Yannis Schumann
| Snapshot Date: 2026-04-23 13:40 -0400 (Thu, 23 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 2026-04-24 11:35 -0400 (Fri, 24 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4958 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4705 |
| 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 170/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.4 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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-04-23 21:39:14 -0400 (Thu, 23 Apr 2026) |
| EndedAt: 2026-04-23 21:40:53 -0400 (Thu, 23 Apr 2026) |
| EllapsedTime: 99.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-24 01:39:14 UTC
* 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 loading without being on the library search path ... 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 24.276 1.729 17.524
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
2026-04-23 21:40:08.409851 INFO::Formatting Data.
2026-04-23 21:40:08.411304 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:08.422776 INFO::Removing potential empty rows and columns
2026-04-23 21:40:08.733619 INFO::Found 0 missing values.
2026-04-23 21:40:08.737382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:08.738083 INFO::Done
2026-04-23 21:40:08.738739 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:08.752225 INFO::Starting hierarchical adjustment
2026-04-23 21:40:08.753195 INFO::Found 3 batches.
2026-04-23 21:40:08.753849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:08.755065 INFO::Using default BPPARAM
2026-04-23 21:40:08.755701 INFO::Processing subtree level 1
2026-04-23 21:40:08.862422 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:40:08.86451 INFO::Done
2026-04-23 21:40:08.865357 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:08.868167 INFO::ASW Batch was -0.00452854663976625 prior to batch effect correction and is now -0.00452854663976625 .
2026-04-23 21:40:08.869375 INFO::Total function execution time is 0.460240364074707 s and adjustment time is 0.11149787902832 s ( 24.23 )
2026-04-23 21:40:08.88461 INFO::Formatting Data.
2026-04-23 21:40:08.88549 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:08.886525 INFO::Removing potential empty rows and columns
2026-04-23 21:40:08.887865 INFO::Found 0 missing values.
2026-04-23 21:40:08.88896 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.
2026-04-23 21:40:08.901508 INFO::Formatting Data.
2026-04-23 21:40:08.902361 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:08.903426 INFO::Removing potential empty rows and columns
2026-04-23 21:40:08.904815 INFO::Found 0 missing values.
2026-04-23 21:40:08.905863 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.
2026-04-23 21:40:08.923912 INFO::Formatting Data.
2026-04-23 21:40:08.924839 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:08.925867 INFO::Removing potential empty rows and columns
2026-04-23 21:40:08.926947 INFO::Found 0 missing values.
2026-04-23 21:40:08.927967 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.
2026-04-23 21:40:08.932929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:08.933586 INFO::Done
2026-04-23 21:40:08.934234 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:08.936562 INFO::Starting hierarchical adjustment
2026-04-23 21:40:08.937453 INFO::Found 2 batches.
2026-04-23 21:40:08.938115 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:08.938905 INFO::Using default BPPARAM
2026-04-23 21:40:08.939519 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:08.940694 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:40:08.965757 INFO::Done
2026-04-23 21:40:08.966697 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:08.969156 INFO::ASW Batch was 0.0177111275464239 prior to batch effect correction and is now -0.115446343940017 .
2026-04-23 21:40:08.970175 INFO::Total function execution time is 0.0463292598724365 s and adjustment time is 0.0284299850463867 s ( 61.37 )
2026-04-23 21:40:08.973602 INFO::Formatting Data.
2026-04-23 21:40:08.974357 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:08.985103 INFO::Formatting Data.
2026-04-23 21:40:08.986176 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:08.987252 INFO::Removing potential empty rows and columns
2026-04-23 21:40:08.98852 INFO::Found 0 missing values.
2026-04-23 21:40:08.992033 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:08.992716 INFO::Done
2026-04-23 21:40:08.993303 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:08.995629 INFO::Starting hierarchical adjustment
2026-04-23 21:40:08.996409 INFO::Found 2 batches.
2026-04-23 21:40:08.997036 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:08.997785 INFO::Using default BPPARAM
2026-04-23 21:40:08.998396 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:08.999404 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:40:09.016761 INFO::Done
2026-04-23 21:40:09.017604 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:09.019977 INFO::ASW Batch was 0.0747178146787717 prior to batch effect correction and is now -0.0972314196312199 .
2026-04-23 21:40:09.02098 INFO::Total function execution time is 0.0359821319580078 s and adjustment time is 0.0204257965087891 s ( 56.77 )
2026-04-23 21:40:09.022228 INFO::Formatting Data.
2026-04-23 21:40:09.022945 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:09.023911 INFO::Removing potential empty rows and columns
2026-04-23 21:40:09.025098 INFO::Found 0 missing values.
2026-04-23 21:40:09.028306 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:09.028961 INFO::Done
2026-04-23 21:40:09.029545 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:09.031961 INFO::Starting hierarchical adjustment
2026-04-23 21:40:09.032782 INFO::Found 2 batches.
2026-04-23 21:40:09.033411 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:09.034122 INFO::Using default BPPARAM
2026-04-23 21:40:09.034763 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:09.03578 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:40:09.051433 INFO::Done
2026-04-23 21:40:09.052219 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:09.054312 INFO::ASW Batch was 0.0747178146787717 prior to batch effect correction and is now -0.0972314196312199 .
2026-04-23 21:40:09.055191 INFO::Total function execution time is 0.0329825878143311 s and adjustment time is 0.018812894821167 s ( 57.04 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-04-23 21:40:12.332922 INFO::Formatting Data.
2026-04-23 21:40:12.333823 INFO::Recognized SummarizedExperiment
2026-04-23 21:40:12.334404 INFO::Typecasting input to dataframe.
2026-04-23 21:40:12.366737 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:12.368287 INFO::Removing potential empty rows and columns
2026-04-23 21:40:12.371921 INFO::Found 0 missing values.
2026-04-23 21:40:12.378608 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:12.379301 INFO::Done
2026-04-23 21:40:12.379879 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:12.38366 INFO::Starting hierarchical adjustment
2026-04-23 21:40:12.384528 INFO::Found 2 batches.
2026-04-23 21:40:12.385148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:12.386541 INFO::Using default BPPARAM
2026-04-23 21:40:12.387114 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:12.388132 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:40:12.442174 INFO::Done
2026-04-23 21:40:12.442987 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:12.446406 INFO::ASW Batch was -0.0059456192933864 prior to batch effect correction and is now -0.0941523508916379 .
2026-04-23 21:40:12.447305 INFO::Total function execution time is 0.114729404449463 s and adjustment time is 0.0578062534332275 s ( 50.38 )
Warning: stack imbalance in '{', 73 then 75
2026-04-23 21:40:12.466259 INFO::Formatting Data.
2026-04-23 21:40:12.467087 INFO::Recognized SummarizedExperiment
2026-04-23 21:40:12.467649 INFO::Typecasting input to dataframe.
2026-04-23 21:40:12.476494 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:12.477618 INFO::Removing potential empty rows and columns
2026-04-23 21:40:12.481022 INFO::Found 0 missing values.
2026-04-23 21:40:12.487906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:12.48852 INFO::Done
2026-04-23 21:40:12.48911 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:12.492651 INFO::Starting hierarchical adjustment
2026-04-23 21:40:12.493416 INFO::Found 2 batches.
2026-04-23 21:40:12.493971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:12.494618 INFO::Using default BPPARAM
2026-04-23 21:40:12.495181 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:12.496192 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:40:12.522394 INFO::Done
2026-04-23 21:40:12.523225 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:12.527081 INFO::ASW Batch was -0.0267607278125563 prior to batch effect correction and is now -0.0267607278125563 .
2026-04-23 21:40:12.52804 INFO::Total function execution time is 0.061776876449585 s and adjustment time is 0.0290758609771729 s ( 47.07 )
2026-04-23 21:40:12.54839 INFO::Formatting Data.
2026-04-23 21:40:12.549408 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:12.550434 INFO::Removing potential empty rows and columns
2026-04-23 21:40:12.551579 INFO::Found 0 missing values.
2026-04-23 21:40:12.554762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:12.555351 INFO::Done
2026-04-23 21:40:12.555943 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:12.558207 INFO::Starting hierarchical adjustment
2026-04-23 21:40:12.559013 INFO::Found 3 batches.
2026-04-23 21:40:12.559594 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:12.56027 INFO::Using default BPPARAM
2026-04-23 21:40:12.560873 INFO::Processing subtree level 1
2026-04-23 21:40:12.711144 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:40:12.713593 INFO::Done
2026-04-23 21:40:12.714384 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:12.717222 INFO::ASW Batch was -0.105868744828911 prior to batch effect correction and is now -0.1633571400943 .
2026-04-23 21:40:12.718281 INFO::Total function execution time is 0.169959783554077 s and adjustment time is 0.154731273651123 s ( 91.04 )
2026-04-23 21:40:12.733961 INFO::Skipping initial DF formatting
2026-04-23 21:40:12.734784 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:12.73939 INFO::Starting hierarchical adjustment
2026-04-23 21:40:12.740404 INFO::Found 5 batches.
2026-04-23 21:40:12.741066 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:12.741789 INFO::Using default BPPARAM
2026-04-23 21:40:12.742373 INFO::Processing subtree level 1
2026-04-23 21:40:12.900718 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:12.903304 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:40:12.928488 INFO::Done
2026-04-23 21:40:12.929664 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:12.935425 INFO::ASW Batch was 0.588307968237801 prior to batch effect correction and is now 0.588307968237801 .
2026-04-23 21:40:12.936296 INFO::ASW Label was 0.283659677218313 prior to batch effect correction and is now 0.283659677218313 .
2026-04-23 21:40:12.937438 INFO::Total function execution time is 0.20356273651123 s and adjustment time is 0.188209772109985 s ( 92.46 )
2026-04-23 21:40:12.959783 INFO::Formatting Data.
2026-04-23 21:40:12.960921 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:12.962121 INFO::Removing potential empty rows and columns
2026-04-23 21:40:12.963375 INFO::Found 0 missing values.
2026-04-23 21:40:12.968533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:12.969279 INFO::Done
2026-04-23 21:40:12.969964 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:12.973968 INFO::Starting hierarchical adjustment
2026-04-23 21:40:12.974874 INFO::Found 5 batches.
2026-04-23 21:40:12.975529 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:12.976336 INFO::Using default BPPARAM
2026-04-23 21:40:12.977013 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.
2026-04-23 21:40:13.136414 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:13.139685 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:40:13.165571 INFO::Done
2026-04-23 21:40:13.16687 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:13.17134 INFO::ASW Batch was 0.513548437460563 prior to batch effect correction and is now -0.0731481218285616 .
2026-04-23 21:40:13.17231 INFO::ASW Label was 0.304675901019983 prior to batch effect correction and is now 0.782336717600571 .
2026-04-23 21:40:13.173417 INFO::Total function execution time is 0.21379542350769 s and adjustment time is 0.190784454345703 s ( 89.24 )
2026-04-23 21:40:13.17451 INFO::Formatting Data.
2026-04-23 21:40:13.175324 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:13.176485 INFO::Removing potential empty rows and columns
2026-04-23 21:40:13.177824 INFO::Found 0 missing values.
2026-04-23 21:40:13.183092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:13.183856 INFO::Done
2026-04-23 21:40:13.184509 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:13.188661 INFO::Starting hierarchical adjustment
2026-04-23 21:40:13.189588 INFO::Found 5 batches.
2026-04-23 21:40:13.190285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:13.191118 INFO::Using default BPPARAM
2026-04-23 21:40:13.191824 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.
2026-04-23 21:40:13.358524 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:13.360624 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:40:13.379138 INFO::Done
2026-04-23 21:40:13.380088 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:13.383941 INFO::ASW Batch was 0.513548437460563 prior to batch effect correction and is now -0.0731481218285616 .
2026-04-23 21:40:13.384618 INFO::ASW Label was 0.304675901019983 prior to batch effect correction and is now 0.782336717600571 .
2026-04-23 21:40:13.385615 INFO::Total function execution time is 0.211137294769287 s and adjustment time is 0.189726829528809 s ( 89.86 )
2026-04-23 21:40:13.40153 INFO::Formatting Data.
2026-04-23 21:40:13.402473 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:13.40352 INFO::Removing potential empty rows and columns
2026-04-23 21:40:13.404652 INFO::Found 0 missing values.
2026-04-23 21:40:13.409131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:13.409784 INFO::Done
2026-04-23 21:40:13.410408 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:13.413817 INFO::Starting hierarchical adjustment
2026-04-23 21:40:13.414616 INFO::Found 5 batches.
2026-04-23 21:40:13.415252 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:13.415987 INFO::Using default BPPARAM
2026-04-23 21:40:13.416576 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.
2026-04-23 21:40:13.561644 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:13.563864 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:40:13.582953 INFO::Done
2026-04-23 21:40:13.584057 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:13.588326 INFO::ASW Batch was 0.519332555189149 prior to batch effect correction and is now -0.108402280043441 .
2026-04-23 21:40:13.589233 INFO::ASW Label was 0.234923181863154 prior to batch effect correction and is now 0.861635111614905 .
2026-04-23 21:40:13.59034 INFO::Total function execution time is 0.188887596130371 s and adjustment time is 0.168385982513428 s ( 89.15 )
2026-04-23 21:40:13.591398 INFO::Formatting Data.
2026-04-23 21:40:13.592172 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:13.593295 INFO::Removing potential empty rows and columns
2026-04-23 21:40:13.59447 INFO::Found 0 missing values.
2026-04-23 21:40:13.599094 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:13.599797 INFO::Done
2026-04-23 21:40:13.600392 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:13.604109 INFO::Starting hierarchical adjustment
2026-04-23 21:40:13.60496 INFO::Found 5 batches.
2026-04-23 21:40:13.605575 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:13.606282 INFO::Using default BPPARAM
2026-04-23 21:40:13.606883 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.
2026-04-23 21:40:13.753471 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:13.755602 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:40:13.773362 INFO::Done
2026-04-23 21:40:13.774328 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:13.77813 INFO::ASW Batch was 0.519332555189149 prior to batch effect correction and is now -0.108402280043441 .
2026-04-23 21:40:13.778858 INFO::ASW Label was 0.234923181863154 prior to batch effect correction and is now 0.861635111614905 .
2026-04-23 21:40:13.779882 INFO::Total function execution time is 0.188499450683594 s and adjustment time is 0.16852879524231 s ( 89.41 )
2026-04-23 21:40:13.794318 INFO::Formatting Data.
2026-04-23 21:40:13.795248 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:13.7963 INFO::Removing potential empty rows and columns
2026-04-23 21:40:13.797425 INFO::Found 0 missing values.
2026-04-23 21:40:13.800472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:13.8012 INFO::Done
2026-04-23 21:40:13.801802 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:13.805218 INFO::Starting hierarchical adjustment
2026-04-23 21:40:13.806036 INFO::Found 2 batches.
2026-04-23 21:40:13.806646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:13.807395 INFO::Using default BPPARAM
2026-04-23 21:40:13.80806 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:13.809096 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:40:13.825855 INFO::Done
2026-04-23 21:40:13.826724 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:13.830134 INFO::ASW Batch was 0.546126016380734 prior to batch effect correction and is now 0.0989549104718239 .
2026-04-23 21:40:13.830832 INFO::ASW Label was 0.583790874906469 prior to batch effect correction and is now 0.866917613970157 .
2026-04-23 21:40:13.831772 INFO::Total function execution time is 0.0375087261199951 s and adjustment time is 0.0199682712554932 s ( 53.24 )
2026-04-23 21:40:13.832708 INFO::Formatting Data.
2026-04-23 21:40:13.83341 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:13.834408 INFO::Removing potential empty rows and columns
2026-04-23 21:40:13.835545 INFO::Found 0 missing values.
2026-04-23 21:40:13.838726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:13.839362 INFO::Done
2026-04-23 21:40:13.839978 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:13.843265 INFO::Starting hierarchical adjustment
2026-04-23 21:40:13.844072 INFO::Found 2 batches.
2026-04-23 21:40:13.844659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:13.845381 INFO::Using default BPPARAM
2026-04-23 21:40:13.846012 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:13.847051 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-04-23 21:40:13.863245 INFO::Done
2026-04-23 21:40:13.864113 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:13.867477 INFO::ASW Batch was 0.546126016380734 prior to batch effect correction and is now 0.0989549104718239 .
2026-04-23 21:40:13.868151 INFO::ASW Label was 0.583790874906469 prior to batch effect correction and is now 0.866917613970157 .
2026-04-23 21:40:13.869091 INFO::Total function execution time is 0.0364389419555664 s and adjustment time is 0.0193016529083252 s ( 52.97 )
2026-04-23 21:40:13.885658 INFO::Formatting Data.
2026-04-23 21:40:13.88696 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:13.888253 INFO::Removing potential empty rows and columns
2026-04-23 21:40:13.889656 INFO::Found 0 missing values.
2026-04-23 21:40:13.89291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:13.89362 INFO::Done
2026-04-23 21:40:13.894286 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:13.897409 INFO::Starting hierarchical adjustment
2026-04-23 21:40:13.898329 INFO::Found 2 batches.
2026-04-23 21:40:13.898975 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:13.899789 INFO::Using default BPPARAM
2026-04-23 21:40:13.900484 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:13.901652 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:40:13.940669 INFO::Done
2026-04-23 21:40:13.941641 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:13.944164 INFO::ASW Batch was 0.147176920941232 prior to batch effect correction and is now -0.112988821285096 .
2026-04-23 21:40:13.945138 INFO::Total function execution time is 0.0596997737884521 s and adjustment time is 0.0424752235412598 s ( 71.15 )
2026-04-23 21:40:13.959245 INFO::Formatting Data.
2026-04-23 21:40:13.960257 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:13.961348 INFO::Removing potential empty rows and columns
2026-04-23 21:40:13.962532 INFO::Found 0 missing values.
2026-04-23 21:40:13.963891 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.
2026-04-23 21:40:13.969069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:13.969974 INFO::Done
2026-04-23 21:40:13.970564 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:13.973866 INFO::Starting hierarchical adjustment
2026-04-23 21:40:13.97465 INFO::Found 2 batches.
2026-04-23 21:40:13.97524 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:13.975921 INFO::Using default BPPARAM
2026-04-23 21:40:13.976533 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:13.977554 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:40:13.995755 INFO::Done
2026-04-23 21:40:13.99667 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:14.000109 INFO::ASW Batch was 0.417554823976129 prior to batch effect correction and is now 0.196554564791511 .
2026-04-23 21:40:14.000817 INFO::ASW Label was 0.707291967936483 prior to batch effect correction and is now 0.803108551085473 .
2026-04-23 21:40:14.00176 INFO::Total function execution time is 0.0426318645477295 s and adjustment time is 0.0212037563323975 s ( 49.74 )
2026-04-23 21:40:14.002651 INFO::Formatting Data.
2026-04-23 21:40:14.003356 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:14.004799 INFO::Removing potential empty rows and columns
2026-04-23 21:40:14.005921 INFO::Found 0 missing values.
2026-04-23 21:40:14.006953 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.
2026-04-23 21:40:14.012019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:14.012615 INFO::Done
2026-04-23 21:40:14.013209 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:14.016388 INFO::Starting hierarchical adjustment
2026-04-23 21:40:14.01717 INFO::Found 2 batches.
2026-04-23 21:40:14.017817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:14.01849 INFO::Using default BPPARAM
2026-04-23 21:40:14.019094 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:14.020125 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:40:14.039226 INFO::Done
2026-04-23 21:40:14.040219 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:14.043743 INFO::ASW Batch was 0.417554823976129 prior to batch effect correction and is now 0.196554564791511 .
2026-04-23 21:40:14.044464 INFO::ASW Label was 0.707291967936483 prior to batch effect correction and is now 0.803108551085473 .
2026-04-23 21:40:14.045382 INFO::Total function execution time is 0.0427584648132324 s and adjustment time is 0.0221595764160156 s ( 51.83 )
2026-04-23 21:40:14.26394 INFO::Formatting Data.
2026-04-23 21:40:14.264851 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:14.265856 INFO::Removing potential empty rows and columns
2026-04-23 21:40:14.266987 INFO::Found 0 missing values.
2026-04-23 21:40:14.270164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:14.270772 INFO::Done
2026-04-23 21:40:14.271347 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:14.27345 INFO::Starting hierarchical adjustment
2026-04-23 21:40:14.274248 INFO::Found 3 batches.
2026-04-23 21:40:14.274833 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:14.275522 INFO::Using default BPPARAM
2026-04-23 21:40:14.276108 INFO::Processing subtree level 1
2026-04-23 21:40:14.367751 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:40:14.369662 INFO::Done
2026-04-23 21:40:14.370421 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:14.373138 INFO::ASW Batch was -0.0843558545704551 prior to batch effect correction and is now -0.0843558545704551 .
2026-04-23 21:40:14.37423 INFO::Total function execution time is 0.110361099243164 s and adjustment time is 0.0955421924591064 s ( 86.57 )
2026-04-23 21:40:14.375364 INFO::Formatting Data.
2026-04-23 21:40:14.376101 INFO::Typecasting input to dataframe.
2026-04-23 21:40:14.376934 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:14.377925 INFO::Removing potential empty rows and columns
2026-04-23 21:40:14.379067 INFO::Found 0 missing values.
2026-04-23 21:40:14.382247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:14.38291 INFO::Done
2026-04-23 21:40:14.383502 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:14.385654 INFO::Starting hierarchical adjustment
2026-04-23 21:40:14.386447 INFO::Found 3 batches.
2026-04-23 21:40:14.387048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:14.387744 INFO::Using default BPPARAM
2026-04-23 21:40:14.388349 INFO::Processing subtree level 1
2026-04-23 21:40:14.479223 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:40:14.481649 INFO::Done
2026-04-23 21:40:14.482397 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:14.485194 INFO::ASW Batch was -0.0843558545704551 prior to batch effect correction and is now -0.0843558545704551 .
2026-04-23 21:40:14.486269 INFO::Total function execution time is 0.110896110534668 s and adjustment time is 0.0953409671783447 s ( 85.97 )
2026-04-23 21:40:14.50106 INFO::Formatting Data.
2026-04-23 21:40:14.501927 INFO::Typecasting input to dataframe.
2026-04-23 21:40:14.502851 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:14.503919 INFO::Removing potential empty rows and columns
2026-04-23 21:40:14.505079 INFO::Found 0 missing values.
2026-04-23 21:40:14.508229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:14.508827 INFO::Done
2026-04-23 21:40:14.509392 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:14.511516 INFO::Starting hierarchical adjustment
2026-04-23 21:40:14.512277 INFO::Found 3 batches.
2026-04-23 21:40:14.512888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:14.513556 INFO::Using default BPPARAM
2026-04-23 21:40:14.514176 INFO::Processing subtree level 1
2026-04-23 21:40:14.603193 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:40:14.605111 INFO::Done
2026-04-23 21:40:14.605895 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:14.608521 INFO::ASW Batch was -0.00960635644926393 prior to batch effect correction and is now -0.00960635644926393 .
2026-04-23 21:40:14.609535 INFO::Total function execution time is 0.108526468276978 s and adjustment time is 0.0929567813873291 s ( 85.65 )
2026-04-23 21:40:14.761355 INFO::Formatting Data.
2026-04-23 21:40:14.762267 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:14.763477 INFO::Removing potential empty rows and columns
2026-04-23 21:40:14.766509 INFO::Found 1000 missing values.
2026-04-23 21:40:14.786902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:14.787761 INFO::Done
2026-04-23 21:40:14.788399 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:14.794181 INFO::Starting hierarchical adjustment
2026-04-23 21:40:14.795027 INFO::Found 10 batches.
2026-04-23 21:40:14.79561 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:14.796372 INFO::Using default BPPARAM
2026-04-23 21:40:14.796988 INFO::Processing subtree level 1
2026-04-23 21:40:14.953422 INFO::Processing subtree level 2
2026-04-23 21:40:15.103788 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:40:15.106186 INFO::Done
2026-04-23 21:40:15.107083 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:15.11388 INFO::ASW Batch was 0.504430668789342 prior to batch effect correction and is now 0.504430668789342 .
2026-04-23 21:40:15.114835 INFO::ASW Label was 0.316090239445325 prior to batch effect correction and is now 0.316090239445325 .
2026-04-23 21:40:15.116027 INFO::Total function execution time is 0.354698181152344 s and adjustment time is 0.311298847198486 s ( 87.76 )
2026-04-23 21:40:15.11712 INFO::Formatting Data.
2026-04-23 21:40:15.117971 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:15.119559 INFO::Removing potential empty rows and columns
2026-04-23 21:40:15.123073 INFO::Found 1000 missing values.
2026-04-23 21:40:15.146909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:15.14781 INFO::Done
2026-04-23 21:40:15.148498 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:15.154629 INFO::Starting hierarchical adjustment
2026-04-23 21:40:15.155491 INFO::Found 10 batches.
2026-04-23 21:40:16.389704 INFO::Set up parallel execution backend with 2 workers
2026-04-23 21:40:16.393215 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-04-23 21:40:17.797519 INFO::Adjusting the last 2 batches sequentially
2026-04-23 21:40:17.800941 INFO::Adjusting sequential tree level 1 with 2 batches
2026-04-23 21:40:17.817446 INFO::Done
2026-04-23 21:40:17.818211 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:17.822798 INFO::ASW Batch was 0.504430668789342 prior to batch effect correction and is now 0.504430668789342 .
2026-04-23 21:40:17.823431 INFO::ASW Label was 0.316090239445325 prior to batch effect correction and is now 0.316090239445325 .
2026-04-23 21:40:17.824234 INFO::Total function execution time is 2.70717716217041 s and adjustment time is 2.66210079193115 s ( 98.33 )
2026-04-23 21:40:17.982286 INFO::Formatting Data.
2026-04-23 21:40:17.983184 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:17.984189 INFO::Removing potential empty rows and columns
2026-04-23 21:40:17.985311 INFO::Found 0 missing values.
2026-04-23 21:40:17.989103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:17.989701 INFO::Done
2026-04-23 21:40:17.990258 INFO::Acquiring quality metrics before batch effect correction.
2026-04-23 21:40:17.993068 INFO::Starting hierarchical adjustment
2026-04-23 21:40:17.993819 INFO::Found 3 batches.
2026-04-23 21:40:17.994395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-04-23 21:40:17.995106 INFO::Using default BPPARAM
2026-04-23 21:40:17.995707 INFO::Processing subtree level 1
2026-04-23 21:40:18.107585 INFO::Adjusting the last 1 batches sequentially
2026-04-23 21:40:18.109542 INFO::Done
2026-04-23 21:40:18.110286 INFO::Acquiring quality metrics after batch effect correction.
2026-04-23 21:40:18.113636 INFO::ASW Batch was 0.19437878775591 prior to batch effect correction and is now -0.158229732608907 .
2026-04-23 21:40:18.114331 INFO::ASW Label was -0.200926339618325 prior to batch effect correction and is now -0.0783633776354333 .
2026-04-23 21:40:18.115341 INFO::Total function execution time is 0.13311243057251 s and adjustment time is 0.115832567214966 s ( 87.02 )
2026-04-23 21:40:18.252511 INFO::Formatting Data.
2026-04-23 21:40:18.253667 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.254786 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.256018 INFO::Found 2 missing values.
2026-04-23 21:40:18.258939 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.259562 INFO::Done
2026-04-23 21:40:18.287491 INFO::Found NA in Reference column
2026-04-23 21:40:18.296993 INFO::Require at least two references per batch.
2026-04-23 21:40:18.317751 INFO::Formatting Data.
2026-04-23 21:40:18.318578 INFO::Recognized SummarizedExperiment
2026-04-23 21:40:18.319196 INFO::Typecasting input to dataframe.
2026-04-23 21:40:18.329153 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.330404 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.334165 INFO::Found 0 missing values.
2026-04-23 21:40:18.341461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.342215 INFO::Done
2026-04-23 21:40:18.358306 INFO::Formatting Data.
2026-04-23 21:40:18.359208 INFO::Recognized SummarizedExperiment
2026-04-23 21:40:18.359812 INFO::Typecasting input to dataframe.
2026-04-23 21:40:18.379067 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.380387 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.384088 INFO::Found 0 missing values.
2026-04-23 21:40:18.395107 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.39589 INFO::Done
2026-04-23 21:40:18.410878 INFO::Formatting Data.
2026-04-23 21:40:18.411641 INFO::Recognized SummarizedExperiment
2026-04-23 21:40:18.412217 INFO::Typecasting input to dataframe.
2026-04-23 21:40:18.427762 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.428791 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.429894 INFO::Found 0 missing values.
2026-04-23 21:40:18.430808 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.
2026-04-23 21:40:18.435163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.43574 INFO::Done
2026-04-23 21:40:18.445536 INFO::Formatting Data.
2026-04-23 21:40:18.446335 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.447255 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.448266 INFO::Found 0 missing values.
2026-04-23 21:40:18.451145 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.451705 INFO::Done
2026-04-23 21:40:18.462799 INFO::Formatting Data.
2026-04-23 21:40:18.463579 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.464476 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.465528 INFO::Found 0 missing values.
2026-04-23 21:40:18.468409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.469001 INFO::Done
2026-04-23 21:40:18.498769 INFO::Formatting Data.
2026-04-23 21:40:18.499627 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.50075 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.501971 INFO::Found 1 missing values.
2026-04-23 21:40:18.504638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.505286 INFO::Done
2026-04-23 21:40:18.524622 INFO::Formatting Data.
2026-04-23 21:40:18.525498 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.526444 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.527497 INFO::Found 2 missing values.
2026-04-23 21:40:18.528452 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.
2026-04-23 21:40:18.530863 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.531507 INFO::Done
2026-04-23 21:40:18.541703 INFO::Formatting Data.
2026-04-23 21:40:18.542511 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.543438 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.544463 INFO::Found 2 missing values.
2026-04-23 21:40:18.546243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.546949 INFO::Done
2026-04-23 21:40:18.558423 INFO::Formatting Data.
2026-04-23 21:40:18.559262 INFO::Typecasting input to dataframe.
2026-04-23 21:40:18.560133 INFO::Replacing NaNs with NAs.
2026-04-23 21:40:18.56107 INFO::Removing potential empty rows and columns
2026-04-23 21:40:18.562161 INFO::Found 0 missing values.
2026-04-23 21:40:18.565137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-04-23 21:40:18.565728 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.699 4.025 23.268
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.276 | 1.729 | 17.524 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.015 | 0.000 | 0.014 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |