Yannis Schumann
| Snapshot Date: 2026-03-27 13:45 -0400 (Fri, 27 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-28 11:57 -0400 (Sat, 28 Mar 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" | 4893 |
| 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: 2026-03-27 21:15:39 -0400 (Fri, 27 Mar 2026) |
| EndedAt: 2026-03-27 21:17:08 -0400 (Fri, 27 Mar 2026) |
| EllapsedTime: 89.1 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 24.04.4 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 23.33 1.308 16.871
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking 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")
2026-03-27 21:16:30.610265 INFO::Formatting Data.
2026-03-27 21:16:30.611781 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:30.623782 INFO::Removing potential empty rows and columns
2026-03-27 21:16:30.88815 INFO::Found 0 missing values.
2026-03-27 21:16:30.891522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:30.89214 INFO::Done
2026-03-27 21:16:30.892686 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:30.903606 INFO::Starting hierarchical adjustment
2026-03-27 21:16:30.904429 INFO::Found 3 batches.
2026-03-27 21:16:30.90497 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:30.906113 INFO::Using default BPPARAM
2026-03-27 21:16:30.906685 INFO::Processing subtree level 1
2026-03-27 21:16:31.023137 INFO::Adjusting the last 1 batches sequentially
2026-03-27 21:16:31.025038 INFO::Done
2026-03-27 21:16:31.025738 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:31.029778 INFO::ASW Batch was -0.0621593384493172 prior to batch effect correction and is now -0.0621593384493172 .
2026-03-27 21:16:31.031696 INFO::Total function execution time is 0.421923637390137 s and adjustment time is 0.120771646499634 s ( 28.62 )
2026-03-27 21:16:31.053056 INFO::Formatting Data.
2026-03-27 21:16:31.0543 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:31.055745 INFO::Removing potential empty rows and columns
2026-03-27 21:16:31.057574 INFO::Found 0 missing values.
2026-03-27 21:16:31.059052 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-27 21:16:31.077891 INFO::Formatting Data.
2026-03-27 21:16:31.079093 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:31.08052 INFO::Removing potential empty rows and columns
2026-03-27 21:16:31.082189 INFO::Found 0 missing values.
2026-03-27 21:16:31.083651 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-27 21:16:31.110097 INFO::Formatting Data.
2026-03-27 21:16:31.111019 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:31.112056 INFO::Removing potential empty rows and columns
2026-03-27 21:16:31.113294 INFO::Found 0 missing values.
2026-03-27 21:16:31.114339 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-27 21:16:31.119452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:31.120121 INFO::Done
2026-03-27 21:16:31.120732 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:31.12295 INFO::Starting hierarchical adjustment
2026-03-27 21:16:31.12374 INFO::Found 2 batches.
2026-03-27 21:16:31.124329 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:31.125036 INFO::Using default BPPARAM
2026-03-27 21:16:31.125636 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:31.126677 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-27 21:16:31.150858 INFO::Done
2026-03-27 21:16:31.151708 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:31.154296 INFO::ASW Batch was 0.0890699043998164 prior to batch effect correction and is now -0.104846230762781 .
2026-03-27 21:16:31.155334 INFO::Total function execution time is 0.0453004837036133 s and adjustment time is 0.0272252559661865 s ( 60.1 )
2026-03-27 21:16:31.158766 INFO::Formatting Data.
2026-03-27 21:16:31.159518 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:31.169518 INFO::Formatting Data.
2026-03-27 21:16:31.170382 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:31.171428 INFO::Removing potential empty rows and columns
2026-03-27 21:16:31.17265 INFO::Found 0 missing values.
2026-03-27 21:16:31.176028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:31.176664 INFO::Done
2026-03-27 21:16:31.177243 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:31.204611 INFO::Starting hierarchical adjustment
2026-03-27 21:16:31.205989 INFO::Found 2 batches.
2026-03-27 21:16:31.206603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:31.207198 INFO::Using default BPPARAM
2026-03-27 21:16:31.207759 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:31.208755 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:31.224591 INFO::Done
2026-03-27 21:16:31.225258 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:31.227451 INFO::ASW Batch was -0.00764282734844592 prior to batch effect correction and is now -0.0909913858412295 .
2026-03-27 21:16:31.228251 INFO::Total function execution time is 0.0588381290435791 s and adjustment time is 0.018749475479126 s ( 31.87 )
2026-03-27 21:16:31.22934 INFO::Formatting Data.
2026-03-27 21:16:31.230011 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:31.230934 INFO::Removing potential empty rows and columns
2026-03-27 21:16:31.232025 INFO::Found 0 missing values.
2026-03-27 21:16:31.235031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:31.235602 INFO::Done
2026-03-27 21:16:31.236167 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:31.238343 INFO::Starting hierarchical adjustment
2026-03-27 21:16:31.239075 INFO::Found 2 batches.
2026-03-27 21:16:31.239655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:31.240337 INFO::Using default BPPARAM
2026-03-27 21:16:31.240903 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:31.24187 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:31.257861 INFO::Done
2026-03-27 21:16:31.258541 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:31.260444 INFO::ASW Batch was -0.00764282734844592 prior to batch effect correction and is now -0.0909913858412295 .
2026-03-27 21:16:31.261192 INFO::Total function execution time is 0.0318777561187744 s and adjustment time is 0.0189194679260254 s ( 59.35 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-27 21:16:34.196107 INFO::Formatting Data.
2026-03-27 21:16:34.196836 INFO::Recognized SummarizedExperiment
2026-03-27 21:16:34.197317 INFO::Typecasting input to dataframe.
2026-03-27 21:16:34.229985 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:34.231262 INFO::Removing potential empty rows and columns
2026-03-27 21:16:34.235046 INFO::Found 0 missing values.
2026-03-27 21:16:34.242136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:34.242735 INFO::Done
2026-03-27 21:16:34.243257 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:34.246946 INFO::Starting hierarchical adjustment
2026-03-27 21:16:34.247675 INFO::Found 2 batches.
2026-03-27 21:16:34.248197 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:34.249264 INFO::Using default BPPARAM
2026-03-27 21:16:34.249807 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:34.250781 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-27 21:16:34.306803 INFO::Done
2026-03-27 21:16:34.30751 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:34.311069 INFO::ASW Batch was 0.0120096512111505 prior to batch effect correction and is now -0.0851754895546928 .
2026-03-27 21:16:34.311896 INFO::Total function execution time is 0.116075277328491 s and adjustment time is 0.0592670440673828 s ( 51.06 )
Warning: stack imbalance in '{', 73 then 75
2026-03-27 21:16:34.33076 INFO::Formatting Data.
2026-03-27 21:16:34.331496 INFO::Recognized SummarizedExperiment
2026-03-27 21:16:34.332029 INFO::Typecasting input to dataframe.
2026-03-27 21:16:34.341253 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:34.342385 INFO::Removing potential empty rows and columns
2026-03-27 21:16:34.346032 INFO::Found 0 missing values.
2026-03-27 21:16:34.353063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:34.353666 INFO::Done
2026-03-27 21:16:34.354178 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:34.357704 INFO::Starting hierarchical adjustment
2026-03-27 21:16:34.35842 INFO::Found 2 batches.
2026-03-27 21:16:34.358933 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:34.35953 INFO::Using default BPPARAM
2026-03-27 21:16:34.360037 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:34.361001 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-27 21:16:34.386015 INFO::Done
2026-03-27 21:16:34.386732 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:34.390229 INFO::ASW Batch was -0.00227192078208777 prior to batch effect correction and is now -0.00227192078208777 .
2026-03-27 21:16:34.391055 INFO::Total function execution time is 0.0602853298187256 s and adjustment time is 0.0277132987976074 s ( 45.97 )
2026-03-27 21:16:34.408855 INFO::Formatting Data.
2026-03-27 21:16:34.409607 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:34.41048 INFO::Removing potential empty rows and columns
2026-03-27 21:16:34.411491 INFO::Found 0 missing values.
2026-03-27 21:16:34.414382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:34.414978 INFO::Done
2026-03-27 21:16:34.415491 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:34.417434 INFO::Starting hierarchical adjustment
2026-03-27 21:16:34.418111 INFO::Found 3 batches.
2026-03-27 21:16:34.418655 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:34.419241 INFO::Using default BPPARAM
2026-03-27 21:16:34.419756 INFO::Processing subtree level 1
2026-03-27 21:16:34.549061 INFO::Adjusting the last 1 batches sequentially
2026-03-27 21:16:34.550809 INFO::Done
2026-03-27 21:16:34.551438 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:34.553794 INFO::ASW Batch was -0.110533169970201 prior to batch effect correction and is now -0.169786977703514 .
2026-03-27 21:16:34.554688 INFO::Total function execution time is 0.145847082138062 s and adjustment time is 0.132817983627319 s ( 91.07 )
2026-03-27 21:16:34.568802 INFO::Skipping initial DF formatting
2026-03-27 21:16:34.569524 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:34.573539 INFO::Starting hierarchical adjustment
2026-03-27 21:16:34.574325 INFO::Found 5 batches.
2026-03-27 21:16:34.574872 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:34.575498 INFO::Using default BPPARAM
2026-03-27 21:16:34.576032 INFO::Processing subtree level 1
2026-03-27 21:16:34.802644 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:34.804192 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-27 21:16:34.823365 INFO::Done
2026-03-27 21:16:34.824055 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:34.828243 INFO::ASW Batch was 0.521163256172652 prior to batch effect correction and is now 0.521163256172652 .
2026-03-27 21:16:34.828842 INFO::ASW Label was 0.358625288128547 prior to batch effect correction and is now 0.358625288128547 .
2026-03-27 21:16:34.829679 INFO::Total function execution time is 0.260928869247437 s and adjustment time is 0.249191999435425 s ( 95.5 )
2026-03-27 21:16:34.898962 INFO::Formatting Data.
2026-03-27 21:16:34.899758 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:34.900655 INFO::Removing potential empty rows and columns
2026-03-27 21:16:34.901656 INFO::Found 0 missing values.
2026-03-27 21:16:34.905622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:34.906114 INFO::Done
2026-03-27 21:16:34.906602 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:34.909423 INFO::Starting hierarchical adjustment
2026-03-27 21:16:34.910091 INFO::Found 5 batches.
2026-03-27 21:16:34.910601 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:34.911171 INFO::Using default BPPARAM
2026-03-27 21:16:34.9117 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.056105 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.058219 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.079804 INFO::Done
2026-03-27 21:16:35.080822 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.085261 INFO::ASW Batch was 0.494081093011376 prior to batch effect correction and is now -0.0935940863282915 .
2026-03-27 21:16:35.086084 INFO::ASW Label was 0.305402545061027 prior to batch effect correction and is now 0.77652471482516 .
2026-03-27 21:16:35.087061 INFO::Total function execution time is 0.188146114349365 s and adjustment time is 0.169751167297363 s ( 90.22 )
2026-03-27 21:16:35.08805 INFO::Formatting Data.
2026-03-27 21:16:35.088765 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:35.089823 INFO::Removing potential empty rows and columns
2026-03-27 21:16:35.091024 INFO::Found 0 missing values.
2026-03-27 21:16:35.095965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:35.096662 INFO::Done
2026-03-27 21:16:35.097354 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:35.100787 INFO::Starting hierarchical adjustment
2026-03-27 21:16:35.101598 INFO::Found 5 batches.
2026-03-27 21:16:35.102186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:35.102872 INFO::Using default BPPARAM
2026-03-27 21:16:35.103474 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.244458 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.24649 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.26586 INFO::Done
2026-03-27 21:16:35.266787 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.270832 INFO::ASW Batch was 0.494081093011376 prior to batch effect correction and is now -0.0935940863282915 .
2026-03-27 21:16:35.271554 INFO::ASW Label was 0.305402545061027 prior to batch effect correction and is now 0.77652471482516 .
2026-03-27 21:16:35.272441 INFO::Total function execution time is 0.184411764144897 s and adjustment time is 0.164374828338623 s ( 89.13 )
2026-03-27 21:16:35.28714 INFO::Formatting Data.
2026-03-27 21:16:35.287953 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:35.288862 INFO::Removing potential empty rows and columns
2026-03-27 21:16:35.289896 INFO::Found 0 missing values.
2026-03-27 21:16:35.294139 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:35.294701 INFO::Done
2026-03-27 21:16:35.295222 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:35.298341 INFO::Starting hierarchical adjustment
2026-03-27 21:16:35.299064 INFO::Found 5 batches.
2026-03-27 21:16:35.299608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:35.300221 INFO::Using default BPPARAM
2026-03-27 21:16:35.300771 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.441957 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.443849 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.461873 INFO::Done
2026-03-27 21:16:35.462815 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.466841 INFO::ASW Batch was 0.288783833677418 prior to batch effect correction and is now -0.0811017903977911 .
2026-03-27 21:16:35.467593 INFO::ASW Label was 0.284052491424994 prior to batch effect correction and is now 0.884056657965313 .
2026-03-27 21:16:35.468525 INFO::Total function execution time is 0.181416511535645 s and adjustment time is 0.162880897521973 s ( 89.78 )
2026-03-27 21:16:35.469463 INFO::Formatting Data.
2026-03-27 21:16:35.47018 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:35.471292 INFO::Removing potential empty rows and columns
2026-03-27 21:16:35.472485 INFO::Found 0 missing values.
2026-03-27 21:16:35.477138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:35.47782 INFO::Done
2026-03-27 21:16:35.478454 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:35.482036 INFO::Starting hierarchical adjustment
2026-03-27 21:16:35.482906 INFO::Found 5 batches.
2026-03-27 21:16:35.483501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:35.484158 INFO::Using default BPPARAM
2026-03-27 21:16:35.484738 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.654393 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.656198 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.672933 INFO::Done
2026-03-27 21:16:35.673691 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.677306 INFO::ASW Batch was 0.288783833677418 prior to batch effect correction and is now -0.0811017903977911 .
2026-03-27 21:16:35.678016 INFO::ASW Label was 0.284052491424994 prior to batch effect correction and is now 0.884056657965313 .
2026-03-27 21:16:35.678983 INFO::Total function execution time is 0.20952296257019 s and adjustment time is 0.190203905105591 s ( 90.78 )
2026-03-27 21:16:35.693163 INFO::Formatting Data.
2026-03-27 21:16:35.694005 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:35.694963 INFO::Removing potential empty rows and columns
2026-03-27 21:16:35.696011 INFO::Found 0 missing values.
2026-03-27 21:16:35.69871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:35.69925 INFO::Done
2026-03-27 21:16:35.69979 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:35.702744 INFO::Starting hierarchical adjustment
2026-03-27 21:16:35.70347 INFO::Found 2 batches.
2026-03-27 21:16:35.703996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:35.704622 INFO::Using default BPPARAM
2026-03-27 21:16:35.70513 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.706027 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.72039 INFO::Done
2026-03-27 21:16:35.721034 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.723943 INFO::ASW Batch was 0.359073888185324 prior to batch effect correction and is now 0.118764371414385 .
2026-03-27 21:16:35.724525 INFO::ASW Label was 0.517594620228562 prior to batch effect correction and is now 0.824693222685161 .
2026-03-27 21:16:35.725258 INFO::Total function execution time is 0.0321927070617676 s and adjustment time is 0.0170729160308838 s ( 53.03 )
2026-03-27 21:16:35.72604 INFO::Formatting Data.
2026-03-27 21:16:35.72666 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:35.727497 INFO::Removing potential empty rows and columns
2026-03-27 21:16:35.728463 INFO::Found 0 missing values.
2026-03-27 21:16:35.731022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:35.731564 INFO::Done
2026-03-27 21:16:35.732074 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:35.735071 INFO::Starting hierarchical adjustment
2026-03-27 21:16:35.735797 INFO::Found 2 batches.
2026-03-27 21:16:35.73633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:35.736915 INFO::Using default BPPARAM
2026-03-27 21:16:35.737427 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.738306 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-27 21:16:35.752932 INFO::Done
2026-03-27 21:16:35.753638 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.756608 INFO::ASW Batch was 0.359073888185324 prior to batch effect correction and is now 0.118764371414385 .
2026-03-27 21:16:35.757229 INFO::ASW Label was 0.517594620228562 prior to batch effect correction and is now 0.824693222685161 .
2026-03-27 21:16:35.758042 INFO::Total function execution time is 0.0320067405700684 s and adjustment time is 0.0172560214996338 s ( 53.91 )
2026-03-27 21:16:35.769636 INFO::Formatting Data.
2026-03-27 21:16:35.770422 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:35.771348 INFO::Removing potential empty rows and columns
2026-03-27 21:16:35.772291 INFO::Found 0 missing values.
2026-03-27 21:16:35.774489 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:35.775024 INFO::Done
2026-03-27 21:16:35.775556 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:35.777549 INFO::Starting hierarchical adjustment
2026-03-27 21:16:35.778266 INFO::Found 2 batches.
2026-03-27 21:16:35.778809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:35.779437 INFO::Using default BPPARAM
2026-03-27 21:16:35.779962 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.780876 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-27 21:16:35.811518 INFO::Done
2026-03-27 21:16:35.812184 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.814059 INFO::ASW Batch was -0.153044244870355 prior to batch effect correction and is now -0.170630055582939 .
2026-03-27 21:16:35.814826 INFO::Total function execution time is 0.0452895164489746 s and adjustment time is 0.033388614654541 s ( 73.72 )
2026-03-27 21:16:35.826057 INFO::Formatting Data.
2026-03-27 21:16:35.82679 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:35.827627 INFO::Removing potential empty rows and columns
2026-03-27 21:16:35.82859 INFO::Found 0 missing values.
2026-03-27 21:16:35.829695 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-27 21:16:35.833992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:35.834523 INFO::Done
2026-03-27 21:16:35.835013 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:35.837796 INFO::Starting hierarchical adjustment
2026-03-27 21:16:35.838469 INFO::Found 2 batches.
2026-03-27 21:16:35.838971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:35.83955 INFO::Using default BPPARAM
2026-03-27 21:16:35.840037 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.840921 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-27 21:16:35.856438 INFO::Done
2026-03-27 21:16:35.857074 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.859871 INFO::ASW Batch was 0.298520512437232 prior to batch effect correction and is now 0.0648329232106225 .
2026-03-27 21:16:35.860437 INFO::ASW Label was 0.674337627387368 prior to batch effect correction and is now 0.875257171893003 .
2026-03-27 21:16:35.861169 INFO::Total function execution time is 0.035179615020752 s and adjustment time is 0.0180997848510742 s ( 51.45 )
2026-03-27 21:16:35.861928 INFO::Formatting Data.
2026-03-27 21:16:35.86253 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:35.86338 INFO::Removing potential empty rows and columns
2026-03-27 21:16:35.864309 INFO::Found 0 missing values.
2026-03-27 21:16:35.865174 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-27 21:16:35.869372 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:35.86989 INFO::Done
2026-03-27 21:16:35.870391 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:35.873092 INFO::Starting hierarchical adjustment
2026-03-27 21:16:35.87377 INFO::Found 2 batches.
2026-03-27 21:16:35.874259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:35.87484 INFO::Using default BPPARAM
2026-03-27 21:16:35.875338 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:35.876194 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-27 21:16:35.891531 INFO::Done
2026-03-27 21:16:35.892179 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:35.895074 INFO::ASW Batch was 0.298520512437232 prior to batch effect correction and is now 0.0648329232106225 .
2026-03-27 21:16:35.895698 INFO::ASW Label was 0.674337627387368 prior to batch effect correction and is now 0.875257171893003 .
2026-03-27 21:16:35.896499 INFO::Total function execution time is 0.0345699787139893 s and adjustment time is 0.0178823471069336 s ( 51.73 )
2026-03-27 21:16:36.117703 INFO::Formatting Data.
2026-03-27 21:16:36.118587 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:36.119586 INFO::Removing potential empty rows and columns
2026-03-27 21:16:36.120743 INFO::Found 0 missing values.
2026-03-27 21:16:36.124068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:36.124652 INFO::Done
2026-03-27 21:16:36.125203 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:36.127373 INFO::Starting hierarchical adjustment
2026-03-27 21:16:36.128141 INFO::Found 3 batches.
2026-03-27 21:16:36.12875 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:36.129399 INFO::Using default BPPARAM
2026-03-27 21:16:36.129985 INFO::Processing subtree level 1
2026-03-27 21:16:36.214346 INFO::Adjusting the last 1 batches sequentially
2026-03-27 21:16:36.216156 INFO::Done
2026-03-27 21:16:36.216811 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:36.219379 INFO::ASW Batch was -0.0731878727709833 prior to batch effect correction and is now -0.0731878727709833 .
2026-03-27 21:16:36.220377 INFO::Total function execution time is 0.102701902389526 s and adjustment time is 0.0881667137145996 s ( 85.85 )
2026-03-27 21:16:36.221463 INFO::Formatting Data.
2026-03-27 21:16:36.222171 INFO::Typecasting input to dataframe.
2026-03-27 21:16:36.223012 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:36.224023 INFO::Removing potential empty rows and columns
2026-03-27 21:16:36.225217 INFO::Found 0 missing values.
2026-03-27 21:16:36.228585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:36.229203 INFO::Done
2026-03-27 21:16:36.229797 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:36.236853 INFO::Starting hierarchical adjustment
2026-03-27 21:16:36.237781 INFO::Found 3 batches.
2026-03-27 21:16:36.238396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:36.239105 INFO::Using default BPPARAM
2026-03-27 21:16:36.239722 INFO::Processing subtree level 1
2026-03-27 21:16:36.322423 INFO::Adjusting the last 1 batches sequentially
2026-03-27 21:16:36.324222 INFO::Done
2026-03-27 21:16:36.324914 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:36.327442 INFO::ASW Batch was -0.0731878727709833 prior to batch effect correction and is now -0.0731878727709833 .
2026-03-27 21:16:36.328483 INFO::Total function execution time is 0.106982946395874 s and adjustment time is 0.0866284370422363 s ( 80.97 )
2026-03-27 21:16:36.342477 INFO::Formatting Data.
2026-03-27 21:16:36.343291 INFO::Typecasting input to dataframe.
2026-03-27 21:16:36.34421 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:36.345203 INFO::Removing potential empty rows and columns
2026-03-27 21:16:36.346444 INFO::Found 0 missing values.
2026-03-27 21:16:36.349761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:36.350345 INFO::Done
2026-03-27 21:16:36.350924 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:36.35305 INFO::Starting hierarchical adjustment
2026-03-27 21:16:36.353802 INFO::Found 3 batches.
2026-03-27 21:16:36.354423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:36.355074 INFO::Using default BPPARAM
2026-03-27 21:16:36.355697 INFO::Processing subtree level 1
2026-03-27 21:16:36.438361 INFO::Adjusting the last 1 batches sequentially
2026-03-27 21:16:36.440238 INFO::Done
2026-03-27 21:16:36.440965 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:36.443671 INFO::ASW Batch was -0.113203900604439 prior to batch effect correction and is now -0.113203900604439 .
2026-03-27 21:16:36.444649 INFO::Total function execution time is 0.102225065231323 s and adjustment time is 0.0865893363952637 s ( 84.7 )
2026-03-27 21:16:36.580502 INFO::Formatting Data.
2026-03-27 21:16:36.581357 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:36.582571 INFO::Removing potential empty rows and columns
2026-03-27 21:16:36.585523 INFO::Found 1000 missing values.
2026-03-27 21:16:36.606419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:36.607189 INFO::Done
2026-03-27 21:16:36.607829 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:36.613647 INFO::Starting hierarchical adjustment
2026-03-27 21:16:36.614432 INFO::Found 10 batches.
2026-03-27 21:16:36.615014 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:36.615692 INFO::Using default BPPARAM
2026-03-27 21:16:36.616504 INFO::Processing subtree level 1
2026-03-27 21:16:36.754506 INFO::Processing subtree level 2
2026-03-27 21:16:36.912966 INFO::Adjusting the last 1 batches sequentially
2026-03-27 21:16:36.91626 INFO::Done
2026-03-27 21:16:36.917236 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:36.923452 INFO::ASW Batch was 0.499166441130061 prior to batch effect correction and is now 0.499166441130061 .
2026-03-27 21:16:36.924224 INFO::ASW Label was 0.327995014075361 prior to batch effect correction and is now 0.327995014075361 .
2026-03-27 21:16:36.925332 INFO::Total function execution time is 0.344855546951294 s and adjustment time is 0.301889419555664 s ( 87.54 )
2026-03-27 21:16:36.926302 INFO::Formatting Data.
2026-03-27 21:16:36.927028 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:36.928434 INFO::Removing potential empty rows and columns
2026-03-27 21:16:36.940265 INFO::Found 1000 missing values.
2026-03-27 21:16:36.960904 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:36.961748 INFO::Done
2026-03-27 21:16:36.962375 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:36.968039 INFO::Starting hierarchical adjustment
2026-03-27 21:16:36.968852 INFO::Found 10 batches.
2026-03-27 21:16:38.096496 INFO::Set up parallel execution backend with 2 workers
2026-03-27 21:16:38.098381 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-27 21:16:39.205599 INFO::Adjusting the last 2 batches sequentially
2026-03-27 21:16:39.207528 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-27 21:16:39.223224 INFO::Done
2026-03-27 21:16:39.223833 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:39.228183 INFO::ASW Batch was 0.499166441130061 prior to batch effect correction and is now 0.499166441130061 .
2026-03-27 21:16:39.228708 INFO::ASW Label was 0.327995014075361 prior to batch effect correction and is now 0.327995014075361 .
2026-03-27 21:16:39.229392 INFO::Total function execution time is 2.3031690120697 s and adjustment time is 2.25453758239746 s ( 97.89 )
2026-03-27 21:16:39.368815 INFO::Formatting Data.
2026-03-27 21:16:39.369556 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.370423 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.371422 INFO::Found 0 missing values.
2026-03-27 21:16:39.374835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.375342 INFO::Done
2026-03-27 21:16:39.375824 INFO::Acquiring quality metrics before batch effect correction.
2026-03-27 21:16:39.378402 INFO::Starting hierarchical adjustment
2026-03-27 21:16:39.379067 INFO::Found 3 batches.
2026-03-27 21:16:39.379573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-27 21:16:39.38015 INFO::Using default BPPARAM
2026-03-27 21:16:39.380664 INFO::Processing subtree level 1
2026-03-27 21:16:39.478567 INFO::Adjusting the last 1 batches sequentially
2026-03-27 21:16:39.480228 INFO::Done
2026-03-27 21:16:39.48085 INFO::Acquiring quality metrics after batch effect correction.
2026-03-27 21:16:39.483882 INFO::ASW Batch was 0.181046365034671 prior to batch effect correction and is now -0.174547814547169 .
2026-03-27 21:16:39.484489 INFO::ASW Label was -0.235655154477792 prior to batch effect correction and is now -0.0936636901372691 .
2026-03-27 21:16:39.485348 INFO::Total function execution time is 0.116556406021118 s and adjustment time is 0.101278781890869 s ( 86.89 )
2026-03-27 21:16:39.600286 INFO::Formatting Data.
2026-03-27 21:16:39.601113 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.602057 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.603145 INFO::Found 2 missing values.
2026-03-27 21:16:39.606114 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.607425 INFO::Done
2026-03-27 21:16:39.63647 INFO::Found NA in Reference column
2026-03-27 21:16:39.646395 INFO::Require at least two references per batch.
2026-03-27 21:16:39.66773 INFO::Formatting Data.
2026-03-27 21:16:39.668522 INFO::Recognized SummarizedExperiment
2026-03-27 21:16:39.669092 INFO::Typecasting input to dataframe.
2026-03-27 21:16:39.6789 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.680079 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.683693 INFO::Found 0 missing values.
2026-03-27 21:16:39.690388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.690997 INFO::Done
2026-03-27 21:16:39.707084 INFO::Formatting Data.
2026-03-27 21:16:39.707828 INFO::Recognized SummarizedExperiment
2026-03-27 21:16:39.70838 INFO::Typecasting input to dataframe.
2026-03-27 21:16:39.725914 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.727176 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.730696 INFO::Found 0 missing values.
2026-03-27 21:16:39.741674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.742348 INFO::Done
2026-03-27 21:16:39.758421 INFO::Formatting Data.
2026-03-27 21:16:39.759135 INFO::Recognized SummarizedExperiment
2026-03-27 21:16:39.759699 INFO::Typecasting input to dataframe.
2026-03-27 21:16:39.776522 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.777582 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.778695 INFO::Found 0 missing values.
2026-03-27 21:16:39.779623 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-27 21:16:39.784143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.78474 INFO::Done
2026-03-27 21:16:39.795235 INFO::Formatting Data.
2026-03-27 21:16:39.796093 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.796994 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.798036 INFO::Found 0 missing values.
2026-03-27 21:16:39.801054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.801611 INFO::Done
2026-03-27 21:16:39.813197 INFO::Formatting Data.
2026-03-27 21:16:39.814131 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.815186 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.816219 INFO::Found 0 missing values.
2026-03-27 21:16:39.819198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.819798 INFO::Done
2026-03-27 21:16:39.851083 INFO::Formatting Data.
2026-03-27 21:16:39.851969 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.85309 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.854307 INFO::Found 1 missing values.
2026-03-27 21:16:39.857124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.857682 INFO::Done
2026-03-27 21:16:39.878039 INFO::Formatting Data.
2026-03-27 21:16:39.878923 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.879818 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.880857 INFO::Found 2 missing values.
2026-03-27 21:16:39.881816 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2026-03-27 21:16:39.884151 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.884733 INFO::Done
2026-03-27 21:16:39.895231 INFO::Formatting Data.
2026-03-27 21:16:39.89614 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.897059 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.898008 INFO::Found 2 missing values.
2026-03-27 21:16:39.899686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.900242 INFO::Done
2026-03-27 21:16:39.911151 INFO::Formatting Data.
2026-03-27 21:16:39.911969 INFO::Typecasting input to dataframe.
2026-03-27 21:16:39.912789 INFO::Replacing NaNs with NAs.
2026-03-27 21:16:39.913663 INFO::Removing potential empty rows and columns
2026-03-27 21:16:39.914674 INFO::Found 0 missing values.
2026-03-27 21:16:39.917734 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-27 21:16:39.918298 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.123 3.738 20.534
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.330 | 1.308 | 16.871 | |
| compute_asw | 0.026 | 0.002 | 0.029 | |
| count_existing | 0.013 | 0.005 | 0.018 | |
| generate_data_covariables | 0.013 | 0.003 | 0.016 | |
| generate_dataset | 0.012 | 0.003 | 0.016 | |