 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:37.119483 INFO::ASW Batch was 0.636795516939549 prior to batch effect correction and is now 0.0447442786830868 .
2025-11-26 19:36:37.120257 INFO::ASW Label was 0.383935725261939 prior to batch effect correction and is now 0.856457070862132 .
2025-11-26 19:36:37.121412 INFO::Total function execution time is 0.0470459461212158 s and adjustment time is 0.0262401103973389 s ( 55.78 )
2025-11-26 19:36:37.122302 INFO::Formatting Data.
2025-11-26 19:36:37.122994 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:37.123896 INFO::Removing potential empty rows and columns
2025-11-26 19:36:37.12542 INFO::Found 0 missing values.
2025-11-26 19:36:37.129502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:37.130401 INFO::Done
2025-11-26 19:36:37.131477 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:37.135217 INFO::Starting hierarchical adjustment
2025-11-26 19:36:37.136095 INFO::Found 2 batches.
2025-11-26 19:36:37.136986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:37.137748 INFO::Using default BPPARAM
2025-11-26 19:36:37.1383 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:37.139597 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-26 19:36:37.160662 INFO::Done
2025-11-26 19:36:37.161697 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:37.165021 INFO::ASW Batch was 0.636795516939549 prior to batch effect correction and is now 0.0447442786830868 .
2025-11-26 19:36:37.165642 INFO::ASW Label was 0.383935725261939 prior to batch effect correction and is now 0.856457070862132 .
2025-11-26 19:36:37.166413 INFO::Total function execution time is 0.0441160202026367 s and adjustment time is 0.0246360301971436 s ( 55.84 )
2025-11-26 19:36:37.186488 INFO::Formatting Data.
2025-11-26 19:36:37.187285 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:37.188434 INFO::Removing potential empty rows and columns
2025-11-26 19:36:37.189437 INFO::Found 0 missing values.
2025-11-26 19:36:37.192539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:37.193403 INFO::Done
2025-11-26 19:36:37.194073 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:37.195955 INFO::Starting hierarchical adjustment
2025-11-26 19:36:37.197163 INFO::Found 2 batches.
2025-11-26 19:36:37.197739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:37.198299 INFO::Using default BPPARAM
2025-11-26 19:36:37.198822 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:37.199725 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 19:36:37.246429 INFO::Done
2025-11-26 19:36:37.247155 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:37.249115 INFO::ASW Batch was 0.070731682298165 prior to batch effect correction and is now -0.168809866400871 .
2025-11-26 19:36:37.249953 INFO::Total function execution time is 0.063560962677002 s and adjustment time is 0.0494670867919922 s ( 77.83 )
2025-11-26 19:36:37.269325 INFO::Formatting Data.
2025-11-26 19:36:37.270534 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:37.271878 INFO::Removing potential empty rows and columns
2025-11-26 19:36:37.273362 INFO::Found 0 missing values.
2025-11-26 19:36:37.275175 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.
2025-11-26 19:36:37.28 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:37.281108 INFO::Done
2025-11-26 19:36:37.281977 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:37.286608 INFO::Starting hierarchical adjustment
2025-11-26 19:36:37.287767 INFO::Found 2 batches.
2025-11-26 19:36:37.288606 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:37.289462 INFO::Using default BPPARAM
2025-11-26 19:36:37.290176 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:37.291553 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 19:36:37.315515 INFO::Done
2025-11-26 19:36:37.316256 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:37.319811 INFO::ASW Batch was 0.499012181787924 prior to batch effect correction and is now 0.098663363939654 .
2025-11-26 19:36:37.320785 INFO::ASW Label was 0.5866408898616 prior to batch effect correction and is now 0.830008431051729 .
2025-11-26 19:36:37.32196 INFO::Total function execution time is 0.0527739524841309 s and adjustment time is 0.0279920101165771 s ( 53.04 )
2025-11-26 19:36:37.323082 INFO::Formatting Data.
2025-11-26 19:36:37.324032 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:37.325209 INFO::Removing potential empty rows and columns
2025-11-26 19:36:37.326408 INFO::Found 0 missing values.
2025-11-26 19:36:37.327673 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.
2025-11-26 19:36:37.332194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:37.333103 INFO::Done
2025-11-26 19:36:37.333896 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:37.338277 INFO::Starting hierarchical adjustment
2025-11-26 19:36:37.339267 INFO::Found 2 batches.
2025-11-26 19:36:37.340001 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:37.340847 INFO::Using default BPPARAM
2025-11-26 19:36:37.341611 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:37.343004 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 19:36:37.366987 INFO::Done
2025-11-26 19:36:37.368026 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:37.372376 INFO::ASW Batch was 0.499012181787924 prior to batch effect correction and is now 0.098663363939654 .
2025-11-26 19:36:37.373362 INFO::ASW Label was 0.5866408898616 prior to batch effect correction and is now 0.830008431051729 .
2025-11-26 19:36:37.374504 INFO::Total function execution time is 0.0514659881591797 s and adjustment time is 0.027839183807373 s ( 54.09 )
2025-11-26 19:36:37.664334 INFO::Formatting Data.
2025-11-26 19:36:37.665507 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:37.6669 INFO::Removing potential empty rows and columns
2025-11-26 19:36:37.668143 INFO::Found 0 missing values.
2025-11-26 19:36:37.671485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:37.672071 INFO::Done
2025-11-26 19:36:37.673 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:37.67564 INFO::Starting hierarchical adjustment
2025-11-26 19:36:37.676711 INFO::Found 3 batches.
2025-11-26 19:36:37.677454 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:37.678256 INFO::Using default BPPARAM
2025-11-26 19:36:37.678927 INFO::Processing subtree level 1
2025-11-26 19:36:37.813182 INFO::Adjusting the last 1 batches sequentially
2025-11-26 19:36:37.822301 INFO::Done
2025-11-26 19:36:37.824308 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:37.833889 INFO::ASW Batch was -0.0892412297462976 prior to batch effect correction and is now -0.0892412297462976 .
2025-11-26 19:36:37.836278 INFO::Total function execution time is 0.171926975250244 s and adjustment time is 0.145747900009155 s ( 84.77 )
2025-11-26 19:36:37.838074 INFO::Formatting Data.
2025-11-26 19:36:37.8389 INFO::Typecasting input to dataframe.
2025-11-26 19:36:37.840001 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:37.841395 INFO::Removing potential empty rows and columns
2025-11-26 19:36:37.842886 INFO::Found 0 missing values.
2025-11-26 19:36:37.846575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:37.847751 INFO::Done
2025-11-26 19:36:37.848282 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:37.850258 INFO::Starting hierarchical adjustment
2025-11-26 19:36:37.851148 INFO::Found 3 batches.
2025-11-26 19:36:37.852091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:37.852987 INFO::Using default BPPARAM
2025-11-26 19:36:37.853763 INFO::Processing subtree level 1
2025-11-26 19:36:37.993802 INFO::Adjusting the last 1 batches sequentially
2025-11-26 19:36:38.000014 INFO::Done
2025-11-26 19:36:38.001627 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:38.00927 INFO::ASW Batch was -0.0892412297462976 prior to batch effect correction and is now -0.0892412297462976 .
2025-11-26 19:36:38.012236 INFO::Total function execution time is 0.174068927764893 s and adjustment time is 0.149052143096924 s ( 85.63 )
2025-11-26 19:36:38.034624 INFO::Formatting Data.
2025-11-26 19:36:38.035604 INFO::Typecasting input to dataframe.
2025-11-26 19:36:38.036808 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:38.038276 INFO::Removing potential empty rows and columns
2025-11-26 19:36:38.03982 INFO::Found 0 missing values.
2025-11-26 19:36:38.043846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:38.044697 INFO::Done
2025-11-26 19:36:38.045463 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:38.048208 INFO::Starting hierarchical adjustment
2025-11-26 19:36:38.049161 INFO::Found 3 batches.
2025-11-26 19:36:38.049675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:38.050238 INFO::Using default BPPARAM
2025-11-26 19:36:38.050727 INFO::Processing subtree level 1
2025-11-26 19:36:38.185375 INFO::Adjusting the last 1 batches sequentially
2025-11-26 19:36:38.19349 INFO::Done
2025-11-26 19:36:38.196828 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:38.204748 INFO::ASW Batch was -0.0485763457312791 prior to batch effect correction and is now -0.0485763457312791 .
2025-11-26 19:36:38.206915 INFO::Total function execution time is 0.171851873397827 s and adjustment time is 0.144426822662354 s ( 84.04 )
2025-11-26 19:36:38.430436 INFO::Formatting Data.
2025-11-26 19:36:38.431661 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:38.433276 INFO::Removing potential empty rows and columns
2025-11-26 19:36:38.436978 INFO::Found 1000 missing values.
2025-11-26 19:36:38.462641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:38.463639 INFO::Done
2025-11-26 19:36:38.46452 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:38.471344 INFO::Starting hierarchical adjustment
2025-11-26 19:36:38.47232 INFO::Found 10 batches.
2025-11-26 19:36:38.473115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:38.47377 INFO::Using default BPPARAM
2025-11-26 19:36:38.474289 INFO::Processing subtree level 1
2025-11-26 19:36:38.643893 INFO::Processing subtree level 2
2025-11-26 19:36:38.879778 INFO::Adjusting the last 1 batches sequentially
2025-11-26 19:36:38.892558 INFO::Done
2025-11-26 19:36:38.894448 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:38.907256 INFO::ASW Batch was 0.510285423819019 prior to batch effect correction and is now 0.510285423819019 .
2025-11-26 19:36:38.90878 INFO::ASW Label was 0.29190598874713 prior to batch effect correction and is now 0.29190598874713 .
2025-11-26 19:36:38.910758 INFO::Total function execution time is 0.480332851409912 s and adjustment time is 0.420430898666382 s ( 87.53 )
2025-11-26 19:36:38.912358 INFO::Formatting Data.
2025-11-26 19:36:38.913438 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:38.915727 INFO::Removing potential empty rows and columns
2025-11-26 19:36:38.920204 INFO::Found 1000 missing values.
2025-11-26 19:36:38.941815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:38.942577 INFO::Done
2025-11-26 19:36:38.943133 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:38.948355 INFO::Starting hierarchical adjustment
2025-11-26 19:36:38.949557 INFO::Found 10 batches.
2025-11-26 19:36:40.066729 INFO::Set up parallel execution backend with 2 workers
2025-11-26 19:36:40.067708 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-26 19:36:41.433433 INFO::Adjusting the last 2 batches sequentially
2025-11-26 19:36:41.435227 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-26 19:36:41.457274 INFO::Done
2025-11-26 19:36:41.458183 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:41.463729 INFO::ASW Batch was 0.510285423819019 prior to batch effect correction and is now 0.510285423819019 .
2025-11-26 19:36:41.464387 INFO::ASW Label was 0.29190598874713 prior to batch effect correction and is now 0.29190598874713 .
2025-11-26 19:36:41.465106 INFO::Total function execution time is 2.55297303199768 s and adjustment time is 2.50790214538574 s ( 98.23 )
2025-11-26 19:36:41.691913 INFO::Formatting Data.
2025-11-26 19:36:41.693225 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:41.694901 INFO::Removing potential empty rows and columns
2025-11-26 19:36:41.696342 INFO::Found 0 missing values.
2025-11-26 19:36:41.701625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:41.702324 INFO::Done
2025-11-26 19:36:41.702958 INFO::Acquiring quality metrics before batch effect correction.
2025-11-26 19:36:41.706941 INFO::Starting hierarchical adjustment
2025-11-26 19:36:41.707761 INFO::Found 3 batches.
2025-11-26 19:36:41.708491 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-26 19:36:41.709478 INFO::Using default BPPARAM
2025-11-26 19:36:41.71033 INFO::Processing subtree level 1
2025-11-26 19:36:41.876651 INFO::Adjusting the last 1 batches sequentially
2025-11-26 19:36:41.886184 INFO::Done
2025-11-26 19:36:41.887702 INFO::Acquiring quality metrics after batch effect correction.
2025-11-26 19:36:41.895805 INFO::ASW Batch was 0.255818507692699 prior to batch effect correction and is now -0.148130769829216 .
2025-11-26 19:36:41.897407 INFO::ASW Label was -0.166276258731404 prior to batch effect correction and is now 0.0369015489491307 .
2025-11-26 19:36:41.89854 INFO::Total function execution time is 0.206799983978271 s and adjustment time is 0.178478956222534 s ( 86.31 )
2025-11-26 19:36:42.106345 INFO::Formatting Data.
2025-11-26 19:36:42.107451 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.108436 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.110188 INFO::Found 2 missing values.
2025-11-26 19:36:42.114727 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.115678 INFO::Done
2025-11-26 19:36:42.165836 INFO::Found NA in Reference column
2025-11-26 19:36:42.182418 INFO::Require at least two references per batch.
2025-11-26 19:36:42.212178 INFO::Formatting Data.
2025-11-26 19:36:42.213091 INFO::Recognized SummarizedExperiment
2025-11-26 19:36:42.213892 INFO::Typecasting input to dataframe.
2025-11-26 19:36:42.226221 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.22745 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.231716 INFO::Found 0 missing values.
2025-11-26 19:36:42.239051 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.239697 INFO::Done
2025-11-26 19:36:42.255032 INFO::Formatting Data.
2025-11-26 19:36:42.255835 INFO::Recognized SummarizedExperiment
2025-11-26 19:36:42.256543 INFO::Typecasting input to dataframe.
2025-11-26 19:36:42.276913 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.27863 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.283626 INFO::Found 0 missing values.
2025-11-26 19:36:42.297534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.298522 INFO::Done
2025-11-26 19:36:42.320033 INFO::Formatting Data.
2025-11-26 19:36:42.320932 INFO::Recognized SummarizedExperiment
2025-11-26 19:36:42.321549 INFO::Typecasting input to dataframe.
2025-11-26 19:36:42.343384 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.344729 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.346053 INFO::Found 0 missing values.
2025-11-26 19:36:42.347044 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.
2025-11-26 19:36:42.351859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.352624 INFO::Done
2025-11-26 19:36:42.368564 INFO::Formatting Data.
2025-11-26 19:36:42.369559 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.370693 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.372151 INFO::Found 0 missing values.
2025-11-26 19:36:42.376439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.378259 INFO::Done
2025-11-26 19:36:42.396509 INFO::Formatting Data.
2025-11-26 19:36:42.397558 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.399024 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.400458 INFO::Found 0 missing values.
2025-11-26 19:36:42.403239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.404052 INFO::Done
2025-11-26 19:36:42.450767 INFO::Formatting Data.
2025-11-26 19:36:42.451861 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.453291 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.454758 INFO::Found 1 missing values.
2025-11-26 19:36:42.457355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.457916 INFO::Done
2025-11-26 19:36:42.489783 INFO::Formatting Data.
2025-11-26 19:36:42.490984 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.49231 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.494686 INFO::Found 2 missing values.
2025-11-26 19:36:42.497259 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.
2025-11-26 19:36:42.500765 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.501364 INFO::Done
2025-11-26 19:36:42.516447 INFO::Formatting Data.
2025-11-26 19:36:42.517572 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.518908 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.520258 INFO::Found 2 missing values.
2025-11-26 19:36:42.522522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.523273 INFO::Done
2025-11-26 19:36:42.539726 INFO::Formatting Data.
2025-11-26 19:36:42.540518 INFO::Typecasting input to dataframe.
2025-11-26 19:36:42.541303 INFO::Replacing NaNs with NAs.
2025-11-26 19:36:42.542143 INFO::Removing potential empty rows and columns
2025-11-26 19:36:42.543497 INFO::Found 0 missing values.
2025-11-26 19:36:42.547325 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-26 19:36:42.548237 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.613 4.485 26.576
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.308 | 1.616 | 20.121 | |
| compute_asw | 0.029 | 0.002 | 0.030 | |
| count_existing | 0.012 | 0.002 | 0.014 | |
| generate_data_covariables | 0.011 | 0.002 | 0.012 | |
| generate_dataset | 0.012 | 0.001 | 0.012 | |