Yannis Schumann
| Snapshot Date: 2026-03-05 13:40 -0500 (Thu, 05 Mar 2026) |
| 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 2026-03-06 11:35 -0500 (Fri, 06 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4891 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4593 |
| 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 169/2357 | 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 | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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: 2026-03-05 18:39:17 -0500 (Thu, 05 Mar 2026) |
| EndedAt: 2026-03-05 18:39:56 -0500 (Thu, 05 Mar 2026) |
| EllapsedTime: 38.5 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) (2026-01-15 r89304)
* 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 Sonoma 14.8.3
* 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 10.564 0.47 7.871
* 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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")
2026-03-05 18:39:46.12743 INFO::Formatting Data.
2026-03-05 18:39:46.128987 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:46.133351 INFO::Removing potential empty rows and columns
2026-03-05 18:39:46.247727 INFO::Found 0 missing values.
2026-03-05 18:39:46.249031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:46.249248 INFO::Done
2026-03-05 18:39:46.24944 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:46.257407 INFO::Starting hierarchical adjustment
2026-03-05 18:39:46.257794 INFO::Found 3 batches.
2026-03-05 18:39:46.257999 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:46.258477 INFO::Using default BPPARAM
2026-03-05 18:39:46.258663 INFO::Processing subtree level 1
2026-03-05 18:39:46.362107 INFO::Adjusting the last 1 batches sequentially
2026-03-05 18:39:46.36307 INFO::Done
2026-03-05 18:39:46.363355 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:46.364506 INFO::ASW Batch was 0.0339898300334132 prior to batch effect correction and is now 0.0339898300334132 .
2026-03-05 18:39:46.364981 INFO::Total function execution time is 0.237909078598022 s and adjustment time is 0.105350017547607 s ( 44.28 )
2026-03-05 18:39:46.372202 INFO::Formatting Data.
2026-03-05 18:39:46.372497 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:46.372866 INFO::Removing potential empty rows and columns
2026-03-05 18:39:46.373438 INFO::Found 0 missing values.
2026-03-05 18:39:46.373836 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.
2026-03-05 18:39:46.37888 INFO::Formatting Data.
2026-03-05 18:39:46.37915 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:46.379449 INFO::Removing potential empty rows and columns
2026-03-05 18:39:46.379846 INFO::Found 0 missing values.
2026-03-05 18:39:46.380187 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.
2026-03-05 18:39:46.387137 INFO::Formatting Data.
2026-03-05 18:39:46.387412 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:46.387756 INFO::Removing potential empty rows and columns
2026-03-05 18:39:46.388215 INFO::Found 0 missing values.
2026-03-05 18:39:46.388577 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.
2026-03-05 18:39:46.390527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:46.390747 INFO::Done
2026-03-05 18:39:46.390965 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:46.39183 INFO::Starting hierarchical adjustment
2026-03-05 18:39:46.392112 INFO::Found 2 batches.
2026-03-05 18:39:46.392313 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:46.392629 INFO::Using default BPPARAM
2026-03-05 18:39:46.392842 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:46.393213 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 18:39:46.402911 INFO::Done
2026-03-05 18:39:46.403214 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:46.403989 INFO::ASW Batch was -0.0315582883237981 prior to batch effect correction and is now -0.128205022469476 .
2026-03-05 18:39:46.404275 INFO::Total function execution time is 0.017164945602417 s and adjustment time is 0.0108299255371094 s ( 63.09 )
2026-03-05 18:39:46.405503 INFO::Formatting Data.
2026-03-05 18:39:46.405716 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:46.409498 INFO::Formatting Data.
2026-03-05 18:39:46.409765 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:46.410073 INFO::Removing potential empty rows and columns
2026-03-05 18:39:46.410468 INFO::Found 0 missing values.
2026-03-05 18:39:46.411581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:46.41178 INFO::Done
2026-03-05 18:39:46.411962 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:46.41269 INFO::Starting hierarchical adjustment
2026-03-05 18:39:46.412931 INFO::Found 2 batches.
2026-03-05 18:39:46.413108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:46.413317 INFO::Using default BPPARAM
2026-03-05 18:39:46.432676 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:46.435995 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 18:39:46.441481 INFO::Done
2026-03-05 18:39:46.441736 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:46.442511 INFO::ASW Batch was -0.00486458225539113 prior to batch effect correction and is now -0.0962168793751147 .
2026-03-05 18:39:46.442812 INFO::Total function execution time is 0.0333337783813477 s and adjustment time is 0.0285840034484863 s ( 85.75 )
2026-03-05 18:39:46.443202 INFO::Formatting Data.
2026-03-05 18:39:46.443416 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:46.443689 INFO::Removing potential empty rows and columns
2026-03-05 18:39:46.444025 INFO::Found 0 missing values.
2026-03-05 18:39:46.445062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:46.445262 INFO::Done
2026-03-05 18:39:46.445432 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:46.446171 INFO::Starting hierarchical adjustment
2026-03-05 18:39:46.446445 INFO::Found 2 batches.
2026-03-05 18:39:46.446652 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:46.446876 INFO::Using default BPPARAM
2026-03-05 18:39:46.447038 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:46.447357 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 18:39:46.459811 INFO::Done
2026-03-05 18:39:46.460077 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:46.460805 INFO::ASW Batch was -0.00486458225539113 prior to batch effect correction and is now -0.0962168793751147 .
2026-03-05 18:39:46.461087 INFO::Total function execution time is 0.0178799629211426 s and adjustment time is 0.013408899307251 s ( 74.99 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-05 18:39:47.717366 INFO::Formatting Data.
2026-03-05 18:39:47.717631 INFO::Recognized SummarizedExperiment
2026-03-05 18:39:47.717794 INFO::Typecasting input to dataframe.
2026-03-05 18:39:47.727796 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:47.728208 INFO::Removing potential empty rows and columns
2026-03-05 18:39:47.729379 INFO::Found 0 missing values.
2026-03-05 18:39:47.731721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:47.731892 INFO::Done
2026-03-05 18:39:47.732048 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:47.733245 INFO::Starting hierarchical adjustment
2026-03-05 18:39:47.733467 INFO::Found 2 batches.
2026-03-05 18:39:47.733621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:47.733934 INFO::Using default BPPARAM
2026-03-05 18:39:47.734089 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:47.734383 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 18:39:47.752083 INFO::Done
2026-03-05 18:39:47.752299 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:47.753496 INFO::ASW Batch was -0.00381093538273996 prior to batch effect correction and is now -0.0988627037890089 .
2026-03-05 18:39:47.753743 INFO::Total function execution time is 0.0364780426025391 s and adjustment time is 0.0186519622802734 s ( 51.13 )
Warning: stack imbalance in '{', 73 then 75
2026-03-05 18:39:47.760214 INFO::Formatting Data.
2026-03-05 18:39:47.760464 INFO::Recognized SummarizedExperiment
2026-03-05 18:39:47.760636 INFO::Typecasting input to dataframe.
2026-03-05 18:39:47.763601 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:47.763962 INFO::Removing potential empty rows and columns
2026-03-05 18:39:47.765146 INFO::Found 0 missing values.
2026-03-05 18:39:47.767358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:47.767523 INFO::Done
2026-03-05 18:39:47.767676 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:47.768869 INFO::Starting hierarchical adjustment
2026-03-05 18:39:47.769086 INFO::Found 2 batches.
2026-03-05 18:39:47.769236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:47.76942 INFO::Using default BPPARAM
2026-03-05 18:39:47.769566 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:47.769851 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 18:39:47.778041 INFO::Done
2026-03-05 18:39:47.778254 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:47.779434 INFO::ASW Batch was -0.00491460446213398 prior to batch effect correction and is now -0.00491460446213398 .
2026-03-05 18:39:47.779695 INFO::Total function execution time is 0.0194799900054932 s and adjustment time is 0.00899600982666016 s ( 46.18 )
2026-03-05 18:39:47.786274 INFO::Formatting Data.
2026-03-05 18:39:47.78653 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:47.786815 INFO::Removing potential empty rows and columns
2026-03-05 18:39:47.787133 INFO::Found 0 missing values.
2026-03-05 18:39:47.788025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:47.788188 INFO::Done
2026-03-05 18:39:47.788339 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:47.789013 INFO::Starting hierarchical adjustment
2026-03-05 18:39:47.789226 INFO::Found 3 batches.
2026-03-05 18:39:47.789373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:47.789567 INFO::Using default BPPARAM
2026-03-05 18:39:47.789713 INFO::Processing subtree level 1
2026-03-05 18:39:47.928232 INFO::Adjusting the last 1 batches sequentially
2026-03-05 18:39:47.929702 INFO::Done
2026-03-05 18:39:47.929982 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:47.931214 INFO::ASW Batch was -0.00566555387962995 prior to batch effect correction and is now -0.152063783035087 .
2026-03-05 18:39:47.931656 INFO::Total function execution time is 0.145380973815918 s and adjustment time is 0.140511989593506 s ( 96.65 )
2026-03-05 18:39:47.938272 INFO::Skipping initial DF formatting
2026-03-05 18:39:47.938482 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:47.939765 INFO::Starting hierarchical adjustment
2026-03-05 18:39:47.940007 INFO::Found 5 batches.
2026-03-05 18:39:47.940185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:47.940407 INFO::Using default BPPARAM
2026-03-05 18:39:47.940586 INFO::Processing subtree level 1
2026-03-05 18:39:48.174755 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.176923 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 18:39:48.187197 INFO::Done
2026-03-05 18:39:48.187469 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.230125 INFO::ASW Batch was 0.479275018665631 prior to batch effect correction and is now 0.479275018665631 .
2026-03-05 18:39:48.230475 INFO::ASW Label was 0.386644890572133 prior to batch effect correction and is now 0.386644890572133 .
2026-03-05 18:39:48.230941 INFO::Total function execution time is 0.292654037475586 s and adjustment time is 0.247229099273682 s ( 84.48 )
2026-03-05 18:39:48.239953 INFO::Formatting Data.
2026-03-05 18:39:48.240207 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.240608 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.241001 INFO::Found 0 missing values.
2026-03-05 18:39:48.242595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.242914 INFO::Done
2026-03-05 18:39:48.243154 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.244281 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.244521 INFO::Found 5 batches.
2026-03-05 18:39:48.244696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.245017 INFO::Using default BPPARAM
2026-03-05 18:39:48.245242 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.
2026-03-05 18:39:48.373122 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.375142 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 18:39:48.384794 INFO::Done
2026-03-05 18:39:48.385137 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.387155 INFO::ASW Batch was 0.541508775857067 prior to batch effect correction and is now -0.0660522745634534 .
2026-03-05 18:39:48.387515 INFO::ASW Label was 0.168992480508784 prior to batch effect correction and is now 0.772357806231986 .
2026-03-05 18:39:48.388021 INFO::Total function execution time is 0.148026943206787 s and adjustment time is 0.140277862548828 s ( 94.77 )
2026-03-05 18:39:48.388558 INFO::Formatting Data.
2026-03-05 18:39:48.388812 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.389262 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.38973 INFO::Found 0 missing values.
2026-03-05 18:39:48.391379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.391601 INFO::Done
2026-03-05 18:39:48.392173 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.393421 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.39377 INFO::Found 5 batches.
2026-03-05 18:39:48.394039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.394316 INFO::Using default BPPARAM
2026-03-05 18:39:48.394556 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.
2026-03-05 18:39:48.483587 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.485199 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 18:39:48.494234 INFO::Done
2026-03-05 18:39:48.494563 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.496052 INFO::ASW Batch was 0.541508775857067 prior to batch effect correction and is now -0.0660522745634534 .
2026-03-05 18:39:48.496312 INFO::ASW Label was 0.168992480508784 prior to batch effect correction and is now 0.772357806231986 .
2026-03-05 18:39:48.496718 INFO::Total function execution time is 0.108129978179932 s and adjustment time is 0.100538015365601 s ( 92.98 )
2026-03-05 18:39:48.504602 INFO::Formatting Data.
2026-03-05 18:39:48.50522 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.506074 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.506607 INFO::Found 0 missing values.
2026-03-05 18:39:48.508553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.508848 INFO::Done
2026-03-05 18:39:48.509096 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.510631 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.51099 INFO::Found 5 batches.
2026-03-05 18:39:48.511212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.511475 INFO::Using default BPPARAM
2026-03-05 18:39:48.5117 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.
2026-03-05 18:39:48.597648 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.599671 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 18:39:48.607074 INFO::Done
2026-03-05 18:39:48.607326 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.609367 INFO::ASW Batch was 0.44408485935103 prior to batch effect correction and is now -0.0269712437294161 .
2026-03-05 18:39:48.60971 INFO::ASW Label was 0.315409245117082 prior to batch effect correction and is now 0.760513554728094 .
2026-03-05 18:39:48.610178 INFO::Total function execution time is 0.105598926544189 s and adjustment time is 0.0961630344390869 s ( 91.06 )
2026-03-05 18:39:48.610532 INFO::Formatting Data.
2026-03-05 18:39:48.610757 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.611128 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.611516 INFO::Found 0 missing values.
2026-03-05 18:39:48.613036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.613282 INFO::Done
2026-03-05 18:39:48.61356 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.614691 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.614972 INFO::Found 5 batches.
2026-03-05 18:39:48.615149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.615387 INFO::Using default BPPARAM
2026-03-05 18:39:48.615562 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.
2026-03-05 18:39:48.706451 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.707528 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 18:39:48.717368 INFO::Done
2026-03-05 18:39:48.717665 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.719646 INFO::ASW Batch was 0.44408485935103 prior to batch effect correction and is now -0.0269712437294161 .
2026-03-05 18:39:48.719942 INFO::ASW Label was 0.315409245117082 prior to batch effect correction and is now 0.760513554728094 .
2026-03-05 18:39:48.720314 INFO::Total function execution time is 0.109739065170288 s and adjustment time is 0.102470874786377 s ( 93.38 )
2026-03-05 18:39:48.727854 INFO::Formatting Data.
2026-03-05 18:39:48.728153 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.728476 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.728872 INFO::Found 0 missing values.
2026-03-05 18:39:48.729837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.730017 INFO::Done
2026-03-05 18:39:48.730188 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.731217 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.731474 INFO::Found 2 batches.
2026-03-05 18:39:48.73165 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.731885 INFO::Using default BPPARAM
2026-03-05 18:39:48.732069 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.732351 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 18:39:48.737619 INFO::Done
2026-03-05 18:39:48.737832 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.738773 INFO::ASW Batch was 0.503957008732694 prior to batch effect correction and is now 0.129249717773466 .
2026-03-05 18:39:48.738963 INFO::ASW Label was 0.465689011071426 prior to batch effect correction and is now 0.84309835602442 .
2026-03-05 18:39:48.73921 INFO::Total function execution time is 0.0113890171051025 s and adjustment time is 0.00619196891784668 s ( 54.37 )
2026-03-05 18:39:48.739441 INFO::Formatting Data.
2026-03-05 18:39:48.739624 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.739885 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.740181 INFO::Found 0 missing values.
2026-03-05 18:39:48.741038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.741214 INFO::Done
2026-03-05 18:39:48.741379 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.742251 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.742477 INFO::Found 2 batches.
2026-03-05 18:39:48.742652 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.74285 INFO::Using default BPPARAM
2026-03-05 18:39:48.743018 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.743286 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-05 18:39:48.74804 INFO::Done
2026-03-05 18:39:48.748243 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.749168 INFO::ASW Batch was 0.503957008732694 prior to batch effect correction and is now 0.129249717773466 .
2026-03-05 18:39:48.749362 INFO::ASW Label was 0.465689011071426 prior to batch effect correction and is now 0.84309835602442 .
2026-03-05 18:39:48.749605 INFO::Total function execution time is 0.0101549625396729 s and adjustment time is 0.00559806823730469 s ( 55.13 )
2026-03-05 18:39:48.754602 INFO::Formatting Data.
2026-03-05 18:39:48.75483 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.755116 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.755417 INFO::Found 0 missing values.
2026-03-05 18:39:48.756097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.756278 INFO::Done
2026-03-05 18:39:48.756461 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.757067 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.757277 INFO::Found 2 batches.
2026-03-05 18:39:48.757446 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.757669 INFO::Using default BPPARAM
2026-03-05 18:39:48.757833 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.758142 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 18:39:48.771677 INFO::Done
2026-03-05 18:39:48.771976 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.772719 INFO::ASW Batch was -0.0443675803895196 prior to batch effect correction and is now -0.0825742001123271 .
2026-03-05 18:39:48.773008 INFO::Total function execution time is 0.0184168815612793 s and adjustment time is 0.014409065246582 s ( 78.24 )
2026-03-05 18:39:48.778049 INFO::Formatting Data.
2026-03-05 18:39:48.778388 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.778775 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.779222 INFO::Found 0 missing values.
2026-03-05 18:39:48.779745 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.
2026-03-05 18:39:48.781588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.781825 INFO::Done
2026-03-05 18:39:48.782047 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.78323 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.783515 INFO::Found 2 batches.
2026-03-05 18:39:48.783719 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.783962 INFO::Using default BPPARAM
2026-03-05 18:39:48.784161 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.7845 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 18:39:48.792336 INFO::Done
2026-03-05 18:39:48.792623 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.793783 INFO::ASW Batch was 0.502523389535439 prior to batch effect correction and is now 0.210865278881919 .
2026-03-05 18:39:48.794018 INFO::ASW Label was 0.668779878798757 prior to batch effect correction and is now 0.798662654765408 .
2026-03-05 18:39:48.794304 INFO::Total function execution time is 0.0162899494171143 s and adjustment time is 0.0088651180267334 s ( 54.42 )
2026-03-05 18:39:48.794593 INFO::Formatting Data.
2026-03-05 18:39:48.794799 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.795107 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.79544 INFO::Found 0 missing values.
2026-03-05 18:39:48.795739 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.
2026-03-05 18:39:48.797203 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.797393 INFO::Done
2026-03-05 18:39:48.797566 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.798523 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.798743 INFO::Found 2 batches.
2026-03-05 18:39:48.798915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.799128 INFO::Using default BPPARAM
2026-03-05 18:39:48.799305 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:48.799606 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 18:39:48.805093 INFO::Done
2026-03-05 18:39:48.805293 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.806182 INFO::ASW Batch was 0.502523389535439 prior to batch effect correction and is now 0.210865278881919 .
2026-03-05 18:39:48.806366 INFO::ASW Label was 0.668779878798757 prior to batch effect correction and is now 0.798662654765408 .
2026-03-05 18:39:48.806601 INFO::Total function execution time is 0.0120089054107666 s and adjustment time is 0.00639104843139648 s ( 53.22 )
2026-03-05 18:39:48.872289 INFO::Formatting Data.
2026-03-05 18:39:48.872552 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.872847 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.873172 INFO::Found 0 missing values.
2026-03-05 18:39:48.874058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.874232 INFO::Done
2026-03-05 18:39:48.874392 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.875026 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.875229 INFO::Found 3 batches.
2026-03-05 18:39:48.875371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.875552 INFO::Using default BPPARAM
2026-03-05 18:39:48.875705 INFO::Processing subtree level 1
2026-03-05 18:39:48.941255 INFO::Adjusting the last 1 batches sequentially
2026-03-05 18:39:48.943131 INFO::Done
2026-03-05 18:39:48.943402 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:48.944736 INFO::ASW Batch was -0.0926091969850278 prior to batch effect correction and is now -0.0926091969850278 .
2026-03-05 18:39:48.945193 INFO::Total function execution time is 0.0729219913482666 s and adjustment time is 0.0679140090942383 s ( 93.13 )
2026-03-05 18:39:48.945611 INFO::Formatting Data.
2026-03-05 18:39:48.945826 INFO::Typecasting input to dataframe.
2026-03-05 18:39:48.946154 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:48.946492 INFO::Removing potential empty rows and columns
2026-03-05 18:39:48.946933 INFO::Found 0 missing values.
2026-03-05 18:39:48.947954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:48.948141 INFO::Done
2026-03-05 18:39:48.948367 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:48.949141 INFO::Starting hierarchical adjustment
2026-03-05 18:39:48.949397 INFO::Found 3 batches.
2026-03-05 18:39:48.949581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:48.949848 INFO::Using default BPPARAM
2026-03-05 18:39:48.950039 INFO::Processing subtree level 1
2026-03-05 18:39:49.015244 INFO::Adjusting the last 1 batches sequentially
2026-03-05 18:39:49.016401 INFO::Done
2026-03-05 18:39:49.016664 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:49.017838 INFO::ASW Batch was -0.0926091969850278 prior to batch effect correction and is now -0.0926091969850278 .
2026-03-05 18:39:49.018299 INFO::Total function execution time is 0.07265305519104 s and adjustment time is 0.0670559406280518 s ( 92.3 )
2026-03-05 18:39:49.025269 INFO::Formatting Data.
2026-03-05 18:39:49.025533 INFO::Typecasting input to dataframe.
2026-03-05 18:39:49.025813 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:49.02616 INFO::Removing potential empty rows and columns
2026-03-05 18:39:49.026661 INFO::Found 0 missing values.
2026-03-05 18:39:49.027623 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:49.027792 INFO::Done
2026-03-05 18:39:49.027966 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:49.02869 INFO::Starting hierarchical adjustment
2026-03-05 18:39:49.028909 INFO::Found 3 batches.
2026-03-05 18:39:49.029112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:49.029333 INFO::Using default BPPARAM
2026-03-05 18:39:49.029491 INFO::Processing subtree level 1
2026-03-05 18:39:49.091873 INFO::Adjusting the last 1 batches sequentially
2026-03-05 18:39:49.09345 INFO::Done
2026-03-05 18:39:49.093775 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:49.095311 INFO::ASW Batch was -0.0744166118993923 prior to batch effect correction and is now -0.0744166118993923 .
2026-03-05 18:39:49.095891 INFO::Total function execution time is 0.0706019401550293 s and adjustment time is 0.0645689964294434 s ( 91.45 )
2026-03-05 18:39:49.201014 INFO::Formatting Data.
2026-03-05 18:39:49.201313 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:49.201707 INFO::Removing potential empty rows and columns
2026-03-05 18:39:49.202697 INFO::Found 1000 missing values.
2026-03-05 18:39:49.208695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:49.208941 INFO::Done
2026-03-05 18:39:49.209119 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:49.211956 INFO::Starting hierarchical adjustment
2026-03-05 18:39:49.212339 INFO::Found 10 batches.
2026-03-05 18:39:49.212577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:49.212863 INFO::Using default BPPARAM
2026-03-05 18:39:49.213074 INFO::Processing subtree level 1
2026-03-05 18:39:49.321841 INFO::Processing subtree level 2
2026-03-05 18:39:49.399723 INFO::Adjusting the last 1 batches sequentially
2026-03-05 18:39:49.400817 INFO::Done
2026-03-05 18:39:49.401082 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:49.403671 INFO::ASW Batch was 0.541723920375937 prior to batch effect correction and is now 0.541723920375937 .
2026-03-05 18:39:49.40392 INFO::ASW Label was 0.28386931496386 prior to batch effect correction and is now 0.28386931496386 .
2026-03-05 18:39:49.404327 INFO::Total function execution time is 0.203341960906982 s and adjustment time is 0.188560009002686 s ( 92.73 )
2026-03-05 18:39:49.404654 INFO::Formatting Data.
2026-03-05 18:39:49.404858 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:49.40529 INFO::Removing potential empty rows and columns
2026-03-05 18:39:49.406363 INFO::Found 1000 missing values.
2026-03-05 18:39:49.413513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:49.413886 INFO::Done
2026-03-05 18:39:49.414122 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:49.416536 INFO::Starting hierarchical adjustment
2026-03-05 18:39:49.416804 INFO::Found 10 batches.
2026-03-05 18:39:49.88587 INFO::Set up parallel execution backend with 2 workers
2026-03-05 18:39:49.886163 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-05 18:39:50.495877 INFO::Adjusting the last 2 batches sequentially
2026-03-05 18:39:50.496517 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-05 18:39:50.503384 INFO::Done
2026-03-05 18:39:50.503643 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:50.50582 INFO::ASW Batch was 0.541723920375937 prior to batch effect correction and is now 0.541723920375937 .
2026-03-05 18:39:50.506019 INFO::ASW Label was 0.28386931496386 prior to batch effect correction and is now 0.28386931496386 .
2026-03-05 18:39:50.506302 INFO::Total function execution time is 1.10165500640869 s and adjustment time is 1.08662986755371 s ( 98.64 )
2026-03-05 18:39:50.684558 INFO::Formatting Data.
2026-03-05 18:39:50.684929 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.685372 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.685936 INFO::Found 0 missing values.
2026-03-05 18:39:50.687722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.687975 INFO::Done
2026-03-05 18:39:50.688208 INFO::Acquiring quality metrics before batch effect correction.
2026-03-05 18:39:50.68951 INFO::Starting hierarchical adjustment
2026-03-05 18:39:50.689827 INFO::Found 3 batches.
2026-03-05 18:39:50.690016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-05 18:39:50.690283 INFO::Using default BPPARAM
2026-03-05 18:39:50.690502 INFO::Processing subtree level 1
2026-03-05 18:39:50.786529 INFO::Adjusting the last 1 batches sequentially
2026-03-05 18:39:50.788198 INFO::Done
2026-03-05 18:39:50.788484 INFO::Acquiring quality metrics after batch effect correction.
2026-03-05 18:39:50.790179 INFO::ASW Batch was 0.19715747140256 prior to batch effect correction and is now -0.138268487074733 .
2026-03-05 18:39:50.790492 INFO::ASW Label was -0.213309566451918 prior to batch effect correction and is now -0.0733137566266599 .
2026-03-05 18:39:50.791129 INFO::Total function execution time is 0.106564044952393 s and adjustment time is 0.0984170436859131 s ( 92.35 )
2026-03-05 18:39:50.858996 INFO::Formatting Data.
2026-03-05 18:39:50.859387 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.859763 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.86018 INFO::Found 2 missing values.
2026-03-05 18:39:50.861151 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.861329 INFO::Done
2026-03-05 18:39:50.872476 INFO::Found NA in Reference column
2026-03-05 18:39:50.876722 INFO::Require at least two references per batch.
2026-03-05 18:39:50.885515 INFO::Formatting Data.
2026-03-05 18:39:50.88578 INFO::Recognized SummarizedExperiment
2026-03-05 18:39:50.885985 INFO::Typecasting input to dataframe.
2026-03-05 18:39:50.890809 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.891346 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.893309 INFO::Found 0 missing values.
2026-03-05 18:39:50.8964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.89666 INFO::Done
2026-03-05 18:39:50.90397 INFO::Formatting Data.
2026-03-05 18:39:50.904274 INFO::Recognized SummarizedExperiment
2026-03-05 18:39:50.904495 INFO::Typecasting input to dataframe.
2026-03-05 18:39:50.911144 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.911647 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.91304 INFO::Found 0 missing values.
2026-03-05 18:39:50.917367 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.917577 INFO::Done
2026-03-05 18:39:50.923716 INFO::Formatting Data.
2026-03-05 18:39:50.923992 INFO::Recognized SummarizedExperiment
2026-03-05 18:39:50.924195 INFO::Typecasting input to dataframe.
2026-03-05 18:39:50.931341 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.931748 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.932154 INFO::Found 0 missing values.
2026-03-05 18:39:50.932476 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.
2026-03-05 18:39:50.934056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.934247 INFO::Done
2026-03-05 18:39:50.938693 INFO::Formatting Data.
2026-03-05 18:39:50.93894 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.939219 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.93954 INFO::Found 0 missing values.
2026-03-05 18:39:50.940546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.94073 INFO::Done
2026-03-05 18:39:50.94643 INFO::Formatting Data.
2026-03-05 18:39:50.94676 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.947102 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.947568 INFO::Found 0 missing values.
2026-03-05 18:39:50.948715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.948906 INFO::Done
2026-03-05 18:39:50.960573 INFO::Formatting Data.
2026-03-05 18:39:50.960958 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.961339 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.961782 INFO::Found 1 missing values.
2026-03-05 18:39:50.962717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.962909 INFO::Done
2026-03-05 18:39:50.971313 INFO::Formatting Data.
2026-03-05 18:39:50.971661 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.972015 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.972466 INFO::Found 2 missing values.
2026-03-05 18:39:50.972825 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.
2026-03-05 18:39:50.973807 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.974031 INFO::Done
2026-03-05 18:39:50.979432 INFO::Formatting Data.
2026-03-05 18:39:50.979818 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.980192 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.980658 INFO::Found 2 missing values.
2026-03-05 18:39:50.981281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.98153 INFO::Done
2026-03-05 18:39:50.986366 INFO::Formatting Data.
2026-03-05 18:39:50.98668 INFO::Typecasting input to dataframe.
2026-03-05 18:39:50.986982 INFO::Replacing NaNs with NAs.
2026-03-05 18:39:50.987284 INFO::Removing potential empty rows and columns
2026-03-05 18:39:50.987661 INFO::Found 0 missing values.
2026-03-05 18:39:50.98875 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-05 18:39:50.988961 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.343 2.328 10.083
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.564 | 0.470 | 7.871 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.007 | 0.000 | 0.007 | |
| generate_data_covariables | 0.005 | 0.001 | 0.006 | |
| generate_dataset | 0.005 | 0.000 | 0.005 | |