Yannis Schumann
| Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 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 2025-11-28 11:39 -0500 (Fri, 28 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" | 4866 |
| 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: 2025-11-27 18:42:47 -0500 (Thu, 27 Nov 2025) |
| EndedAt: 2025-11-27 18:43:24 -0500 (Thu, 27 Nov 2025) |
| EllapsedTime: 37.6 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) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
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 10.584 0.436 8.061
* 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-arm64/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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
2025-11-27 18:43:15.557845 INFO::Formatting Data.
2025-11-27 18:43:15.559637 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:15.565757 INFO::Removing potential empty rows and columns
2025-11-27 18:43:15.69541 INFO::Found 0 missing values.
2025-11-27 18:43:15.696769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:15.697006 INFO::Done
2025-11-27 18:43:15.69723 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:15.703775 INFO::Starting hierarchical adjustment
2025-11-27 18:43:15.704184 INFO::Found 3 batches.
2025-11-27 18:43:15.704411 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:15.70489 INFO::Using default BPPARAM
2025-11-27 18:43:15.705079 INFO::Processing subtree level 1
2025-11-27 18:43:15.773524 INFO::Adjusting the last 1 batches sequentially
2025-11-27 18:43:15.775083 INFO::Done
2025-11-27 18:43:15.775345 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:15.776991 INFO::ASW Batch was 0.0154770321412596 prior to batch effect correction and is now 0.0154770321412596 .
2025-11-27 18:43:15.777648 INFO::Total function execution time is 0.220184087753296 s and adjustment time is 0.0709781646728516 s ( 32.24 )
2025-11-27 18:43:15.786627 INFO::Formatting Data.
2025-11-27 18:43:15.786925 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:15.787302 INFO::Removing potential empty rows and columns
2025-11-27 18:43:15.787826 INFO::Found 0 missing values.
2025-11-27 18:43:15.788206 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.
2025-11-27 18:43:15.795714 INFO::Formatting Data.
2025-11-27 18:43:15.796062 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:15.796443 INFO::Removing potential empty rows and columns
2025-11-27 18:43:15.796975 INFO::Found 0 missing values.
2025-11-27 18:43:15.797357 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.
2025-11-27 18:43:15.806164 INFO::Formatting Data.
2025-11-27 18:43:15.80653 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:15.80694 INFO::Removing potential empty rows and columns
2025-11-27 18:43:15.80744 INFO::Found 0 missing values.
2025-11-27 18:43:15.807803 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.
2025-11-27 18:43:15.809723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:15.809949 INFO::Done
2025-11-27 18:43:15.810167 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:15.811207 INFO::Starting hierarchical adjustment
2025-11-27 18:43:15.811528 INFO::Found 2 batches.
2025-11-27 18:43:15.811762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:15.812066 INFO::Using default BPPARAM
2025-11-27 18:43:15.812339 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:15.812908 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 18:43:15.829155 INFO::Done
2025-11-27 18:43:15.829559 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:15.830661 INFO::ASW Batch was 0.0177316958806372 prior to batch effect correction and is now -0.0783882737021634 .
2025-11-27 18:43:15.831008 INFO::Total function execution time is 0.0248980522155762 s and adjustment time is 0.017664909362793 s ( 70.95 )
2025-11-27 18:43:15.832519 INFO::Formatting Data.
2025-11-27 18:43:15.832968 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:15.837667 INFO::Formatting Data.
2025-11-27 18:43:15.837913 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:15.838238 INFO::Removing potential empty rows and columns
2025-11-27 18:43:15.838659 INFO::Found 0 missing values.
2025-11-27 18:43:15.840084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:15.840345 INFO::Done
2025-11-27 18:43:15.840581 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:15.841527 INFO::Starting hierarchical adjustment
2025-11-27 18:43:15.841823 INFO::Found 2 batches.
2025-11-27 18:43:15.84206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:15.842327 INFO::Using default BPPARAM
2025-11-27 18:43:15.842566 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:15.842943 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 18:43:15.872694 INFO::Done
2025-11-27 18:43:15.872951 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:15.873619 INFO::ASW Batch was -0.00927335032240277 prior to batch effect correction and is now -0.125702679724584 .
2025-11-27 18:43:15.873867 INFO::Total function execution time is 0.036221981048584 s and adjustment time is 0.0309338569641113 s ( 85.4 )
2025-11-27 18:43:15.874199 INFO::Formatting Data.
2025-11-27 18:43:15.874379 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:15.874647 INFO::Removing potential empty rows and columns
2025-11-27 18:43:15.874968 INFO::Found 0 missing values.
2025-11-27 18:43:15.875872 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:15.876053 INFO::Done
2025-11-27 18:43:15.876206 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:15.876806 INFO::Starting hierarchical adjustment
2025-11-27 18:43:15.877047 INFO::Found 2 batches.
2025-11-27 18:43:15.877221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:15.877423 INFO::Using default BPPARAM
2025-11-27 18:43:15.877594 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:15.87787 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 18:43:15.882649 INFO::Done
2025-11-27 18:43:15.882852 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:15.883457 INFO::ASW Batch was -0.00927335032240277 prior to batch effect correction and is now -0.125702679724584 .
2025-11-27 18:43:15.883704 INFO::Total function execution time is 0.009490966796875 s and adjustment time is 0.00564718246459961 s ( 59.5 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-27 18:43:17.220434 INFO::Formatting Data.
2025-11-27 18:43:17.220785 INFO::Recognized SummarizedExperiment
2025-11-27 18:43:17.221015 INFO::Typecasting input to dataframe.
2025-11-27 18:43:17.234689 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.235181 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.236446 INFO::Found 0 missing values.
2025-11-27 18:43:17.238483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.238756 INFO::Done
2025-11-27 18:43:17.239081 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.240406 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.240655 INFO::Found 2 batches.
2025-11-27 18:43:17.24082 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.241154 INFO::Using default BPPARAM
2025-11-27 18:43:17.2413 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.241588 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 18:43:17.258889 INFO::Done
2025-11-27 18:43:17.259147 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.2604 INFO::ASW Batch was -0.00219727212367033 prior to batch effect correction and is now -0.0957741055805369 .
2025-11-27 18:43:17.260675 INFO::Total function execution time is 0.0403749942779541 s and adjustment time is 0.018251895904541 s ( 45.21 )
Warning: stack imbalance in '{', 73 then 75
2025-11-27 18:43:17.26776 INFO::Formatting Data.
2025-11-27 18:43:17.268079 INFO::Recognized SummarizedExperiment
2025-11-27 18:43:17.268288 INFO::Typecasting input to dataframe.
2025-11-27 18:43:17.271863 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.272319 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.273617 INFO::Found 0 missing values.
2025-11-27 18:43:17.276182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.276369 INFO::Done
2025-11-27 18:43:17.276537 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.278025 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.278318 INFO::Found 2 batches.
2025-11-27 18:43:17.278515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.278754 INFO::Using default BPPARAM
2025-11-27 18:43:17.278944 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.279291 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 18:43:17.290055 INFO::Done
2025-11-27 18:43:17.290338 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.29173 INFO::ASW Batch was 0.00180265740869669 prior to batch effect correction and is now 0.00180265740869669 .
2025-11-27 18:43:17.292039 INFO::Total function execution time is 0.024306058883667 s and adjustment time is 0.0117850303649902 s ( 48.49 )
2025-11-27 18:43:17.29964 INFO::Formatting Data.
2025-11-27 18:43:17.299875 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.300146 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.300459 INFO::Found 0 missing values.
2025-11-27 18:43:17.301334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.301552 INFO::Done
2025-11-27 18:43:17.30175 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.302784 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.303057 INFO::Found 3 batches.
2025-11-27 18:43:17.303252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.303487 INFO::Using default BPPARAM
2025-11-27 18:43:17.303675 INFO::Processing subtree level 1
2025-11-27 18:43:17.393286 INFO::Adjusting the last 1 batches sequentially
2025-11-27 18:43:17.39531 INFO::Done
2025-11-27 18:43:17.39578 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.397967 INFO::ASW Batch was -0.00680442081003698 prior to batch effect correction and is now -0.169174992741438 .
2025-11-27 18:43:17.398942 INFO::Total function execution time is 0.099153995513916 s and adjustment time is 0.0923140048980713 s ( 93.1 )
2025-11-27 18:43:17.406829 INFO::Skipping initial DF formatting
2025-11-27 18:43:17.407161 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.408835 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.409114 INFO::Found 5 batches.
2025-11-27 18:43:17.409321 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.409563 INFO::Using default BPPARAM
2025-11-27 18:43:17.409732 INFO::Processing subtree level 1
2025-11-27 18:43:17.476651 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.478849 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 18:43:17.488243 INFO::Done
2025-11-27 18:43:17.488666 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.490715 INFO::ASW Batch was 0.507183903736989 prior to batch effect correction and is now 0.507183903736989 .
2025-11-27 18:43:17.490936 INFO::ASW Label was 0.41519608333562 prior to batch effect correction and is now 0.41519608333562 .
2025-11-27 18:43:17.491699 INFO::Total function execution time is 0.0847198963165283 s and adjustment time is 0.0791800022125244 s ( 93.46 )
2025-11-27 18:43:17.501695 INFO::Formatting Data.
2025-11-27 18:43:17.501954 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.502318 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.502861 INFO::Found 0 missing values.
2025-11-27 18:43:17.504105 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.504289 INFO::Done
2025-11-27 18:43:17.504466 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.506196 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.506445 INFO::Found 5 batches.
2025-11-27 18:43:17.506607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.506966 INFO::Using default BPPARAM
2025-11-27 18:43:17.507138 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.
2025-11-27 18:43:17.559379 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.564297 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 18:43:17.576141 INFO::Done
2025-11-27 18:43:17.576558 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.578607 INFO::ASW Batch was 0.516005133561199 prior to batch effect correction and is now -0.0708945010995046 .
2025-11-27 18:43:17.578863 INFO::ASW Label was 0.203053235212577 prior to batch effect correction and is now 0.789089316204463 .
2025-11-27 18:43:17.579727 INFO::Total function execution time is 0.0778119564056396 s and adjustment time is 0.0697369575500488 s ( 89.62 )
2025-11-27 18:43:17.580371 INFO::Formatting Data.
2025-11-27 18:43:17.580593 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.581083 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.581478 INFO::Found 0 missing values.
2025-11-27 18:43:17.584384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.584699 INFO::Done
2025-11-27 18:43:17.584953 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.586269 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.586727 INFO::Found 5 batches.
2025-11-27 18:43:17.586914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.587423 INFO::Using default BPPARAM
2025-11-27 18:43:17.587657 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.
2025-11-27 18:43:17.652338 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.656474 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 18:43:17.666529 INFO::Done
2025-11-27 18:43:17.666914 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.668394 INFO::ASW Batch was 0.516005133561199 prior to batch effect correction and is now -0.0708945010995046 .
2025-11-27 18:43:17.66859 INFO::ASW Label was 0.203053235212577 prior to batch effect correction and is now 0.789089316204463 .
2025-11-27 18:43:17.669093 INFO::Total function execution time is 0.0885839462280273 s and adjustment time is 0.0800268650054932 s ( 90.34 )
2025-11-27 18:43:17.677731 INFO::Formatting Data.
2025-11-27 18:43:17.678064 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.678489 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.679105 INFO::Found 0 missing values.
2025-11-27 18:43:17.680574 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.68076 INFO::Done
2025-11-27 18:43:17.680925 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.68199 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.682224 INFO::Found 5 batches.
2025-11-27 18:43:17.68241 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.682845 INFO::Using default BPPARAM
2025-11-27 18:43:17.683023 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.
2025-11-27 18:43:17.732309 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.738337 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 18:43:17.747836 INFO::Done
2025-11-27 18:43:17.748249 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.750131 INFO::ASW Batch was 0.56552446630578 prior to batch effect correction and is now -0.102542184581902 .
2025-11-27 18:43:17.750362 INFO::ASW Label was 0.297864860634499 prior to batch effect correction and is now 0.731332464213824 .
2025-11-27 18:43:17.7514 INFO::Total function execution time is 0.0731680393218994 s and adjustment time is 0.0656528472900391 s ( 89.73 )
2025-11-27 18:43:17.752055 INFO::Formatting Data.
2025-11-27 18:43:17.752281 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.752604 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.752972 INFO::Found 0 missing values.
2025-11-27 18:43:17.754294 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.754482 INFO::Done
2025-11-27 18:43:17.754646 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.757595 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.758285 INFO::Found 5 batches.
2025-11-27 18:43:17.758603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.758925 INFO::Using default BPPARAM
2025-11-27 18:43:17.759189 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.
2025-11-27 18:43:17.826536 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.830222 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 18:43:17.838589 INFO::Done
2025-11-27 18:43:17.839089 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.840349 INFO::ASW Batch was 0.56552446630578 prior to batch effect correction and is now -0.102542184581902 .
2025-11-27 18:43:17.840558 INFO::ASW Label was 0.297864860634499 prior to batch effect correction and is now 0.731332464213824 .
2025-11-27 18:43:17.841261 INFO::Total function execution time is 0.0887999534606934 s and adjustment time is 0.0806150436401367 s ( 90.78 )
2025-11-27 18:43:17.848851 INFO::Formatting Data.
2025-11-27 18:43:17.849158 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.849494 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.849875 INFO::Found 0 missing values.
2025-11-27 18:43:17.850765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.850942 INFO::Done
2025-11-27 18:43:17.851103 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.852163 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.852425 INFO::Found 2 batches.
2025-11-27 18:43:17.85259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.85283 INFO::Using default BPPARAM
2025-11-27 18:43:17.852992 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.853278 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 18:43:17.859343 INFO::Done
2025-11-27 18:43:17.859639 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.860834 INFO::ASW Batch was 0.516319429558793 prior to batch effect correction and is now -0.0070396785553692 .
2025-11-27 18:43:17.861059 INFO::ASW Label was 0.513680953944929 prior to batch effect correction and is now 0.894450200929536 .
2025-11-27 18:43:17.86138 INFO::Total function execution time is 0.0125901699066162 s and adjustment time is 0.00695204734802246 s ( 55.22 )
2025-11-27 18:43:17.861673 INFO::Formatting Data.
2025-11-27 18:43:17.861907 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.862231 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.863255 INFO::Found 0 missing values.
2025-11-27 18:43:17.864288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.864501 INFO::Done
2025-11-27 18:43:17.864705 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.865791 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.866065 INFO::Found 2 batches.
2025-11-27 18:43:17.866272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.866468 INFO::Using default BPPARAM
2025-11-27 18:43:17.866618 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.866878 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 18:43:17.871727 INFO::Done
2025-11-27 18:43:17.871943 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.872984 INFO::ASW Batch was 0.516319429558793 prior to batch effect correction and is now -0.0070396785553692 .
2025-11-27 18:43:17.873162 INFO::ASW Label was 0.513680953944929 prior to batch effect correction and is now 0.894450200929536 .
2025-11-27 18:43:17.873602 INFO::Total function execution time is 0.0119287967681885 s and adjustment time is 0.0057070255279541 s ( 47.84 )
2025-11-27 18:43:17.87865 INFO::Formatting Data.
2025-11-27 18:43:17.878923 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.879208 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.879517 INFO::Found 0 missing values.
2025-11-27 18:43:17.880203 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.880399 INFO::Done
2025-11-27 18:43:17.880591 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.88132 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.88157 INFO::Found 2 batches.
2025-11-27 18:43:17.881738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.881969 INFO::Using default BPPARAM
2025-11-27 18:43:17.882161 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.882449 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 18:43:17.896589 INFO::Done
2025-11-27 18:43:17.896926 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.897756 INFO::ASW Batch was 0.0654426080964803 prior to batch effect correction and is now -0.0756849561924638 .
2025-11-27 18:43:17.898094 INFO::Total function execution time is 0.019474983215332 s and adjustment time is 0.0150341987609863 s ( 77.2 )
2025-11-27 18:43:17.903886 INFO::Formatting Data.
2025-11-27 18:43:17.904231 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.904593 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.905002 INFO::Found 0 missing values.
2025-11-27 18:43:17.905535 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.
2025-11-27 18:43:17.907229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.90748 INFO::Done
2025-11-27 18:43:17.907675 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.908825 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.909087 INFO::Found 2 batches.
2025-11-27 18:43:17.909245 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.909439 INFO::Using default BPPARAM
2025-11-27 18:43:17.909598 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.909878 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 18:43:17.915383 INFO::Done
2025-11-27 18:43:17.915587 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.916495 INFO::ASW Batch was 0.47388082187322 prior to batch effect correction and is now 0.0570407721634455 .
2025-11-27 18:43:17.916678 INFO::ASW Label was 0.605468373061827 prior to batch effect correction and is now 0.882628858194371 .
2025-11-27 18:43:17.916921 INFO::Total function execution time is 0.0131030082702637 s and adjustment time is 0.00634407997131348 s ( 48.42 )
2025-11-27 18:43:17.917161 INFO::Formatting Data.
2025-11-27 18:43:17.917346 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:17.917612 INFO::Removing potential empty rows and columns
2025-11-27 18:43:17.917905 INFO::Found 0 missing values.
2025-11-27 18:43:17.918164 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.
2025-11-27 18:43:17.919436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:17.919606 INFO::Done
2025-11-27 18:43:17.91976 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:17.920637 INFO::Starting hierarchical adjustment
2025-11-27 18:43:17.920851 INFO::Found 2 batches.
2025-11-27 18:43:17.921005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:17.921189 INFO::Using default BPPARAM
2025-11-27 18:43:17.921335 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:17.921597 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 18:43:17.926856 INFO::Done
2025-11-27 18:43:17.927066 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:17.928064 INFO::ASW Batch was 0.47388082187322 prior to batch effect correction and is now 0.0570407721634455 .
2025-11-27 18:43:17.928234 INFO::ASW Label was 0.605468373061827 prior to batch effect correction and is now 0.882628858194371 .
2025-11-27 18:43:17.928485 INFO::Total function execution time is 0.0113179683685303 s and adjustment time is 0.0060431957244873 s ( 53.39 )
2025-11-27 18:43:18.00453 INFO::Formatting Data.
2025-11-27 18:43:18.004875 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:18.00537 INFO::Removing potential empty rows and columns
2025-11-27 18:43:18.005706 INFO::Found 0 missing values.
2025-11-27 18:43:18.006607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:18.006784 INFO::Done
2025-11-27 18:43:18.006955 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:18.007657 INFO::Starting hierarchical adjustment
2025-11-27 18:43:18.007877 INFO::Found 3 batches.
2025-11-27 18:43:18.008027 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:18.008214 INFO::Using default BPPARAM
2025-11-27 18:43:18.008369 INFO::Processing subtree level 1
2025-11-27 18:43:18.067066 INFO::Adjusting the last 1 batches sequentially
2025-11-27 18:43:18.069942 INFO::Done
2025-11-27 18:43:18.070526 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:18.072662 INFO::ASW Batch was -0.0845489265477642 prior to batch effect correction and is now -0.0845489265477642 .
2025-11-27 18:43:18.073532 INFO::Total function execution time is 0.0689170360565186 s and adjustment time is 0.06209397315979 s ( 90.1 )
2025-11-27 18:43:18.073939 INFO::Formatting Data.
2025-11-27 18:43:18.074184 INFO::Typecasting input to dataframe.
2025-11-27 18:43:18.074482 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:18.074972 INFO::Removing potential empty rows and columns
2025-11-27 18:43:18.075522 INFO::Found 0 missing values.
2025-11-27 18:43:18.07681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:18.077036 INFO::Done
2025-11-27 18:43:18.07724 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:18.07804 INFO::Starting hierarchical adjustment
2025-11-27 18:43:18.078346 INFO::Found 3 batches.
2025-11-27 18:43:18.078538 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:18.078911 INFO::Using default BPPARAM
2025-11-27 18:43:18.079079 INFO::Processing subtree level 1
2025-11-27 18:43:18.123197 INFO::Adjusting the last 1 batches sequentially
2025-11-27 18:43:18.124777 INFO::Done
2025-11-27 18:43:18.125267 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:18.127062 INFO::ASW Batch was -0.0845489265477642 prior to batch effect correction and is now -0.0845489265477642 .
2025-11-27 18:43:18.127876 INFO::Total function execution time is 0.0537669658660889 s and adjustment time is 0.0464890003204346 s ( 86.46 )
2025-11-27 18:43:18.135443 INFO::Formatting Data.
2025-11-27 18:43:18.135741 INFO::Typecasting input to dataframe.
2025-11-27 18:43:18.136023 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:18.136344 INFO::Removing potential empty rows and columns
2025-11-27 18:43:18.1368 INFO::Found 0 missing values.
2025-11-27 18:43:18.138462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:18.138653 INFO::Done
2025-11-27 18:43:18.138824 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:18.13957 INFO::Starting hierarchical adjustment
2025-11-27 18:43:18.13983 INFO::Found 3 batches.
2025-11-27 18:43:18.140006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:18.140249 INFO::Using default BPPARAM
2025-11-27 18:43:18.140407 INFO::Processing subtree level 1
2025-11-27 18:43:18.187802 INFO::Adjusting the last 1 batches sequentially
2025-11-27 18:43:18.189688 INFO::Done
2025-11-27 18:43:18.190099 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:18.191769 INFO::ASW Batch was -0.0354558223560791 prior to batch effect correction and is now -0.0354558223560791 .
2025-11-27 18:43:18.192413 INFO::Total function execution time is 0.0568749904632568 s and adjustment time is 0.0498909950256348 s ( 87.72 )
2025-11-27 18:43:18.276139 INFO::Formatting Data.
2025-11-27 18:43:18.276437 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:18.276869 INFO::Removing potential empty rows and columns
2025-11-27 18:43:18.277817 INFO::Found 1000 missing values.
2025-11-27 18:43:18.283628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:18.284297 INFO::Done
2025-11-27 18:43:18.284506 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:18.286739 INFO::Starting hierarchical adjustment
2025-11-27 18:43:18.287017 INFO::Found 10 batches.
2025-11-27 18:43:18.287194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:18.287446 INFO::Using default BPPARAM
2025-11-27 18:43:18.287634 INFO::Processing subtree level 1
2025-11-27 18:43:18.348966 INFO::Processing subtree level 2
2025-11-27 18:43:18.487058 INFO::Adjusting the last 1 batches sequentially
2025-11-27 18:43:18.488758 INFO::Done
2025-11-27 18:43:18.489005 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:18.492358 INFO::ASW Batch was 0.51311621580814 prior to batch effect correction and is now 0.51311621580814 .
2025-11-27 18:43:18.492706 INFO::ASW Label was 0.331289461785586 prior to batch effect correction and is now 0.331289461785586 .
2025-11-27 18:43:18.494218 INFO::Total function execution time is 0.217967987060547 s and adjustment time is 0.201792001724243 s ( 92.58 )
2025-11-27 18:43:18.495123 INFO::Formatting Data.
2025-11-27 18:43:18.495429 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:18.496035 INFO::Removing potential empty rows and columns
2025-11-27 18:43:18.542347 INFO::Found 1000 missing values.
2025-11-27 18:43:18.551489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:18.55209 INFO::Done
2025-11-27 18:43:18.552594 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:18.55503 INFO::Starting hierarchical adjustment
2025-11-27 18:43:18.555354 INFO::Found 10 batches.
2025-11-27 18:43:19.143189 INFO::Set up parallel execution backend with 2 workers
2025-11-27 18:43:19.143618 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-27 18:43:19.860364 INFO::Adjusting the last 2 batches sequentially
2025-11-27 18:43:19.860961 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 18:43:19.866349 INFO::Done
2025-11-27 18:43:19.866538 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:19.868416 INFO::ASW Batch was 0.51311621580814 prior to batch effect correction and is now 0.51311621580814 .
2025-11-27 18:43:19.868599 INFO::ASW Label was 0.331289461785586 prior to batch effect correction and is now 0.331289461785586 .
2025-11-27 18:43:19.868841 INFO::Total function execution time is 1.37373995780945 s and adjustment time is 1.31106090545654 s ( 95.44 )
2025-11-27 18:43:19.9471 INFO::Formatting Data.
2025-11-27 18:43:19.947575 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:19.948074 INFO::Removing potential empty rows and columns
2025-11-27 18:43:19.948708 INFO::Found 0 missing values.
2025-11-27 18:43:19.950972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:19.951397 INFO::Done
2025-11-27 18:43:19.95167 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 18:43:19.953588 INFO::Starting hierarchical adjustment
2025-11-27 18:43:19.954354 INFO::Found 3 batches.
2025-11-27 18:43:19.954617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 18:43:19.954918 INFO::Using default BPPARAM
2025-11-27 18:43:19.955142 INFO::Processing subtree level 1
2025-11-27 18:43:20.028344 INFO::Adjusting the last 1 batches sequentially
2025-11-27 18:43:20.029927 INFO::Done
2025-11-27 18:43:20.030282 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 18:43:20.032444 INFO::ASW Batch was 0.0914081778405461 prior to batch effect correction and is now -0.164441870381959 .
2025-11-27 18:43:20.032775 INFO::ASW Label was -0.145374985930144 prior to batch effect correction and is now 0.0580753301532095 .
2025-11-27 18:43:20.033347 INFO::Total function execution time is 0.0862710475921631 s and adjustment time is 0.0758647918701172 s ( 87.94 )
2025-11-27 18:43:20.113417 INFO::Formatting Data.
2025-11-27 18:43:20.113831 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.114303 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.114842 INFO::Found 2 missing values.
2025-11-27 18:43:20.116314 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.116609 INFO::Done
2025-11-27 18:43:20.131817 INFO::Found NA in Reference column
2025-11-27 18:43:20.136765 INFO::Require at least two references per batch.
2025-11-27 18:43:20.151953 INFO::Formatting Data.
2025-11-27 18:43:20.152449 INFO::Recognized SummarizedExperiment
2025-11-27 18:43:20.152703 INFO::Typecasting input to dataframe.
2025-11-27 18:43:20.158902 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.159461 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.161257 INFO::Found 0 missing values.
2025-11-27 18:43:20.165006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.165243 INFO::Done
2025-11-27 18:43:20.173662 INFO::Formatting Data.
2025-11-27 18:43:20.174056 INFO::Recognized SummarizedExperiment
2025-11-27 18:43:20.174356 INFO::Typecasting input to dataframe.
2025-11-27 18:43:20.182842 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.18348 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.18531 INFO::Found 0 missing values.
2025-11-27 18:43:20.191075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.191394 INFO::Done
2025-11-27 18:43:20.199859 INFO::Formatting Data.
2025-11-27 18:43:20.200218 INFO::Recognized SummarizedExperiment
2025-11-27 18:43:20.200481 INFO::Typecasting input to dataframe.
2025-11-27 18:43:20.207978 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.208409 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.208896 INFO::Found 0 missing values.
2025-11-27 18:43:20.209295 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.
2025-11-27 18:43:20.211471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.211739 INFO::Done
2025-11-27 18:43:20.217686 INFO::Formatting Data.
2025-11-27 18:43:20.218034 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.21846 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.218948 INFO::Found 0 missing values.
2025-11-27 18:43:20.220323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.220566 INFO::Done
2025-11-27 18:43:20.247914 INFO::Formatting Data.
2025-11-27 18:43:20.24947 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.25031 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.25093 INFO::Found 0 missing values.
2025-11-27 18:43:20.252355 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.252817 INFO::Done
2025-11-27 18:43:20.273606 INFO::Formatting Data.
2025-11-27 18:43:20.273994 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.274744 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.275459 INFO::Found 1 missing values.
2025-11-27 18:43:20.27658 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.276826 INFO::Done
2025-11-27 18:43:20.292261 INFO::Formatting Data.
2025-11-27 18:43:20.292672 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.293066 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.293444 INFO::Found 2 missing values.
2025-11-27 18:43:20.294221 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.
2025-11-27 18:43:20.295188 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.295572 INFO::Done
2025-11-27 18:43:20.304133 INFO::Formatting Data.
2025-11-27 18:43:20.304848 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.305336 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.305776 INFO::Found 2 missing values.
2025-11-27 18:43:20.306467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.306678 INFO::Done
2025-11-27 18:43:20.312963 INFO::Formatting Data.
2025-11-27 18:43:20.313557 INFO::Typecasting input to dataframe.
2025-11-27 18:43:20.313956 INFO::Replacing NaNs with NAs.
2025-11-27 18:43:20.314358 INFO::Removing potential empty rows and columns
2025-11-27 18:43:20.314856 INFO::Found 0 missing values.
2025-11-27 18:43:20.316202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 18:43:20.316435 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.286 1.962 10.122
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.584 | 0.436 | 8.061 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.006 | |
| generate_data_covariables | 0.005 | 0.000 | 0.006 | |
| generate_dataset | 0.004 | 0.000 | 0.004 | |