Yannis Schumann
| Snapshot Date: 2025-12-03 13:40 -0500 (Wed, 03 Dec 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 2025-12-04 11:35 -0500 (Thu, 04 Dec 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" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 168/2331 | 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 | | ||||||||
| 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: 2025-12-03 19:08:13 -0500 (Wed, 03 Dec 2025) |
| EndedAt: 2025-12-03 19:12:51 -0500 (Wed, 03 Dec 2025) |
| EllapsedTime: 277.9 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 12.531 0.582 13.858
* 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")
2025-12-03 19:12:44.027784 INFO::Formatting Data.
2025-12-03 19:12:44.029455 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:44.03388 INFO::Removing potential empty rows and columns
2025-12-03 19:12:44.136504 INFO::Found 0 missing values.
2025-12-03 19:12:44.137888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:44.13815 INFO::Done
2025-12-03 19:12:44.138368 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:44.143971 INFO::Starting hierarchical adjustment
2025-12-03 19:12:44.144294 INFO::Found 3 batches.
2025-12-03 19:12:44.144508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:44.14493 INFO::Using default BPPARAM
2025-12-03 19:12:44.145122 INFO::Processing subtree level 1
2025-12-03 19:12:44.209749 INFO::Adjusting the last 1 batches sequentially
2025-12-03 19:12:44.210981 INFO::Done
2025-12-03 19:12:44.211374 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:44.212719 INFO::ASW Batch was -0.0736271987873201 prior to batch effect correction and is now -0.0736271987873201 .
2025-12-03 19:12:44.213137 INFO::Total function execution time is 0.185763835906982 s and adjustment time is 0.0667581558227539 s ( 35.94 )
2025-12-03 19:12:44.219677 INFO::Formatting Data.
2025-12-03 19:12:44.219933 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:44.22026 INFO::Removing potential empty rows and columns
2025-12-03 19:12:44.22071 INFO::Found 0 missing values.
2025-12-03 19:12:44.221031 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-03 19:12:44.225581 INFO::Formatting Data.
2025-12-03 19:12:44.225841 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:44.226217 INFO::Removing potential empty rows and columns
2025-12-03 19:12:44.230304 INFO::Found 0 missing values.
2025-12-03 19:12:44.230838 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-03 19:12:44.238637 INFO::Formatting Data.
2025-12-03 19:12:44.238904 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:44.239213 INFO::Removing potential empty rows and columns
2025-12-03 19:12:44.239576 INFO::Found 0 missing values.
2025-12-03 19:12:44.23987 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-03 19:12:44.241309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:44.241511 INFO::Done
2025-12-03 19:12:44.241688 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:44.242483 INFO::Starting hierarchical adjustment
2025-12-03 19:12:44.242741 INFO::Found 2 batches.
2025-12-03 19:12:44.242938 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:44.243207 INFO::Using default BPPARAM
2025-12-03 19:12:44.243411 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:44.243798 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-03 19:12:44.252385 INFO::Done
2025-12-03 19:12:44.252622 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:44.253286 INFO::ASW Batch was -0.0322100038301394 prior to batch effect correction and is now -0.129595403614662 .
2025-12-03 19:12:44.25355 INFO::Total function execution time is 0.0149509906768799 s and adjustment time is 0.00969386100769043 s ( 64.84 )
2025-12-03 19:12:44.255111 INFO::Formatting Data.
2025-12-03 19:12:44.255496 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:44.25915 INFO::Formatting Data.
2025-12-03 19:12:44.259384 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:44.259706 INFO::Removing potential empty rows and columns
2025-12-03 19:12:44.260101 INFO::Found 0 missing values.
2025-12-03 19:12:44.261146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:44.261329 INFO::Done
2025-12-03 19:12:44.2615 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:44.262156 INFO::Starting hierarchical adjustment
2025-12-03 19:12:44.262385 INFO::Found 2 batches.
2025-12-03 19:12:44.262556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:44.262764 INFO::Using default BPPARAM
2025-12-03 19:12:44.262932 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:44.263211 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:44.286918 INFO::Done
2025-12-03 19:12:44.287166 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:44.287802 INFO::ASW Batch was 0.0119600757166793 prior to batch effect correction and is now -0.111141532024387 .
2025-12-03 19:12:44.288058 INFO::Total function execution time is 0.0289130210876465 s and adjustment time is 0.0245699882507324 s ( 84.98 )
2025-12-03 19:12:44.288382 INFO::Formatting Data.
2025-12-03 19:12:44.288564 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:44.288825 INFO::Removing potential empty rows and columns
2025-12-03 19:12:44.289135 INFO::Found 0 missing values.
2025-12-03 19:12:44.290018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:44.290187 INFO::Done
2025-12-03 19:12:44.290345 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:44.290944 INFO::Starting hierarchical adjustment
2025-12-03 19:12:44.291182 INFO::Found 2 batches.
2025-12-03 19:12:44.291364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:44.291569 INFO::Using default BPPARAM
2025-12-03 19:12:44.291727 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:44.291987 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:44.296707 INFO::Done
2025-12-03 19:12:44.296926 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:44.297578 INFO::ASW Batch was 0.0119600757166793 prior to batch effect correction and is now -0.111141532024387 .
2025-12-03 19:12:44.297814 INFO::Total function execution time is 0.00942015647888184 s and adjustment time is 0.00556206703186035 s ( 59.04 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-03 19:12:45.601708 INFO::Formatting Data.
2025-12-03 19:12:45.601964 INFO::Recognized SummarizedExperiment
2025-12-03 19:12:45.602119 INFO::Typecasting input to dataframe.
2025-12-03 19:12:45.612016 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:45.612413 INFO::Removing potential empty rows and columns
2025-12-03 19:12:45.613455 INFO::Found 0 missing values.
2025-12-03 19:12:45.615352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:45.615523 INFO::Done
2025-12-03 19:12:45.61566 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:45.616744 INFO::Starting hierarchical adjustment
2025-12-03 19:12:45.616963 INFO::Found 2 batches.
2025-12-03 19:12:45.617104 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:45.617433 INFO::Using default BPPARAM
2025-12-03 19:12:45.617573 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:45.617832 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-03 19:12:45.636717 INFO::Done
2025-12-03 19:12:45.636996 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:45.638438 INFO::ASW Batch was 0.000531634089831337 prior to batch effect correction and is now -0.0916759147421536 .
2025-12-03 19:12:45.638758 INFO::Total function execution time is 0.037128210067749 s and adjustment time is 0.0197889804840088 s ( 53.3 )
Warning: stack imbalance in '{', 73 then 75
2025-12-03 19:12:45.6461 INFO::Formatting Data.
2025-12-03 19:12:45.646404 INFO::Recognized SummarizedExperiment
2025-12-03 19:12:45.646601 INFO::Typecasting input to dataframe.
2025-12-03 19:12:45.649856 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:45.650238 INFO::Removing potential empty rows and columns
2025-12-03 19:12:45.651391 INFO::Found 0 missing values.
2025-12-03 19:12:45.653558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:45.653727 INFO::Done
2025-12-03 19:12:45.653882 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:45.655108 INFO::Starting hierarchical adjustment
2025-12-03 19:12:45.655341 INFO::Found 2 batches.
2025-12-03 19:12:45.655504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:45.655692 INFO::Using default BPPARAM
2025-12-03 19:12:45.655847 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:45.656145 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-03 19:12:45.665526 INFO::Done
2025-12-03 19:12:45.66576 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:45.666974 INFO::ASW Batch was -0.00556163418226034 prior to batch effect correction and is now -0.00556163418226034 .
2025-12-03 19:12:45.667255 INFO::Total function execution time is 0.0211668014526367 s and adjustment time is 0.0102288722991943 s ( 48.33 )
2025-12-03 19:12:45.673938 INFO::Formatting Data.
2025-12-03 19:12:45.674171 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:45.674455 INFO::Removing potential empty rows and columns
2025-12-03 19:12:45.674768 INFO::Found 0 missing values.
2025-12-03 19:12:45.675624 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:45.675787 INFO::Done
2025-12-03 19:12:45.67594 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:45.676547 INFO::Starting hierarchical adjustment
2025-12-03 19:12:45.676753 INFO::Found 3 batches.
2025-12-03 19:12:45.676926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:45.677109 INFO::Using default BPPARAM
2025-12-03 19:12:45.677257 INFO::Processing subtree level 1
2025-12-03 19:12:45.740254 INFO::Adjusting the last 1 batches sequentially
2025-12-03 19:12:45.741287 INFO::Done
2025-12-03 19:12:45.741528 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:45.743108 INFO::ASW Batch was -0.0295474284602939 prior to batch effect correction and is now -0.16594548387102 .
2025-12-03 19:12:45.743812 INFO::Total function execution time is 0.0698719024658203 s and adjustment time is 0.0645599365234375 s ( 92.4 )
2025-12-03 19:12:45.7507 INFO::Skipping initial DF formatting
2025-12-03 19:12:45.750935 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:45.752311 INFO::Starting hierarchical adjustment
2025-12-03 19:12:45.752551 INFO::Found 5 batches.
2025-12-03 19:12:45.752722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:45.752929 INFO::Using default BPPARAM
2025-12-03 19:12:45.753096 INFO::Processing subtree level 1
2025-12-03 19:12:45.806558 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:45.807746 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-03 19:12:45.816952 INFO::Done
2025-12-03 19:12:45.81724 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:45.819931 INFO::ASW Batch was 0.496304134412891 prior to batch effect correction and is now 0.496304134412891 .
2025-12-03 19:12:45.820357 INFO::ASW Label was 0.382316816284791 prior to batch effect correction and is now 0.382316816284791 .
2025-12-03 19:12:45.82072 INFO::Total function execution time is 0.0700211524963379 s and adjustment time is 0.0644409656524658 s ( 92.03 )
2025-12-03 19:12:45.828637 INFO::Formatting Data.
2025-12-03 19:12:45.828906 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:45.829249 INFO::Removing potential empty rows and columns
2025-12-03 19:12:45.829602 INFO::Found 0 missing values.
2025-12-03 19:12:45.830836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:45.831023 INFO::Done
2025-12-03 19:12:45.831188 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:45.832174 INFO::Starting hierarchical adjustment
2025-12-03 19:12:45.832411 INFO::Found 5 batches.
2025-12-03 19:12:45.832582 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:45.832795 INFO::Using default BPPARAM
2025-12-03 19:12:45.832957 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:45.883451 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:45.884809 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:45.894788 INFO::Done
2025-12-03 19:12:45.89504 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:45.896612 INFO::ASW Batch was 0.47455511062515 prior to batch effect correction and is now -0.0977866714167203 .
2025-12-03 19:12:45.896886 INFO::ASW Label was 0.287191557719274 prior to batch effect correction and is now 0.834644387216737 .
2025-12-03 19:12:45.897203 INFO::Total function execution time is 0.0685930252075195 s and adjustment time is 0.0624179840087891 s ( 91 )
2025-12-03 19:12:45.897493 INFO::Formatting Data.
2025-12-03 19:12:45.897893 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:45.898187 INFO::Removing potential empty rows and columns
2025-12-03 19:12:45.898508 INFO::Found 0 missing values.
2025-12-03 19:12:45.899877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:45.900092 INFO::Done
2025-12-03 19:12:45.900273 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:45.901335 INFO::Starting hierarchical adjustment
2025-12-03 19:12:45.901584 INFO::Found 5 batches.
2025-12-03 19:12:45.901761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:45.901981 INFO::Using default BPPARAM
2025-12-03 19:12:45.90214 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:45.951637 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:45.953033 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:45.964189 INFO::Done
2025-12-03 19:12:45.964474 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:45.968428 INFO::ASW Batch was 0.47455511062515 prior to batch effect correction and is now -0.0977866714167203 .
2025-12-03 19:12:45.968671 INFO::ASW Label was 0.287191557719274 prior to batch effect correction and is now 0.834644387216737 .
2025-12-03 19:12:45.968989 INFO::Total function execution time is 0.071462869644165 s and adjustment time is 0.0626449584960938 s ( 87.66 )
2025-12-03 19:12:45.979525 INFO::Formatting Data.
2025-12-03 19:12:45.980123 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:45.980456 INFO::Removing potential empty rows and columns
2025-12-03 19:12:45.980857 INFO::Found 0 missing values.
2025-12-03 19:12:45.982191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:45.982387 INFO::Done
2025-12-03 19:12:45.982555 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:45.983558 INFO::Starting hierarchical adjustment
2025-12-03 19:12:45.98384 INFO::Found 5 batches.
2025-12-03 19:12:45.984017 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:45.984501 INFO::Using default BPPARAM
2025-12-03 19:12:45.984697 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:46.031254 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:46.033345 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:46.042097 INFO::Done
2025-12-03 19:12:46.042351 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.043753 INFO::ASW Batch was 0.36365854046675 prior to batch effect correction and is now -0.00648619738987983 .
2025-12-03 19:12:46.043961 INFO::ASW Label was 0.455050722879517 prior to batch effect correction and is now 0.828885264622065 .
2025-12-03 19:12:46.044263 INFO::Total function execution time is 0.0647659301757812 s and adjustment time is 0.0583000183105469 s ( 90.02 )
2025-12-03 19:12:46.044577 INFO::Formatting Data.
2025-12-03 19:12:46.044905 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.045187 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.045506 INFO::Found 0 missing values.
2025-12-03 19:12:46.046864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.047103 INFO::Done
2025-12-03 19:12:46.047284 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.04828 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.048658 INFO::Found 5 batches.
2025-12-03 19:12:46.048837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.04906 INFO::Using default BPPARAM
2025-12-03 19:12:46.049227 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:46.099967 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:46.101707 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:46.109959 INFO::Done
2025-12-03 19:12:46.110219 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.111714 INFO::ASW Batch was 0.36365854046675 prior to batch effect correction and is now -0.00648619738987983 .
2025-12-03 19:12:46.111948 INFO::ASW Label was 0.455050722879517 prior to batch effect correction and is now 0.828885264622065 .
2025-12-03 19:12:46.112279 INFO::Total function execution time is 0.0676698684692383 s and adjustment time is 0.0613391399383545 s ( 90.64 )
2025-12-03 19:12:46.118738 INFO::Formatting Data.
2025-12-03 19:12:46.118999 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.119305 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.119657 INFO::Found 0 missing values.
2025-12-03 19:12:46.120497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.120668 INFO::Done
2025-12-03 19:12:46.120828 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.12184 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.122079 INFO::Found 2 batches.
2025-12-03 19:12:46.122242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.122459 INFO::Using default BPPARAM
2025-12-03 19:12:46.12262 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:46.122892 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:46.128214 INFO::Done
2025-12-03 19:12:46.128441 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.129333 INFO::ASW Batch was 0.428498909466654 prior to batch effect correction and is now -0.0217479679873761 .
2025-12-03 19:12:46.129521 INFO::ASW Label was 0.667299229325456 prior to batch effect correction and is now 0.948843163033256 .
2025-12-03 19:12:46.129763 INFO::Total function execution time is 0.0110788345336914 s and adjustment time is 0.00617098808288574 s ( 55.7 )
2025-12-03 19:12:46.129995 INFO::Formatting Data.
2025-12-03 19:12:46.130162 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.130419 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.1309 INFO::Found 0 missing values.
2025-12-03 19:12:46.131686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.131857 INFO::Done
2025-12-03 19:12:46.132118 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.13293 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.133157 INFO::Found 2 batches.
2025-12-03 19:12:46.133313 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.133493 INFO::Using default BPPARAM
2025-12-03 19:12:46.133642 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:46.133896 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-03 19:12:46.138466 INFO::Done
2025-12-03 19:12:46.138659 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.139518 INFO::ASW Batch was 0.428498909466654 prior to batch effect correction and is now -0.0217479679873761 .
2025-12-03 19:12:46.13969 INFO::ASW Label was 0.667299229325456 prior to batch effect correction and is now 0.948843163033256 .
2025-12-03 19:12:46.139912 INFO::Total function execution time is 0.00990891456604004 s and adjustment time is 0.00536108016967773 s ( 54.1 )
2025-12-03 19:12:46.14449 INFO::Formatting Data.
2025-12-03 19:12:46.144732 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.144992 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.145255 INFO::Found 0 missing values.
2025-12-03 19:12:46.145864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.146023 INFO::Done
2025-12-03 19:12:46.146177 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.146735 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.146938 INFO::Found 2 batches.
2025-12-03 19:12:46.147115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.147302 INFO::Using default BPPARAM
2025-12-03 19:12:46.147608 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:46.147852 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-03 19:12:46.158089 INFO::Done
2025-12-03 19:12:46.158311 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.15893 INFO::ASW Batch was 0.158232269215301 prior to batch effect correction and is now -0.138578798315255 .
2025-12-03 19:12:46.159177 INFO::Total function execution time is 0.0146970748901367 s and adjustment time is 0.0111780166625977 s ( 76.06 )
2025-12-03 19:12:46.16376 INFO::Formatting Data.
2025-12-03 19:12:46.163975 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.164236 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.164535 INFO::Found 0 missing values.
2025-12-03 19:12:46.16492 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-03 19:12:46.16651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.166703 INFO::Done
2025-12-03 19:12:46.16687 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.167965 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.168232 INFO::Found 2 batches.
2025-12-03 19:12:46.168433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.168633 INFO::Using default BPPARAM
2025-12-03 19:12:46.168809 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:46.169161 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-03 19:12:46.175188 INFO::Done
2025-12-03 19:12:46.175424 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.176496 INFO::ASW Batch was 0.290682999875962 prior to batch effect correction and is now -0.0242782271316112 .
2025-12-03 19:12:46.176724 INFO::ASW Label was 0.624991405400319 prior to batch effect correction and is now 0.923416341172493 .
2025-12-03 19:12:46.177013 INFO::Total function execution time is 0.0132501125335693 s and adjustment time is 0.00700807571411133 s ( 52.89 )
2025-12-03 19:12:46.177312 INFO::Formatting Data.
2025-12-03 19:12:46.177527 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.17786 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.178189 INFO::Found 0 missing values.
2025-12-03 19:12:46.178493 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-03 19:12:46.179979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.180163 INFO::Done
2025-12-03 19:12:46.180343 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.181317 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.181567 INFO::Found 2 batches.
2025-12-03 19:12:46.181735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.181944 INFO::Using default BPPARAM
2025-12-03 19:12:46.182107 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:46.182424 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-03 19:12:46.188424 INFO::Done
2025-12-03 19:12:46.188683 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.189618 INFO::ASW Batch was 0.290682999875962 prior to batch effect correction and is now -0.0242782271316112 .
2025-12-03 19:12:46.189814 INFO::ASW Label was 0.624991405400319 prior to batch effect correction and is now 0.923416341172493 .
2025-12-03 19:12:46.190065 INFO::Total function execution time is 0.0127580165863037 s and adjustment time is 0.00689291954040527 s ( 54.03 )
2025-12-03 19:12:46.262394 INFO::Formatting Data.
2025-12-03 19:12:46.262705 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.263047 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.263423 INFO::Found 0 missing values.
2025-12-03 19:12:46.264345 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.264513 INFO::Done
2025-12-03 19:12:46.26468 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.265353 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.265585 INFO::Found 3 batches.
2025-12-03 19:12:46.265738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.265927 INFO::Using default BPPARAM
2025-12-03 19:12:46.266086 INFO::Processing subtree level 1
2025-12-03 19:12:46.311596 INFO::Adjusting the last 1 batches sequentially
2025-12-03 19:12:46.313259 INFO::Done
2025-12-03 19:12:46.313504 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.315197 INFO::ASW Batch was -0.0723865918599854 prior to batch effect correction and is now -0.0723865918599854 .
2025-12-03 19:12:46.315666 INFO::Total function execution time is 0.053292989730835 s and adjustment time is 0.0477209091186523 s ( 89.54 )
2025-12-03 19:12:46.316091 INFO::Formatting Data.
2025-12-03 19:12:46.316522 INFO::Typecasting input to dataframe.
2025-12-03 19:12:46.316754 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.317077 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.317528 INFO::Found 0 missing values.
2025-12-03 19:12:46.318626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.31885 INFO::Done
2025-12-03 19:12:46.319029 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.319751 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.319991 INFO::Found 3 batches.
2025-12-03 19:12:46.320172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.320442 INFO::Using default BPPARAM
2025-12-03 19:12:46.320621 INFO::Processing subtree level 1
2025-12-03 19:12:46.368224 INFO::Adjusting the last 1 batches sequentially
2025-12-03 19:12:46.369821 INFO::Done
2025-12-03 19:12:46.370055 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.371656 INFO::ASW Batch was -0.0723865918599854 prior to batch effect correction and is now -0.0723865918599854 .
2025-12-03 19:12:46.372131 INFO::Total function execution time is 0.0559189319610596 s and adjustment time is 0.049868106842041 s ( 89.18 )
2025-12-03 19:12:46.377831 INFO::Formatting Data.
2025-12-03 19:12:46.37808 INFO::Typecasting input to dataframe.
2025-12-03 19:12:46.378341 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.378647 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.379006 INFO::Found 0 missing values.
2025-12-03 19:12:46.379896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.380067 INFO::Done
2025-12-03 19:12:46.380236 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.380864 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.381078 INFO::Found 3 batches.
2025-12-03 19:12:46.381229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.381431 INFO::Using default BPPARAM
2025-12-03 19:12:46.381585 INFO::Processing subtree level 1
2025-12-03 19:12:46.417159 INFO::Adjusting the last 1 batches sequentially
2025-12-03 19:12:46.418619 INFO::Done
2025-12-03 19:12:46.418876 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.420271 INFO::ASW Batch was 0.00594323594515337 prior to batch effect correction and is now 0.00594323594515337 .
2025-12-03 19:12:46.420652 INFO::Total function execution time is 0.0428438186645508 s and adjustment time is 0.0375781059265137 s ( 87.71 )
2025-12-03 19:12:46.483822 INFO::Formatting Data.
2025-12-03 19:12:46.484113 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.484512 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.485506 INFO::Found 1000 missing values.
2025-12-03 19:12:46.491771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.492005 INFO::Done
2025-12-03 19:12:46.492231 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.494203 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.494448 INFO::Found 10 batches.
2025-12-03 19:12:46.494618 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:46.494826 INFO::Using default BPPARAM
2025-12-03 19:12:46.494995 INFO::Processing subtree level 1
2025-12-03 19:12:46.541895 INFO::Processing subtree level 2
2025-12-03 19:12:46.670759 INFO::Adjusting the last 1 batches sequentially
2025-12-03 19:12:46.674017 INFO::Done
2025-12-03 19:12:46.674559 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:46.678568 INFO::ASW Batch was 0.534934474062996 prior to batch effect correction and is now 0.534934474062996 .
2025-12-03 19:12:46.678933 INFO::ASW Label was 0.290938171272272 prior to batch effect correction and is now 0.290938171272272 .
2025-12-03 19:12:46.706115 INFO::Total function execution time is 0.222265005111694 s and adjustment time is 0.179592132568359 s ( 80.8 )
2025-12-03 19:12:46.706509 INFO::Formatting Data.
2025-12-03 19:12:46.706726 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:46.707249 INFO::Removing potential empty rows and columns
2025-12-03 19:12:46.708472 INFO::Found 1000 missing values.
2025-12-03 19:12:46.71566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:46.715879 INFO::Done
2025-12-03 19:12:46.716054 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:46.718432 INFO::Starting hierarchical adjustment
2025-12-03 19:12:46.718711 INFO::Found 10 batches.
2025-12-03 19:12:47.178237 INFO::Set up parallel execution backend with 2 workers
2025-12-03 19:12:47.178522 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-03 19:12:47.694192 INFO::Adjusting the last 2 batches sequentially
2025-12-03 19:12:47.694744 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-03 19:12:47.700329 INFO::Done
2025-12-03 19:12:47.70054 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:47.702336 INFO::ASW Batch was 0.534934474062996 prior to batch effect correction and is now 0.534934474062996 .
2025-12-03 19:12:47.702514 INFO::ASW Label was 0.290938171272272 prior to batch effect correction and is now 0.290938171272272 .
2025-12-03 19:12:47.702748 INFO::Total function execution time is 0.996265172958374 s and adjustment time is 0.981667995452881 s ( 98.53 )
2025-12-03 19:12:47.769694 INFO::Formatting Data.
2025-12-03 19:12:47.769949 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.770252 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.770621 INFO::Found 0 missing values.
2025-12-03 19:12:47.771771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.771951 INFO::Done
2025-12-03 19:12:47.772127 INFO::Acquiring quality metrics before batch effect correction.
2025-12-03 19:12:47.773002 INFO::Starting hierarchical adjustment
2025-12-03 19:12:47.773241 INFO::Found 3 batches.
2025-12-03 19:12:47.773513 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-03 19:12:47.773713 INFO::Using default BPPARAM
2025-12-03 19:12:47.773868 INFO::Processing subtree level 1
2025-12-03 19:12:47.827273 INFO::Adjusting the last 1 batches sequentially
2025-12-03 19:12:47.828425 INFO::Done
2025-12-03 19:12:47.829223 INFO::Acquiring quality metrics after batch effect correction.
2025-12-03 19:12:47.833253 INFO::ASW Batch was 0.124496938584671 prior to batch effect correction and is now -0.12063764922517 .
2025-12-03 19:12:47.833468 INFO::ASW Label was -0.193596809947822 prior to batch effect correction and is now -0.0731235061050875 .
2025-12-03 19:12:47.833836 INFO::Total function execution time is 0.0641520023345947 s and adjustment time is 0.055217981338501 s ( 86.07 )
2025-12-03 19:12:47.887194 INFO::Formatting Data.
2025-12-03 19:12:47.887567 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.887909 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.888297 INFO::Found 2 missing values.
2025-12-03 19:12:47.889277 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.88945 INFO::Done
2025-12-03 19:12:47.900871 INFO::Found NA in Reference column
2025-12-03 19:12:47.904466 INFO::Require at least two references per batch.
2025-12-03 19:12:47.912613 INFO::Formatting Data.
2025-12-03 19:12:47.912862 INFO::Recognized SummarizedExperiment
2025-12-03 19:12:47.913031 INFO::Typecasting input to dataframe.
2025-12-03 19:12:47.916725 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.917137 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.918413 INFO::Found 0 missing values.
2025-12-03 19:12:47.920827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.921003 INFO::Done
2025-12-03 19:12:47.926538 INFO::Formatting Data.
2025-12-03 19:12:47.92678 INFO::Recognized SummarizedExperiment
2025-12-03 19:12:47.926964 INFO::Typecasting input to dataframe.
2025-12-03 19:12:47.933086 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.933573 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.935104 INFO::Found 0 missing values.
2025-12-03 19:12:47.939393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.939586 INFO::Done
2025-12-03 19:12:47.944964 INFO::Formatting Data.
2025-12-03 19:12:47.94517 INFO::Recognized SummarizedExperiment
2025-12-03 19:12:47.945345 INFO::Typecasting input to dataframe.
2025-12-03 19:12:47.951082 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.951461 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.951853 INFO::Found 0 missing values.
2025-12-03 19:12:47.952209 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-03 19:12:47.95387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.954088 INFO::Done
2025-12-03 19:12:47.958686 INFO::Formatting Data.
2025-12-03 19:12:47.958978 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.959301 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.959653 INFO::Found 0 missing values.
2025-12-03 19:12:47.960667 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.960859 INFO::Done
2025-12-03 19:12:47.965699 INFO::Formatting Data.
2025-12-03 19:12:47.966014 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.966328 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.966682 INFO::Found 0 missing values.
2025-12-03 19:12:47.967645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.967814 INFO::Done
2025-12-03 19:12:47.978591 INFO::Formatting Data.
2025-12-03 19:12:47.978864 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.979269 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.979698 INFO::Found 1 missing values.
2025-12-03 19:12:47.980634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.980813 INFO::Done
2025-12-03 19:12:47.988884 INFO::Formatting Data.
2025-12-03 19:12:47.989142 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.989412 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.989713 INFO::Found 2 missing values.
2025-12-03 19:12:47.989991 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-12-03 19:12:47.990724 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.990891 INFO::Done
2025-12-03 19:12:47.994939 INFO::Formatting Data.
2025-12-03 19:12:47.995261 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:47.995576 INFO::Removing potential empty rows and columns
2025-12-03 19:12:47.995879 INFO::Found 2 missing values.
2025-12-03 19:12:47.996392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:47.996554 INFO::Done
2025-12-03 19:12:48.000486 INFO::Formatting Data.
2025-12-03 19:12:48.000751 INFO::Typecasting input to dataframe.
2025-12-03 19:12:48.001008 INFO::Replacing NaNs with NAs.
2025-12-03 19:12:48.001284 INFO::Removing potential empty rows and columns
2025-12-03 19:12:48.001596 INFO::Found 0 missing values.
2025-12-03 19:12:48.002492 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-03 19:12:48.002673 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.227 1.494 9.110
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 12.531 | 0.582 | 13.858 | |
| compute_asw | 0.010 | 0.001 | 0.012 | |
| count_existing | 0.010 | 0.001 | 0.019 | |
| generate_data_covariables | 0.005 | 0.000 | 0.005 | |
| generate_dataset | 0.009 | 0.001 | 0.017 | |