Yannis Schumann
| Snapshot Date: 2026-02-02 13:45 -0500 (Mon, 02 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-05 11:57 -0500 (Thu, 05 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4888 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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: 1.6.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz |
| StartedAt: 2026-02-03 21:12:13 -0500 (Tue, 03 Feb 2026) |
| EndedAt: 2026-02-03 21:13:45 -0500 (Tue, 03 Feb 2026) |
| EllapsedTime: 92.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* 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 25.656 1.4 18.552
* 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-3.22-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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")
2026-02-03 21:13:06.385002 INFO::Formatting Data.
2026-02-03 21:13:06.386347 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:06.398274 INFO::Removing potential empty rows and columns
2026-02-03 21:13:06.668278 INFO::Found 0 missing values.
2026-02-03 21:13:06.671793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:06.672476 INFO::Done
2026-02-03 21:13:06.673059 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:06.684748 INFO::Starting hierarchical adjustment
2026-02-03 21:13:06.685681 INFO::Found 3 batches.
2026-02-03 21:13:06.686274 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:06.687468 INFO::Using default BPPARAM
2026-02-03 21:13:06.688069 INFO::Processing subtree level 1
2026-02-03 21:13:06.791303 INFO::Adjusting the last 1 batches sequentially
2026-02-03 21:13:06.793247 INFO::Done
2026-02-03 21:13:06.793981 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:06.7968 INFO::ASW Batch was -0.0858701474691842 prior to batch effect correction and is now -0.0858701474691842 .
2026-02-03 21:13:06.797961 INFO::Total function execution time is 0.413635969161987 s and adjustment time is 0.107748031616211 s ( 26.05 )
2026-02-03 21:13:06.813663 INFO::Formatting Data.
2026-02-03 21:13:06.814549 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:06.815621 INFO::Removing potential empty rows and columns
2026-02-03 21:13:06.816905 INFO::Found 0 missing values.
2026-02-03 21:13:06.817942 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.
2026-02-03 21:13:06.830467 INFO::Formatting Data.
2026-02-03 21:13:06.831404 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:06.832481 INFO::Removing potential empty rows and columns
2026-02-03 21:13:06.833694 INFO::Found 0 missing values.
2026-02-03 21:13:06.834776 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.
2026-02-03 21:13:06.852739 INFO::Formatting Data.
2026-02-03 21:13:06.853544 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:06.8545 INFO::Removing potential empty rows and columns
2026-02-03 21:13:06.855648 INFO::Found 0 missing values.
2026-02-03 21:13:06.856665 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.
2026-02-03 21:13:06.861387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:06.862022 INFO::Done
2026-02-03 21:13:06.862592 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:06.864722 INFO::Starting hierarchical adjustment
2026-02-03 21:13:06.865466 INFO::Found 2 batches.
2026-02-03 21:13:06.866041 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:06.866722 INFO::Using default BPPARAM
2026-02-03 21:13:06.867268 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:06.868264 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-03 21:13:06.889949 INFO::Done
2026-02-03 21:13:06.890656 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:06.892914 INFO::ASW Batch was 0.0163744743704567 prior to batch effect correction and is now -0.124968286933781 .
2026-02-03 21:13:06.89396 INFO::Total function execution time is 0.0412490367889404 s and adjustment time is 0.0246026515960693 s ( 59.64 )
2026-02-03 21:13:06.89687 INFO::Formatting Data.
2026-02-03 21:13:06.897537 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:06.906755 INFO::Formatting Data.
2026-02-03 21:13:06.907568 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:06.908541 INFO::Removing potential empty rows and columns
2026-02-03 21:13:06.90966 INFO::Found 0 missing values.
2026-02-03 21:13:06.912882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:06.913482 INFO::Done
2026-02-03 21:13:06.914048 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:06.939564 INFO::Starting hierarchical adjustment
2026-02-03 21:13:06.940908 INFO::Found 2 batches.
2026-02-03 21:13:06.941453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:06.942032 INFO::Using default BPPARAM
2026-02-03 21:13:06.942543 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:06.943439 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-03 21:13:06.95737 INFO::Done
2026-02-03 21:13:06.958041 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:06.959982 INFO::ASW Batch was -0.046947917899371 prior to batch effect correction and is now -0.107051178398612 .
2026-02-03 21:13:06.960758 INFO::Total function execution time is 0.0540902614593506 s and adjustment time is 0.0166122913360596 s ( 30.71 )
2026-02-03 21:13:06.961736 INFO::Formatting Data.
2026-02-03 21:13:06.962305 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:06.96313 INFO::Removing potential empty rows and columns
2026-02-03 21:13:06.964093 INFO::Found 0 missing values.
2026-02-03 21:13:06.966745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:06.967264 INFO::Done
2026-02-03 21:13:06.967759 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:06.969636 INFO::Starting hierarchical adjustment
2026-02-03 21:13:06.970306 INFO::Found 2 batches.
2026-02-03 21:13:06.970809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:06.971373 INFO::Using default BPPARAM
2026-02-03 21:13:06.971882 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:06.972743 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-03 21:13:06.986669 INFO::Done
2026-02-03 21:13:06.987318 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:06.989271 INFO::ASW Batch was -0.046947917899371 prior to batch effect correction and is now -0.107051178398612 .
2026-02-03 21:13:06.990033 INFO::Total function execution time is 0.0282857418060303 s and adjustment time is 0.0164730548858643 s ( 58.24 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-03 21:13:10.061759 INFO::Formatting Data.
2026-02-03 21:13:10.062517 INFO::Recognized SummarizedExperiment
2026-02-03 21:13:10.063018 INFO::Typecasting input to dataframe.
2026-02-03 21:13:10.093091 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:10.094411 INFO::Removing potential empty rows and columns
2026-02-03 21:13:10.098352 INFO::Found 0 missing values.
2026-02-03 21:13:10.105717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:10.106383 INFO::Done
2026-02-03 21:13:10.106964 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:10.110783 INFO::Starting hierarchical adjustment
2026-02-03 21:13:10.111572 INFO::Found 2 batches.
2026-02-03 21:13:10.112113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:10.113263 INFO::Using default BPPARAM
2026-02-03 21:13:10.113849 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:10.114913 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-03 21:13:10.174784 INFO::Done
2026-02-03 21:13:10.175594 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:10.179558 INFO::ASW Batch was 0.00665859688850453 prior to batch effect correction and is now -0.100873785964605 .
2026-02-03 21:13:10.180499 INFO::Total function execution time is 0.119015216827393 s and adjustment time is 0.0633513927459717 s ( 53.23 )
Warning: stack imbalance in '{', 73 then 75
2026-02-03 21:13:10.200177 INFO::Formatting Data.
2026-02-03 21:13:10.200992 INFO::Recognized SummarizedExperiment
2026-02-03 21:13:10.201572 INFO::Typecasting input to dataframe.
2026-02-03 21:13:10.211299 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:10.212477 INFO::Removing potential empty rows and columns
2026-02-03 21:13:10.216372 INFO::Found 0 missing values.
2026-02-03 21:13:10.223953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:10.22463 INFO::Done
2026-02-03 21:13:10.225176 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:10.22888 INFO::Starting hierarchical adjustment
2026-02-03 21:13:10.229667 INFO::Found 2 batches.
2026-02-03 21:13:10.230207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:10.23083 INFO::Using default BPPARAM
2026-02-03 21:13:10.231345 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:10.232341 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-03 21:13:10.258611 INFO::Done
2026-02-03 21:13:10.259491 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:10.263874 INFO::ASW Batch was 0.0115600830538541 prior to batch effect correction and is now 0.0115600830538541 .
2026-02-03 21:13:10.264901 INFO::Total function execution time is 0.064687967300415 s and adjustment time is 0.029022216796875 s ( 44.86 )
2026-02-03 21:13:10.285693 INFO::Formatting Data.
2026-02-03 21:13:10.286816 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:10.28792 INFO::Removing potential empty rows and columns
2026-02-03 21:13:10.289117 INFO::Found 0 missing values.
2026-02-03 21:13:10.29244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:10.293067 INFO::Done
2026-02-03 21:13:10.293635 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:10.295949 INFO::Starting hierarchical adjustment
2026-02-03 21:13:10.296718 INFO::Found 3 batches.
2026-02-03 21:13:10.297261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:10.298171 INFO::Using default BPPARAM
2026-02-03 21:13:10.298733 INFO::Processing subtree level 1
2026-02-03 21:13:10.458908 INFO::Adjusting the last 1 batches sequentially
2026-02-03 21:13:10.462131 INFO::Done
2026-02-03 21:13:10.462884 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:10.466519 INFO::ASW Batch was -0.0545861322336412 prior to batch effect correction and is now -0.147572635636536 .
2026-02-03 21:13:10.467647 INFO::Total function execution time is 0.182000160217285 s and adjustment time is 0.165566444396973 s ( 90.97 )
2026-02-03 21:13:10.487263 INFO::Skipping initial DF formatting
2026-02-03 21:13:10.488464 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:10.494759 INFO::Starting hierarchical adjustment
2026-02-03 21:13:10.49603 INFO::Found 5 batches.
2026-02-03 21:13:10.496881 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:10.497804 INFO::Using default BPPARAM
2026-02-03 21:13:10.498582 INFO::Processing subtree level 1
2026-02-03 21:13:10.765674 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:10.768183 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-03 21:13:10.802342 INFO::Done
2026-02-03 21:13:10.803594 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:10.810868 INFO::ASW Batch was 0.559393341821286 prior to batch effect correction and is now 0.559393341821286 .
2026-02-03 21:13:10.81199 INFO::ASW Label was 0.39308856959281 prior to batch effect correction and is now 0.39308856959281 .
2026-02-03 21:13:10.813439 INFO::Total function execution time is 0.326326847076416 s and adjustment time is 0.306521415710449 s ( 93.93 )
2026-02-03 21:13:10.902771 INFO::Formatting Data.
2026-02-03 21:13:10.903666 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:10.904688 INFO::Removing potential empty rows and columns
2026-02-03 21:13:10.905742 INFO::Found 0 missing values.
2026-02-03 21:13:10.909913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:10.910489 INFO::Done
2026-02-03 21:13:10.911026 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:10.914111 INFO::Starting hierarchical adjustment
2026-02-03 21:13:10.91486 INFO::Found 5 batches.
2026-02-03 21:13:10.915387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:10.916027 INFO::Using default BPPARAM
2026-02-03 21:13:10.916559 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.
2026-02-03 21:13:11.059896 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.061641 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-03 21:13:11.07983 INFO::Done
2026-02-03 21:13:11.080669 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.084377 INFO::ASW Batch was 0.38311524749513 prior to batch effect correction and is now -0.0287200342343381 .
2026-02-03 21:13:11.085057 INFO::ASW Label was 0.461778620504641 prior to batch effect correction and is now 0.744059885787554 .
2026-02-03 21:13:11.085921 INFO::Total function execution time is 0.183263778686523 s and adjustment time is 0.165081739425659 s ( 90.08 )
2026-02-03 21:13:11.086833 INFO::Formatting Data.
2026-02-03 21:13:11.087462 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:11.088493 INFO::Removing potential empty rows and columns
2026-02-03 21:13:11.089597 INFO::Found 0 missing values.
2026-02-03 21:13:11.094108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:11.094805 INFO::Done
2026-02-03 21:13:11.095369 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:11.098792 INFO::Starting hierarchical adjustment
2026-02-03 21:13:11.099593 INFO::Found 5 batches.
2026-02-03 21:13:11.100135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:11.100781 INFO::Using default BPPARAM
2026-02-03 21:13:11.101366 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.
2026-02-03 21:13:11.23362 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.235302 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-03 21:13:11.252829 INFO::Done
2026-02-03 21:13:11.253683 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.257189 INFO::ASW Batch was 0.38311524749513 prior to batch effect correction and is now -0.0287200342343381 .
2026-02-03 21:13:11.257834 INFO::ASW Label was 0.461778620504641 prior to batch effect correction and is now 0.744059885787554 .
2026-02-03 21:13:11.258711 INFO::Total function execution time is 0.171880006790161 s and adjustment time is 0.153366088867188 s ( 89.23 )
2026-02-03 21:13:11.27369 INFO::Formatting Data.
2026-02-03 21:13:11.274617 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:11.275657 INFO::Removing potential empty rows and columns
2026-02-03 21:13:11.276772 INFO::Found 0 missing values.
2026-02-03 21:13:11.281044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:11.281642 INFO::Done
2026-02-03 21:13:11.28216 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:11.285381 INFO::Starting hierarchical adjustment
2026-02-03 21:13:11.286186 INFO::Found 5 batches.
2026-02-03 21:13:11.286772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:11.287445 INFO::Using default BPPARAM
2026-02-03 21:13:11.287991 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.
2026-02-03 21:13:11.430348 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.432496 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-03 21:13:11.455841 INFO::Done
2026-02-03 21:13:11.45688 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.461438 INFO::ASW Batch was 0.322190528106318 prior to batch effect correction and is now 0.0318040493943452 .
2026-02-03 21:13:11.46226 INFO::ASW Label was 0.529276133227943 prior to batch effect correction and is now 0.717018479272526 .
2026-02-03 21:13:11.463306 INFO::Total function execution time is 0.189708232879639 s and adjustment time is 0.169738531112671 s ( 89.47 )
2026-02-03 21:13:11.464437 INFO::Formatting Data.
2026-02-03 21:13:11.465262 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:11.466411 INFO::Removing potential empty rows and columns
2026-02-03 21:13:11.467784 INFO::Found 0 missing values.
2026-02-03 21:13:11.473424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:11.474121 INFO::Done
2026-02-03 21:13:11.474835 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:11.479182 INFO::Starting hierarchical adjustment
2026-02-03 21:13:11.480194 INFO::Found 5 batches.
2026-02-03 21:13:11.480944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:11.48182 INFO::Using default BPPARAM
2026-02-03 21:13:11.482581 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.
2026-02-03 21:13:11.637718 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.639697 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-03 21:13:11.66031 INFO::Done
2026-02-03 21:13:11.661388 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.665304 INFO::ASW Batch was 0.322190528106318 prior to batch effect correction and is now 0.0318040493943452 .
2026-02-03 21:13:11.666006 INFO::ASW Label was 0.529276133227943 prior to batch effect correction and is now 0.717018479272526 .
2026-02-03 21:13:11.667005 INFO::Total function execution time is 0.202571868896484 s and adjustment time is 0.180166721343994 s ( 88.94 )
2026-02-03 21:13:11.682715 INFO::Formatting Data.
2026-02-03 21:13:11.683584 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:11.684602 INFO::Removing potential empty rows and columns
2026-02-03 21:13:11.685755 INFO::Found 0 missing values.
2026-02-03 21:13:11.688756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:11.689344 INFO::Done
2026-02-03 21:13:11.689943 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:11.69331 INFO::Starting hierarchical adjustment
2026-02-03 21:13:11.694109 INFO::Found 2 batches.
2026-02-03 21:13:11.694695 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:11.695359 INFO::Using default BPPARAM
2026-02-03 21:13:11.695954 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.696934 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-03 21:13:11.713258 INFO::Done
2026-02-03 21:13:11.714024 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.71747 INFO::ASW Batch was 0.728085677600308 prior to batch effect correction and is now 0.0773362724100669 .
2026-02-03 21:13:11.718153 INFO::ASW Label was 0.370601178370961 prior to batch effect correction and is now 0.838376737086153 .
2026-02-03 21:13:11.719032 INFO::Total function execution time is 0.0364341735839844 s and adjustment time is 0.0192830562591553 s ( 52.93 )
2026-02-03 21:13:11.719926 INFO::Formatting Data.
2026-02-03 21:13:11.720608 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:11.721589 INFO::Removing potential empty rows and columns
2026-02-03 21:13:11.722682 INFO::Found 0 missing values.
2026-02-03 21:13:11.725535 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:11.726106 INFO::Done
2026-02-03 21:13:11.726665 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:11.730031 INFO::Starting hierarchical adjustment
2026-02-03 21:13:11.730801 INFO::Found 2 batches.
2026-02-03 21:13:11.73136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:11.732019 INFO::Using default BPPARAM
2026-02-03 21:13:11.732585 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.733579 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-03 21:13:11.749721 INFO::Done
2026-02-03 21:13:11.750435 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.753777 INFO::ASW Batch was 0.728085677600308 prior to batch effect correction and is now 0.0773362724100669 .
2026-02-03 21:13:11.754427 INFO::ASW Label was 0.370601178370961 prior to batch effect correction and is now 0.838376737086153 .
2026-02-03 21:13:11.755289 INFO::Total function execution time is 0.0353841781616211 s and adjustment time is 0.0190615653991699 s ( 53.87 )
2026-02-03 21:13:11.768977 INFO::Formatting Data.
2026-02-03 21:13:11.769994 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:11.771049 INFO::Removing potential empty rows and columns
2026-02-03 21:13:11.772079 INFO::Found 0 missing values.
2026-02-03 21:13:11.774386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:11.774977 INFO::Done
2026-02-03 21:13:11.775539 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:11.777792 INFO::Starting hierarchical adjustment
2026-02-03 21:13:11.778584 INFO::Found 2 batches.
2026-02-03 21:13:11.779152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:11.779825 INFO::Using default BPPARAM
2026-02-03 21:13:11.780367 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.781378 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-03 21:13:11.81542 INFO::Done
2026-02-03 21:13:11.816253 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.818459 INFO::ASW Batch was -0.023060956464948 prior to batch effect correction and is now -0.117151544846824 .
2026-02-03 21:13:11.819394 INFO::Total function execution time is 0.0507228374481201 s and adjustment time is 0.0369651317596436 s ( 72.88 )
2026-02-03 21:13:11.833193 INFO::Formatting Data.
2026-02-03 21:13:11.834132 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:11.835124 INFO::Removing potential empty rows and columns
2026-02-03 21:13:11.836206 INFO::Found 0 missing values.
2026-02-03 21:13:11.837436 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.
2026-02-03 21:13:11.842474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:11.843127 INFO::Done
2026-02-03 21:13:11.843694 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:11.846879 INFO::Starting hierarchical adjustment
2026-02-03 21:13:11.847662 INFO::Found 2 batches.
2026-02-03 21:13:11.848203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:11.848863 INFO::Using default BPPARAM
2026-02-03 21:13:11.849397 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.850415 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-03 21:13:11.868068 INFO::Done
2026-02-03 21:13:11.868841 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.872005 INFO::ASW Batch was 0.709814669514431 prior to batch effect correction and is now 0.0150244343203917 .
2026-02-03 21:13:11.872699 INFO::ASW Label was 0.314961679878109 prior to batch effect correction and is now 0.83443862641646 .
2026-02-03 21:13:11.873504 INFO::Total function execution time is 0.0404467582702637 s and adjustment time is 0.0205450057983398 s ( 50.8 )
2026-02-03 21:13:11.874336 INFO::Formatting Data.
2026-02-03 21:13:11.874999 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:11.875975 INFO::Removing potential empty rows and columns
2026-02-03 21:13:11.877034 INFO::Found 0 missing values.
2026-02-03 21:13:11.87804 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.
2026-02-03 21:13:11.882985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:11.883621 INFO::Done
2026-02-03 21:13:11.884174 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:11.887497 INFO::Starting hierarchical adjustment
2026-02-03 21:13:11.888345 INFO::Found 2 batches.
2026-02-03 21:13:11.888966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:11.889625 INFO::Using default BPPARAM
2026-02-03 21:13:11.890171 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:11.891209 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-03 21:13:11.909115 INFO::Done
2026-02-03 21:13:11.909934 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:11.913222 INFO::ASW Batch was 0.709814669514431 prior to batch effect correction and is now 0.0150244343203917 .
2026-02-03 21:13:11.913918 INFO::ASW Label was 0.314961679878109 prior to batch effect correction and is now 0.83443862641646 .
2026-02-03 21:13:11.914797 INFO::Total function execution time is 0.0404584407806396 s and adjustment time is 0.0209004878997803 s ( 51.66 )
2026-02-03 21:13:12.157838 INFO::Formatting Data.
2026-02-03 21:13:12.158982 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:12.160054 INFO::Removing potential empty rows and columns
2026-02-03 21:13:12.161316 INFO::Found 0 missing values.
2026-02-03 21:13:12.164697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:12.165303 INFO::Done
2026-02-03 21:13:12.165876 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:12.16825 INFO::Starting hierarchical adjustment
2026-02-03 21:13:12.169053 INFO::Found 3 batches.
2026-02-03 21:13:12.169631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:12.170271 INFO::Using default BPPARAM
2026-02-03 21:13:12.170856 INFO::Processing subtree level 1
2026-02-03 21:13:12.266655 INFO::Adjusting the last 1 batches sequentially
2026-02-03 21:13:12.268625 INFO::Done
2026-02-03 21:13:12.269318 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:12.272075 INFO::ASW Batch was -0.0827797542130967 prior to batch effect correction and is now -0.0827797542130967 .
2026-02-03 21:13:12.273111 INFO::Total function execution time is 0.115357875823975 s and adjustment time is 0.0996987819671631 s ( 86.43 )
2026-02-03 21:13:12.274302 INFO::Formatting Data.
2026-02-03 21:13:12.274996 INFO::Typecasting input to dataframe.
2026-02-03 21:13:12.275819 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:12.276801 INFO::Removing potential empty rows and columns
2026-02-03 21:13:12.277995 INFO::Found 0 missing values.
2026-02-03 21:13:12.281222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:12.281827 INFO::Done
2026-02-03 21:13:12.282381 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:12.284536 INFO::Starting hierarchical adjustment
2026-02-03 21:13:12.285337 INFO::Found 3 batches.
2026-02-03 21:13:12.285885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:12.286582 INFO::Using default BPPARAM
2026-02-03 21:13:12.287152 INFO::Processing subtree level 1
2026-02-03 21:13:12.384287 INFO::Adjusting the last 1 batches sequentially
2026-02-03 21:13:12.386299 INFO::Done
2026-02-03 21:13:12.387028 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:12.389802 INFO::ASW Batch was -0.0827797542130967 prior to batch effect correction and is now -0.0827797542130967 .
2026-02-03 21:13:12.390797 INFO::Total function execution time is 0.11651086807251 s and adjustment time is 0.10108208656311 s ( 86.76 )
2026-02-03 21:13:12.406117 INFO::Formatting Data.
2026-02-03 21:13:12.407043 INFO::Typecasting input to dataframe.
2026-02-03 21:13:12.408004 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:12.408973 INFO::Removing potential empty rows and columns
2026-02-03 21:13:12.410131 INFO::Found 0 missing values.
2026-02-03 21:13:12.413267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:12.413847 INFO::Done
2026-02-03 21:13:12.414381 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:12.416626 INFO::Starting hierarchical adjustment
2026-02-03 21:13:12.417345 INFO::Found 3 batches.
2026-02-03 21:13:12.417898 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:12.418536 INFO::Using default BPPARAM
2026-02-03 21:13:12.419069 INFO::Processing subtree level 1
2026-02-03 21:13:12.519178 INFO::Adjusting the last 1 batches sequentially
2026-02-03 21:13:12.52218 INFO::Done
2026-02-03 21:13:12.523334 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:12.527784 INFO::ASW Batch was -0.0350518913891629 prior to batch effect correction and is now -0.0350518913891629 .
2026-02-03 21:13:12.529282 INFO::Total function execution time is 0.123172998428345 s and adjustment time is 0.104899644851685 s ( 85.16 )
2026-02-03 21:13:12.693559 INFO::Formatting Data.
2026-02-03 21:13:12.694493 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:12.695794 INFO::Removing potential empty rows and columns
2026-02-03 21:13:12.698725 INFO::Found 1000 missing values.
2026-02-03 21:13:12.717972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:12.718851 INFO::Done
2026-02-03 21:13:12.719445 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:12.725255 INFO::Starting hierarchical adjustment
2026-02-03 21:13:12.726072 INFO::Found 10 batches.
2026-02-03 21:13:12.726644 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:12.727274 INFO::Using default BPPARAM
2026-02-03 21:13:12.727849 INFO::Processing subtree level 1
2026-02-03 21:13:12.887135 INFO::Processing subtree level 2
2026-02-03 21:13:13.037648 INFO::Adjusting the last 1 batches sequentially
2026-02-03 21:13:13.039847 INFO::Done
2026-02-03 21:13:13.040614 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:13.046994 INFO::ASW Batch was 0.522869011573305 prior to batch effect correction and is now 0.522869011573305 .
2026-02-03 21:13:13.047771 INFO::ASW Label was 0.314706189605326 prior to batch effect correction and is now 0.314706189605326 .
2026-02-03 21:13:13.048975 INFO::Total function execution time is 0.355495929718018 s and adjustment time is 0.313891887664795 s ( 88.3 )
2026-02-03 21:13:13.049975 INFO::Formatting Data.
2026-02-03 21:13:13.050751 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:13.052158 INFO::Removing potential empty rows and columns
2026-02-03 21:13:13.055386 INFO::Found 1000 missing values.
2026-02-03 21:13:13.078183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:13.079103 INFO::Done
2026-02-03 21:13:13.079777 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:13.085895 INFO::Starting hierarchical adjustment
2026-02-03 21:13:13.086738 INFO::Found 10 batches.
2026-02-03 21:13:14.7593 INFO::Set up parallel execution backend with 2 workers
2026-02-03 21:13:14.76139 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-03 21:13:15.900563 INFO::Adjusting the last 2 batches sequentially
2026-02-03 21:13:15.902301 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-03 21:13:15.917653 INFO::Done
2026-02-03 21:13:15.918204 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:15.92247 INFO::ASW Batch was 0.522869011573305 prior to batch effect correction and is now 0.522869011573305 .
2026-02-03 21:13:15.922976 INFO::ASW Label was 0.314706189605326 prior to batch effect correction and is now 0.314706189605326 .
2026-02-03 21:13:15.923661 INFO::Total function execution time is 2.87376379966736 s and adjustment time is 2.8311140537262 s ( 98.52 )
2026-02-03 21:13:16.068287 INFO::Formatting Data.
2026-02-03 21:13:16.069089 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.069981 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.071021 INFO::Found 0 missing values.
2026-02-03 21:13:16.074471 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.074992 INFO::Done
2026-02-03 21:13:16.075482 INFO::Acquiring quality metrics before batch effect correction.
2026-02-03 21:13:16.078125 INFO::Starting hierarchical adjustment
2026-02-03 21:13:16.078871 INFO::Found 3 batches.
2026-02-03 21:13:16.079373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-03 21:13:16.079966 INFO::Using default BPPARAM
2026-02-03 21:13:16.080451 INFO::Processing subtree level 1
2026-02-03 21:13:16.183758 INFO::Adjusting the last 1 batches sequentially
2026-02-03 21:13:16.18543 INFO::Done
2026-02-03 21:13:16.186048 INFO::Acquiring quality metrics after batch effect correction.
2026-02-03 21:13:16.189111 INFO::ASW Batch was 0.166569256452079 prior to batch effect correction and is now -0.172017245431004 .
2026-02-03 21:13:16.189699 INFO::ASW Label was -0.165467670630992 prior to batch effect correction and is now -0.00132481810218254 .
2026-02-03 21:13:16.19058 INFO::Total function execution time is 0.122348546981812 s and adjustment time is 0.10667610168457 s ( 87.19 )
2026-02-03 21:13:16.309064 INFO::Formatting Data.
2026-02-03 21:13:16.30992 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.310848 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.311912 INFO::Found 2 missing values.
2026-02-03 21:13:16.314723 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.315253 INFO::Done
2026-02-03 21:13:16.344875 INFO::Found NA in Reference column
2026-02-03 21:13:16.355191 INFO::Require at least two references per batch.
2026-02-03 21:13:16.376753 INFO::Formatting Data.
2026-02-03 21:13:16.377622 INFO::Recognized SummarizedExperiment
2026-02-03 21:13:16.37817 INFO::Typecasting input to dataframe.
2026-02-03 21:13:16.388825 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.390191 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.393823 INFO::Found 0 missing values.
2026-02-03 21:13:16.400773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.401551 INFO::Done
2026-02-03 21:13:16.418091 INFO::Formatting Data.
2026-02-03 21:13:16.418932 INFO::Recognized SummarizedExperiment
2026-02-03 21:13:16.419475 INFO::Typecasting input to dataframe.
2026-02-03 21:13:16.438317 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.439765 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.443358 INFO::Found 0 missing values.
2026-02-03 21:13:16.45436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.455189 INFO::Done
2026-02-03 21:13:16.471843 INFO::Formatting Data.
2026-02-03 21:13:16.472775 INFO::Recognized SummarizedExperiment
2026-02-03 21:13:16.473325 INFO::Typecasting input to dataframe.
2026-02-03 21:13:16.491305 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.492544 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.493711 INFO::Found 0 missing values.
2026-02-03 21:13:16.494721 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.
2026-02-03 21:13:16.49927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.499918 INFO::Done
2026-02-03 21:13:16.511066 INFO::Formatting Data.
2026-02-03 21:13:16.511987 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.512963 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.51404 INFO::Found 0 missing values.
2026-02-03 21:13:16.517038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.517598 INFO::Done
2026-02-03 21:13:16.530499 INFO::Formatting Data.
2026-02-03 21:13:16.531539 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.532732 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.533903 INFO::Found 0 missing values.
2026-02-03 21:13:16.537969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.538865 INFO::Done
2026-02-03 21:13:16.576668 INFO::Formatting Data.
2026-02-03 21:13:16.577708 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.578963 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.580286 INFO::Found 1 missing values.
2026-02-03 21:13:16.583341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.583939 INFO::Done
2026-02-03 21:13:16.607281 INFO::Formatting Data.
2026-02-03 21:13:16.608222 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.609225 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.610315 INFO::Found 2 missing values.
2026-02-03 21:13:16.611337 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.
2026-02-03 21:13:16.613912 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.61453 INFO::Done
2026-02-03 21:13:16.626605 INFO::Formatting Data.
2026-02-03 21:13:16.62763 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.628653 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.629743 INFO::Found 2 missing values.
2026-02-03 21:13:16.631629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.632237 INFO::Done
2026-02-03 21:13:16.64492 INFO::Formatting Data.
2026-02-03 21:13:16.645938 INFO::Typecasting input to dataframe.
2026-02-03 21:13:16.646876 INFO::Replacing NaNs with NAs.
2026-02-03 21:13:16.6479 INFO::Removing potential empty rows and columns
2026-02-03 21:13:16.649012 INFO::Found 0 missing values.
2026-02-03 21:13:16.652303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-03 21:13:16.652939 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.160 4.426 21.190
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.656 | 1.400 | 18.552 | |
| compute_asw | 0.024 | 0.004 | 0.028 | |
| count_existing | 0.012 | 0.006 | 0.018 | |
| generate_data_covariables | 0.013 | 0.003 | 0.016 | |
| generate_dataset | 0.014 | 0.001 | 0.015 | |