Yannis Schumann
| Snapshot Date: 2026-04-01 13:40 -0400 (Wed, 01 Apr 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-02 11:35 -0400 (Thu, 02 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4885 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4619 |
| 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 170/2374 | 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: 2026-04-01 18:28:54 -0400 (Wed, 01 Apr 2026) |
| EndedAt: 2026-04-01 18:29:27 -0400 (Wed, 01 Apr 2026) |
| EllapsedTime: 33.4 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 version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-01 22:28:54 UTC
* 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 9.648 0.36 6.941
* 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/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 version 4.6.0 alpha (2026-03-28 r89739)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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")
2026-04-01 18:29:19.166243 INFO::Formatting Data.
2026-04-01 18:29:19.168311 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:19.175168 INFO::Removing potential empty rows and columns
2026-04-01 18:29:19.319807 INFO::Found 0 missing values.
2026-04-01 18:29:19.321383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:19.321794 INFO::Done
2026-04-01 18:29:19.322119 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:19.329679 INFO::Starting hierarchical adjustment
2026-04-01 18:29:19.330254 INFO::Found 3 batches.
2026-04-01 18:29:19.33058 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:19.331138 INFO::Using default BPPARAM
2026-04-01 18:29:19.33146 INFO::Processing subtree level 1
2026-04-01 18:29:19.395291 INFO::Adjusting the last 1 batches sequentially
2026-04-01 18:29:19.396813 INFO::Done
2026-04-01 18:29:19.397261 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:19.398433 INFO::ASW Batch was -0.0817274303372614 prior to batch effect correction and is now -0.0817274303372614 .
2026-04-01 18:29:19.399224 INFO::Total function execution time is 0.233392953872681 s and adjustment time is 0.0666170120239258 s ( 28.54 )
2026-04-01 18:29:19.40878 INFO::Formatting Data.
2026-04-01 18:29:19.409271 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:19.409873 INFO::Removing potential empty rows and columns
2026-04-01 18:29:19.410798 INFO::Found 0 missing values.
2026-04-01 18:29:19.411521 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.
2026-04-01 18:29:19.417822 INFO::Formatting Data.
2026-04-01 18:29:19.418631 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:19.419333 INFO::Removing potential empty rows and columns
2026-04-01 18:29:19.419918 INFO::Found 0 missing values.
2026-04-01 18:29:19.420528 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.
2026-04-01 18:29:19.428917 INFO::Formatting Data.
2026-04-01 18:29:19.429363 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:19.429856 INFO::Removing potential empty rows and columns
2026-04-01 18:29:19.430334 INFO::Found 0 missing values.
2026-04-01 18:29:19.430757 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.
2026-04-01 18:29:19.432278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:19.432639 INFO::Done
2026-04-01 18:29:19.432942 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:19.43378 INFO::Starting hierarchical adjustment
2026-04-01 18:29:19.434147 INFO::Found 2 batches.
2026-04-01 18:29:19.434453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:19.434798 INFO::Using default BPPARAM
2026-04-01 18:29:19.435063 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:19.435471 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-01 18:29:19.44381 INFO::Done
2026-04-01 18:29:19.444198 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:19.44497 INFO::ASW Batch was 0.0842619338436312 prior to batch effect correction and is now -0.118383128497454 .
2026-04-01 18:29:19.445374 INFO::Total function execution time is 0.0164859294891357 s and adjustment time is 0.00969791412353516 s ( 58.83 )
2026-04-01 18:29:19.446519 INFO::Formatting Data.
2026-04-01 18:29:19.446843 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:19.450104 INFO::Formatting Data.
2026-04-01 18:29:19.450515 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:19.450921 INFO::Removing potential empty rows and columns
2026-04-01 18:29:19.451387 INFO::Found 0 missing values.
2026-04-01 18:29:19.45243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:19.452746 INFO::Done
2026-04-01 18:29:19.453057 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:19.453905 INFO::Starting hierarchical adjustment
2026-04-01 18:29:19.454279 INFO::Found 2 batches.
2026-04-01 18:29:19.454579 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:19.454888 INFO::Using default BPPARAM
2026-04-01 18:29:19.455166 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:19.455564 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-01 18:29:19.461478 INFO::Done
2026-04-01 18:29:19.461894 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:19.462683 INFO::ASW Batch was 0.00401016892799284 prior to batch effect correction and is now -0.115270156336211 .
2026-04-01 18:29:19.463108 INFO::Total function execution time is 0.0129740238189697 s and adjustment time is 0.00724005699157715 s ( 55.8 )
2026-04-01 18:29:19.463631 INFO::Formatting Data.
2026-04-01 18:29:19.464013 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:19.464467 INFO::Removing potential empty rows and columns
2026-04-01 18:29:19.465014 INFO::Found 0 missing values.
2026-04-01 18:29:19.466291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:19.466686 INFO::Done
2026-04-01 18:29:19.467113 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:19.46798 INFO::Starting hierarchical adjustment
2026-04-01 18:29:19.468406 INFO::Found 2 batches.
2026-04-01 18:29:19.468732 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:19.469071 INFO::Using default BPPARAM
2026-04-01 18:29:19.469388 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:19.469774 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-01 18:29:19.475452 INFO::Done
2026-04-01 18:29:19.475936 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:19.477705 INFO::ASW Batch was 0.00401016892799284 prior to batch effect correction and is now -0.115270156336211 .
2026-04-01 18:29:19.478411 INFO::Total function execution time is 0.0147120952606201 s and adjustment time is 0.00708699226379395 s ( 48.17 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-01 18:29:20.822243 INFO::Formatting Data.
2026-04-01 18:29:20.822722 INFO::Recognized SummarizedExperiment
2026-04-01 18:29:20.823038 INFO::Typecasting input to dataframe.
2026-04-01 18:29:20.833047 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:20.833919 INFO::Removing potential empty rows and columns
2026-04-01 18:29:20.835876 INFO::Found 0 missing values.
2026-04-01 18:29:20.838186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:20.838537 INFO::Done
2026-04-01 18:29:20.839306 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:20.842106 INFO::Starting hierarchical adjustment
2026-04-01 18:29:20.842557 INFO::Found 2 batches.
2026-04-01 18:29:20.842918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:20.843474 INFO::Using default BPPARAM
2026-04-01 18:29:20.843924 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:20.844507 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-01 18:29:20.865586 INFO::Done
2026-04-01 18:29:20.866162 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:20.867601 INFO::ASW Batch was -0.00924129873734051 prior to batch effect correction and is now -0.0914493644402188 .
2026-04-01 18:29:20.868063 INFO::Total function execution time is 0.0459201335906982 s and adjustment time is 0.0230629444122314 s ( 50.22 )
Warning: stack imbalance in '{', 73 then 75
2026-04-01 18:29:20.876365 INFO::Formatting Data.
2026-04-01 18:29:20.876861 INFO::Recognized SummarizedExperiment
2026-04-01 18:29:20.877237 INFO::Typecasting input to dataframe.
2026-04-01 18:29:20.880818 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:20.881477 INFO::Removing potential empty rows and columns
2026-04-01 18:29:20.884226 INFO::Found 0 missing values.
2026-04-01 18:29:20.887887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:20.888298 INFO::Done
2026-04-01 18:29:20.889221 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:20.891405 INFO::Starting hierarchical adjustment
2026-04-01 18:29:20.891832 INFO::Found 2 batches.
2026-04-01 18:29:20.892325 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:20.892837 INFO::Using default BPPARAM
2026-04-01 18:29:20.893493 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:20.894195 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-01 18:29:20.90665 INFO::Done
2026-04-01 18:29:20.907235 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:20.908983 INFO::ASW Batch was 0.00176507791184969 prior to batch effect correction and is now 0.00176507791184969 .
2026-04-01 18:29:20.909625 INFO::Total function execution time is 0.0332620143890381 s and adjustment time is 0.0148630142211914 s ( 44.68 )
2026-04-01 18:29:20.91729 INFO::Formatting Data.
2026-04-01 18:29:20.917757 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:20.918201 INFO::Removing potential empty rows and columns
2026-04-01 18:29:20.918685 INFO::Found 0 missing values.
2026-04-01 18:29:20.921934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:20.922954 INFO::Done
2026-04-01 18:29:20.923728 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:20.925257 INFO::Starting hierarchical adjustment
2026-04-01 18:29:20.925839 INFO::Found 3 batches.
2026-04-01 18:29:20.92619 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:20.926641 INFO::Using default BPPARAM
2026-04-01 18:29:20.927432 INFO::Processing subtree level 1
2026-04-01 18:29:21.067373 INFO::Adjusting the last 1 batches sequentially
2026-04-01 18:29:21.068715 INFO::Done
2026-04-01 18:29:21.069098 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.070237 INFO::ASW Batch was -0.0902959074989087 prior to batch effect correction and is now -0.172571534350347 .
2026-04-01 18:29:21.070776 INFO::Total function execution time is 0.153488159179688 s and adjustment time is 0.142914056777954 s ( 93.11 )
2026-04-01 18:29:21.079525 INFO::Skipping initial DF formatting
2026-04-01 18:29:21.080048 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.081935 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.082532 INFO::Found 5 batches.
2026-04-01 18:29:21.082924 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.083305 INFO::Using default BPPARAM
2026-04-01 18:29:21.083627 INFO::Processing subtree level 1
2026-04-01 18:29:21.159212 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.160554 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-01 18:29:21.170813 INFO::Done
2026-04-01 18:29:21.171278 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.173672 INFO::ASW Batch was 0.458644606092265 prior to batch effect correction and is now 0.458644606092265 .
2026-04-01 18:29:21.174078 INFO::ASW Label was 0.425637032110895 prior to batch effect correction and is now 0.425637032110895 .
2026-04-01 18:29:21.174741 INFO::Total function execution time is 0.0952699184417725 s and adjustment time is 0.0883498191833496 s ( 92.74 )
2026-04-01 18:29:21.186148 INFO::Formatting Data.
2026-04-01 18:29:21.186668 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.187136 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.188313 INFO::Found 0 missing values.
2026-04-01 18:29:21.190855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.191361 INFO::Done
2026-04-01 18:29:21.191731 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.193749 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.194229 INFO::Found 5 batches.
2026-04-01 18:29:21.19458 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.194994 INFO::Using default BPPARAM
2026-04-01 18:29:21.195494 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.
2026-04-01 18:29:21.274206 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.275759 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-01 18:29:21.282608 INFO::Done
2026-04-01 18:29:21.283019 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.284414 INFO::ASW Batch was 0.612335761550661 prior to batch effect correction and is now -0.0707603851124528 .
2026-04-01 18:29:21.284765 INFO::ASW Label was 0.166189645509805 prior to batch effect correction and is now 0.70985972547981 .
2026-04-01 18:29:21.285178 INFO::Total function execution time is 0.099107027053833 s and adjustment time is 0.0884299278259277 s ( 89.23 )
2026-04-01 18:29:21.285563 INFO::Formatting Data.
2026-04-01 18:29:21.28586 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.286246 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.286686 INFO::Found 0 missing values.
2026-04-01 18:29:21.288102 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.288432 INFO::Done
2026-04-01 18:29:21.28875 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.290263 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.290892 INFO::Found 5 batches.
2026-04-01 18:29:21.291249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.291598 INFO::Using default BPPARAM
2026-04-01 18:29:21.291873 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.
2026-04-01 18:29:21.365762 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.367163 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-01 18:29:21.373821 INFO::Done
2026-04-01 18:29:21.374264 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.375695 INFO::ASW Batch was 0.612335761550661 prior to batch effect correction and is now -0.0707603851124528 .
2026-04-01 18:29:21.376056 INFO::ASW Label was 0.166189645509805 prior to batch effect correction and is now 0.70985972547981 .
2026-04-01 18:29:21.376485 INFO::Total function execution time is 0.0908949375152588 s and adjustment time is 0.0829770565032959 s ( 91.29 )
2026-04-01 18:29:21.382419 INFO::Formatting Data.
2026-04-01 18:29:21.382857 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.383283 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.383731 INFO::Found 0 missing values.
2026-04-01 18:29:21.385019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.38531 INFO::Done
2026-04-01 18:29:21.385596 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.386638 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.386995 INFO::Found 5 batches.
2026-04-01 18:29:21.387316 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.387634 INFO::Using default BPPARAM
2026-04-01 18:29:21.387942 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.
2026-04-01 18:29:21.451974 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.453835 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-01 18:29:21.461146 INFO::Done
2026-04-01 18:29:21.4616 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.463195 INFO::ASW Batch was 0.569060166551263 prior to batch effect correction and is now 0.00965647151625174 .
2026-04-01 18:29:21.463577 INFO::ASW Label was 0.38637138774262 prior to batch effect correction and is now 0.558296915300152 .
2026-04-01 18:29:21.464086 INFO::Total function execution time is 0.0816619396209717 s and adjustment time is 0.0741829872131348 s ( 90.84 )
2026-04-01 18:29:21.464608 INFO::Formatting Data.
2026-04-01 18:29:21.464992 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.465442 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.465975 INFO::Found 0 missing values.
2026-04-01 18:29:21.467713 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.468016 INFO::Done
2026-04-01 18:29:21.468473 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.469696 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.470127 INFO::Found 5 batches.
2026-04-01 18:29:21.470414 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.470778 INFO::Using default BPPARAM
2026-04-01 18:29:21.471194 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.
2026-04-01 18:29:21.532478 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.534193 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-01 18:29:21.540812 INFO::Done
2026-04-01 18:29:21.541272 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.54277 INFO::ASW Batch was 0.569060166551263 prior to batch effect correction and is now 0.00965647151625174 .
2026-04-01 18:29:21.543146 INFO::ASW Label was 0.38637138774262 prior to batch effect correction and is now 0.558296915300152 .
2026-04-01 18:29:21.543641 INFO::Total function execution time is 0.0789928436279297 s and adjustment time is 0.0707290172576904 s ( 89.54 )
2026-04-01 18:29:21.551528 INFO::Formatting Data.
2026-04-01 18:29:21.552036 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.552783 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.553409 INFO::Found 0 missing values.
2026-04-01 18:29:21.554617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.555052 INFO::Done
2026-04-01 18:29:21.555407 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.557719 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.558705 INFO::Found 2 batches.
2026-04-01 18:29:21.559109 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.559642 INFO::Using default BPPARAM
2026-04-01 18:29:21.560048 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.560568 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-01 18:29:21.568969 INFO::Done
2026-04-01 18:29:21.569397 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.570626 INFO::ASW Batch was 0.338948423761991 prior to batch effect correction and is now 0.0643532071370352 .
2026-04-01 18:29:21.571337 INFO::ASW Label was 0.716646496767744 prior to batch effect correction and is now 0.884312804006417 .
2026-04-01 18:29:21.572204 INFO::Total function execution time is 0.0206940174102783 s and adjustment time is 0.0103299617767334 s ( 49.92 )
2026-04-01 18:29:21.572614 INFO::Formatting Data.
2026-04-01 18:29:21.572938 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.573411 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.574151 INFO::Found 0 missing values.
2026-04-01 18:29:21.575428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.575983 INFO::Done
2026-04-01 18:29:21.576335 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.577515 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.577891 INFO::Found 2 batches.
2026-04-01 18:29:21.578213 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.578537 INFO::Using default BPPARAM
2026-04-01 18:29:21.578824 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.579225 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-01 18:29:21.584207 INFO::Done
2026-04-01 18:29:21.584587 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.58563 INFO::ASW Batch was 0.338948423761991 prior to batch effect correction and is now 0.0643532071370352 .
2026-04-01 18:29:21.585932 INFO::ASW Label was 0.716646496767744 prior to batch effect correction and is now 0.884312804006417 .
2026-04-01 18:29:21.586289 INFO::Total function execution time is 0.0136861801147461 s and adjustment time is 0.00636196136474609 s ( 46.48 )
2026-04-01 18:29:21.591022 INFO::Formatting Data.
2026-04-01 18:29:21.591392 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.591806 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.5922 INFO::Found 0 missing values.
2026-04-01 18:29:21.592965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.593257 INFO::Done
2026-04-01 18:29:21.593537 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.59424 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.594591 INFO::Found 2 batches.
2026-04-01 18:29:21.594863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.595188 INFO::Using default BPPARAM
2026-04-01 18:29:21.595485 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.595912 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-01 18:29:21.606991 INFO::Done
2026-04-01 18:29:21.607437 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.60821 INFO::ASW Batch was -0.0227373772164528 prior to batch effect correction and is now -0.0896352239637258 .
2026-04-01 18:29:21.608603 INFO::Total function execution time is 0.0176048278808594 s and adjustment time is 0.0124349594116211 s ( 70.63 )
2026-04-01 18:29:21.613427 INFO::Formatting Data.
2026-04-01 18:29:21.613788 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.614184 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.614613 INFO::Found 0 missing values.
2026-04-01 18:29:21.615233 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.
2026-04-01 18:29:21.616729 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.617043 INFO::Done
2026-04-01 18:29:21.61732 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.618365 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.61871 INFO::Found 2 batches.
2026-04-01 18:29:21.618993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.619287 INFO::Using default BPPARAM
2026-04-01 18:29:21.61954 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.619932 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-01 18:29:21.625437 INFO::Done
2026-04-01 18:29:21.625834 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.626882 INFO::ASW Batch was 0.299021024030231 prior to batch effect correction and is now -0.0343205573755147 .
2026-04-01 18:29:21.627181 INFO::ASW Label was 0.655087221034992 prior to batch effect correction and is now 0.937967813940776 .
2026-04-01 18:29:21.627546 INFO::Total function execution time is 0.01413893699646 s and adjustment time is 0.00677108764648438 s ( 47.89 )
2026-04-01 18:29:21.627893 INFO::Formatting Data.
2026-04-01 18:29:21.628205 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.628593 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.629011 INFO::Found 0 missing values.
2026-04-01 18:29:21.629417 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.
2026-04-01 18:29:21.631508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.632126 INFO::Done
2026-04-01 18:29:21.632812 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.635179 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.635679 INFO::Found 2 batches.
2026-04-01 18:29:21.636049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.636687 INFO::Using default BPPARAM
2026-04-01 18:29:21.637045 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:21.637535 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-01 18:29:21.645741 INFO::Done
2026-04-01 18:29:21.64621 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.647499 INFO::ASW Batch was 0.299021024030231 prior to batch effect correction and is now -0.0343205573755147 .
2026-04-01 18:29:21.647888 INFO::ASW Label was 0.655087221034992 prior to batch effect correction and is now 0.937967813940776 .
2026-04-01 18:29:21.648321 INFO::Total function execution time is 0.0204038619995117 s and adjustment time is 0.0100970268249512 s ( 49.49 )
2026-04-01 18:29:21.739751 INFO::Formatting Data.
2026-04-01 18:29:21.740192 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.740632 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.74109 INFO::Found 0 missing values.
2026-04-01 18:29:21.742119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.742426 INFO::Done
2026-04-01 18:29:21.742695 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.743477 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.743803 INFO::Found 3 batches.
2026-04-01 18:29:21.744069 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.74437 INFO::Using default BPPARAM
2026-04-01 18:29:21.744616 INFO::Processing subtree level 1
2026-04-01 18:29:21.830436 INFO::Adjusting the last 1 batches sequentially
2026-04-01 18:29:21.832168 INFO::Done
2026-04-01 18:29:21.832641 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.835247 INFO::ASW Batch was -0.0657278012712335 prior to batch effect correction and is now -0.0657278012712335 .
2026-04-01 18:29:21.8362 INFO::Total function execution time is 0.0962419509887695 s and adjustment time is 0.0883841514587402 s ( 91.84 )
2026-04-01 18:29:21.837141 INFO::Formatting Data.
2026-04-01 18:29:21.837931 INFO::Typecasting input to dataframe.
2026-04-01 18:29:21.838812 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.839604 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.840743 INFO::Found 0 missing values.
2026-04-01 18:29:21.843646 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.844367 INFO::Done
2026-04-01 18:29:21.844825 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.846025 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.846619 INFO::Found 3 batches.
2026-04-01 18:29:21.847035 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.847468 INFO::Using default BPPARAM
2026-04-01 18:29:21.847874 INFO::Processing subtree level 1
2026-04-01 18:29:21.914606 INFO::Adjusting the last 1 batches sequentially
2026-04-01 18:29:21.916025 INFO::Done
2026-04-01 18:29:21.916409 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:21.917827 INFO::ASW Batch was -0.0657278012712335 prior to batch effect correction and is now -0.0657278012712335 .
2026-04-01 18:29:21.918521 INFO::Total function execution time is 0.0814001560211182 s and adjustment time is 0.0694999694824219 s ( 85.38 )
2026-04-01 18:29:21.925551 INFO::Formatting Data.
2026-04-01 18:29:21.926012 INFO::Typecasting input to dataframe.
2026-04-01 18:29:21.926436 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:21.926902 INFO::Removing potential empty rows and columns
2026-04-01 18:29:21.927435 INFO::Found 0 missing values.
2026-04-01 18:29:21.928694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:21.92908 INFO::Done
2026-04-01 18:29:21.929427 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:21.930373 INFO::Starting hierarchical adjustment
2026-04-01 18:29:21.930811 INFO::Found 3 batches.
2026-04-01 18:29:21.931112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:21.931489 INFO::Using default BPPARAM
2026-04-01 18:29:21.931817 INFO::Processing subtree level 1
2026-04-01 18:29:22.01101 INFO::Adjusting the last 1 batches sequentially
2026-04-01 18:29:22.012577 INFO::Done
2026-04-01 18:29:22.012968 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:22.014475 INFO::ASW Batch was -0.0446070389618128 prior to batch effect correction and is now -0.0446070389618128 .
2026-04-01 18:29:22.01516 INFO::Total function execution time is 0.089601993560791 s and adjustment time is 0.08182692527771 s ( 91.32 )
2026-04-01 18:29:22.117329 INFO::Formatting Data.
2026-04-01 18:29:22.11793 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:22.11856 INFO::Removing potential empty rows and columns
2026-04-01 18:29:22.120287 INFO::Found 1000 missing values.
2026-04-01 18:29:22.130589 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:22.131118 INFO::Done
2026-04-01 18:29:22.131652 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:22.13454 INFO::Starting hierarchical adjustment
2026-04-01 18:29:22.135056 INFO::Found 10 batches.
2026-04-01 18:29:22.135696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:22.136176 INFO::Using default BPPARAM
2026-04-01 18:29:22.136574 INFO::Processing subtree level 1
2026-04-01 18:29:22.237048 INFO::Processing subtree level 2
2026-04-01 18:29:22.358127 INFO::Adjusting the last 1 batches sequentially
2026-04-01 18:29:22.360169 INFO::Done
2026-04-01 18:29:22.360852 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:22.364293 INFO::ASW Batch was 0.488519247044237 prior to batch effect correction and is now 0.488519247044237 .
2026-04-01 18:29:22.365205 INFO::ASW Label was 0.371843914576468 prior to batch effect correction and is now 0.371843914576468 .
2026-04-01 18:29:22.365866 INFO::Total function execution time is 0.248565912246704 s and adjustment time is 0.22517991065979 s ( 90.59 )
2026-04-01 18:29:22.366381 INFO::Formatting Data.
2026-04-01 18:29:22.366832 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:22.367954 INFO::Removing potential empty rows and columns
2026-04-01 18:29:22.369564 INFO::Found 1000 missing values.
2026-04-01 18:29:22.380914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:22.381458 INFO::Done
2026-04-01 18:29:22.381839 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:22.384279 INFO::Starting hierarchical adjustment
2026-04-01 18:29:22.384904 INFO::Found 10 batches.
2026-04-01 18:29:22.790044 INFO::Set up parallel execution backend with 2 workers
2026-04-01 18:29:22.790591 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-01 18:29:23.372055 INFO::Adjusting the last 2 batches sequentially
2026-04-01 18:29:23.3729 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-01 18:29:23.378645 INFO::Done
2026-04-01 18:29:23.378981 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:23.381012 INFO::ASW Batch was 0.488519247044237 prior to batch effect correction and is now 0.488519247044237 .
2026-04-01 18:29:23.382708 INFO::ASW Label was 0.371843914576468 prior to batch effect correction and is now 0.371843914576468 .
2026-04-01 18:29:23.383105 INFO::Total function execution time is 1.01675701141357 s and adjustment time is 0.99380898475647 s ( 97.74 )
2026-04-01 18:29:23.524122 INFO::Formatting Data.
2026-04-01 18:29:23.52467 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.525228 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.52587 INFO::Found 0 missing values.
2026-04-01 18:29:23.527531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.527931 INFO::Done
2026-04-01 18:29:23.528304 INFO::Acquiring quality metrics before batch effect correction.
2026-04-01 18:29:23.529526 INFO::Starting hierarchical adjustment
2026-04-01 18:29:23.529959 INFO::Found 3 batches.
2026-04-01 18:29:23.530317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-01 18:29:23.530705 INFO::Using default BPPARAM
2026-04-01 18:29:23.531014 INFO::Processing subtree level 1
2026-04-01 18:29:23.600135 INFO::Adjusting the last 1 batches sequentially
2026-04-01 18:29:23.602261 INFO::Done
2026-04-01 18:29:23.602816 INFO::Acquiring quality metrics after batch effect correction.
2026-04-01 18:29:23.605057 INFO::ASW Batch was 0.128707057126307 prior to batch effect correction and is now -0.155930619844919 .
2026-04-01 18:29:23.605468 INFO::ASW Label was -0.192573905602748 prior to batch effect correction and is now -0.0665043733021577 .
2026-04-01 18:29:23.606113 INFO::Total function execution time is 0.0819780826568604 s and adjustment time is 0.0723299980163574 s ( 88.23 )
2026-04-01 18:29:23.678798 INFO::Formatting Data.
2026-04-01 18:29:23.679389 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.680014 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.680584 INFO::Found 2 missing values.
2026-04-01 18:29:23.683383 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.683795 INFO::Done
2026-04-01 18:29:23.696134 INFO::Found NA in Reference column
2026-04-01 18:29:23.699942 INFO::Require at least two references per batch.
2026-04-01 18:29:23.707803 INFO::Formatting Data.
2026-04-01 18:29:23.708221 INFO::Recognized SummarizedExperiment
2026-04-01 18:29:23.70854 INFO::Typecasting input to dataframe.
2026-04-01 18:29:23.712564 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.713096 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.714539 INFO::Found 0 missing values.
2026-04-01 18:29:23.717067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.717423 INFO::Done
2026-04-01 18:29:23.722966 INFO::Formatting Data.
2026-04-01 18:29:23.72336 INFO::Recognized SummarizedExperiment
2026-04-01 18:29:23.723655 INFO::Typecasting input to dataframe.
2026-04-01 18:29:23.729372 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.729932 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.731344 INFO::Found 0 missing values.
2026-04-01 18:29:23.73569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.736127 INFO::Done
2026-04-01 18:29:23.742134 INFO::Formatting Data.
2026-04-01 18:29:23.742546 INFO::Recognized SummarizedExperiment
2026-04-01 18:29:23.742866 INFO::Typecasting input to dataframe.
2026-04-01 18:29:23.748685 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.749203 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.749735 INFO::Found 0 missing values.
2026-04-01 18:29:23.750224 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.
2026-04-01 18:29:23.751909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.752229 INFO::Done
2026-04-01 18:29:23.756933 INFO::Formatting Data.
2026-04-01 18:29:23.75735 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.757791 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.758271 INFO::Found 0 missing values.
2026-04-01 18:29:23.759541 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.759884 INFO::Done
2026-04-01 18:29:23.76511 INFO::Formatting Data.
2026-04-01 18:29:23.76556 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.765956 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.766431 INFO::Found 0 missing values.
2026-04-01 18:29:23.767543 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.767872 INFO::Done
2026-04-01 18:29:23.780872 INFO::Formatting Data.
2026-04-01 18:29:23.781407 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.781917 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.782439 INFO::Found 1 missing values.
2026-04-01 18:29:23.783428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.783737 INFO::Done
2026-04-01 18:29:23.792513 INFO::Formatting Data.
2026-04-01 18:29:23.79299 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.793449 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.793937 INFO::Found 2 missing values.
2026-04-01 18:29:23.794385 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.
2026-04-01 18:29:23.795516 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.795866 INFO::Done
2026-04-01 18:29:23.800551 INFO::Formatting Data.
2026-04-01 18:29:23.801 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.801441 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.80187 INFO::Found 2 missing values.
2026-04-01 18:29:23.802537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.802844 INFO::Done
2026-04-01 18:29:23.807551 INFO::Formatting Data.
2026-04-01 18:29:23.807961 INFO::Typecasting input to dataframe.
2026-04-01 18:29:23.808336 INFO::Replacing NaNs with NAs.
2026-04-01 18:29:23.808753 INFO::Removing potential empty rows and columns
2026-04-01 18:29:23.809275 INFO::Found 0 missing values.
2026-04-01 18:29:23.810264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-01 18:29:23.810542 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.305 2.035 9.621
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.648 | 0.360 | 6.941 | |
| compute_asw | 0.011 | 0.001 | 0.012 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.005 | 0.001 | 0.006 | |