Yannis Schumann
| Snapshot Date: 2026-02-16 13:40 -0500 (Mon, 16 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-17 11:32 -0500 (Tue, 17 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4865 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 169/2352 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-16 21:34:35 -0500 (Mon, 16 Feb 2026) |
| EndedAt: 2026-02-16 21:36:03 -0500 (Mon, 16 Feb 2026) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 24.367 1.158 17.226
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2026-02-16 21:35:26.064225 INFO::Formatting Data.
2026-02-16 21:35:26.065485 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:26.076533 INFO::Removing potential empty rows and columns
2026-02-16 21:35:26.311304 INFO::Found 0 missing values.
2026-02-16 21:35:26.314585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:26.315264 INFO::Done
2026-02-16 21:35:26.315842 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:26.327059 INFO::Starting hierarchical adjustment
2026-02-16 21:35:26.32796 INFO::Found 3 batches.
2026-02-16 21:35:26.328538 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:26.329638 INFO::Using default BPPARAM
2026-02-16 21:35:26.330188 INFO::Processing subtree level 1
2026-02-16 21:35:26.425127 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:35:26.426886 INFO::Done
2026-02-16 21:35:26.427559 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:26.430053 INFO::ASW Batch was 0.0251700525290401 prior to batch effect correction and is now 0.0251700525290401 .
2026-02-16 21:35:26.431131 INFO::Total function execution time is 0.367486476898193 s and adjustment time is 0.0990898609161377 s ( 26.96 )
2026-02-16 21:35:26.444594 INFO::Formatting Data.
2026-02-16 21:35:26.445397 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:26.446329 INFO::Removing potential empty rows and columns
2026-02-16 21:35:26.447481 INFO::Found 0 missing values.
2026-02-16 21:35:26.448421 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.
2026-02-16 21:35:26.459291 INFO::Formatting Data.
2026-02-16 21:35:26.460117 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:26.461068 INFO::Removing potential empty rows and columns
2026-02-16 21:35:26.462175 INFO::Found 0 missing values.
2026-02-16 21:35:26.463147 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.
2026-02-16 21:35:26.481309 INFO::Formatting Data.
2026-02-16 21:35:26.482262 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:26.48325 INFO::Removing potential empty rows and columns
2026-02-16 21:35:26.48439 INFO::Found 0 missing values.
2026-02-16 21:35:26.485397 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.
2026-02-16 21:35:26.49033 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:26.490995 INFO::Done
2026-02-16 21:35:26.491563 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:26.493773 INFO::Starting hierarchical adjustment
2026-02-16 21:35:26.494561 INFO::Found 2 batches.
2026-02-16 21:35:26.495134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:26.495817 INFO::Using default BPPARAM
2026-02-16 21:35:26.49638 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:26.497403 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:35:26.51942 INFO::Done
2026-02-16 21:35:26.520207 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:26.522635 INFO::ASW Batch was 0.00501907729992614 prior to batch effect correction and is now -0.113824004199123 .
2026-02-16 21:35:26.523531 INFO::Total function execution time is 0.0423069000244141 s and adjustment time is 0.0249781608581543 s ( 59.04 )
2026-02-16 21:35:26.526601 INFO::Formatting Data.
2026-02-16 21:35:26.527295 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:26.536593 INFO::Formatting Data.
2026-02-16 21:35:26.537465 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:26.538444 INFO::Removing potential empty rows and columns
2026-02-16 21:35:26.539538 INFO::Found 0 missing values.
2026-02-16 21:35:26.542725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:26.543311 INFO::Done
2026-02-16 21:35:26.543865 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:26.546021 INFO::Starting hierarchical adjustment
2026-02-16 21:35:26.546771 INFO::Found 2 batches.
2026-02-16 21:35:26.547323 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:26.54798 INFO::Using default BPPARAM
2026-02-16 21:35:26.548537 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:26.549541 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:35:26.588967 INFO::Done
2026-02-16 21:35:26.589744 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:26.591706 INFO::ASW Batch was -0.00510533738328007 prior to batch effect correction and is now -0.0767917805049414 .
2026-02-16 21:35:26.592506 INFO::Total function execution time is 0.0559883117675781 s and adjustment time is 0.0422985553741455 s ( 75.55 )
2026-02-16 21:35:26.59351 INFO::Formatting Data.
2026-02-16 21:35:26.594094 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:26.59494 INFO::Removing potential empty rows and columns
2026-02-16 21:35:26.595917 INFO::Found 0 missing values.
2026-02-16 21:35:26.598578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:26.599113 INFO::Done
2026-02-16 21:35:26.599627 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:26.601503 INFO::Starting hierarchical adjustment
2026-02-16 21:35:26.602178 INFO::Found 2 batches.
2026-02-16 21:35:26.602678 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:26.603236 INFO::Using default BPPARAM
2026-02-16 21:35:26.603731 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:26.6046 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:35:26.618344 INFO::Done
2026-02-16 21:35:26.619012 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:26.620935 INFO::ASW Batch was -0.00510533738328007 prior to batch effect correction and is now -0.0767917805049414 .
2026-02-16 21:35:26.621699 INFO::Total function execution time is 0.0281970500946045 s and adjustment time is 0.0162827968597412 s ( 57.75 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-16 21:35:29.338201 INFO::Formatting Data.
2026-02-16 21:35:29.33888 INFO::Recognized SummarizedExperiment
2026-02-16 21:35:29.339358 INFO::Typecasting input to dataframe.
2026-02-16 21:35:29.368514 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:29.369717 INFO::Removing potential empty rows and columns
2026-02-16 21:35:29.373688 INFO::Found 0 missing values.
2026-02-16 21:35:29.381255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:29.381966 INFO::Done
2026-02-16 21:35:29.382524 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:29.386102 INFO::Starting hierarchical adjustment
2026-02-16 21:35:29.38687 INFO::Found 2 batches.
2026-02-16 21:35:29.387422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:29.388526 INFO::Using default BPPARAM
2026-02-16 21:35:29.389066 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:29.390051 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:35:29.447276 INFO::Done
2026-02-16 21:35:29.448021 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:29.451617 INFO::ASW Batch was -0.0011344212928233 prior to batch effect correction and is now -0.099440036523355 .
2026-02-16 21:35:29.452476 INFO::Total function execution time is 0.114519357681274 s and adjustment time is 0.0605282783508301 s ( 52.85 )
Warning: stack imbalance in '{', 73 then 75
2026-02-16 21:35:29.471199 INFO::Formatting Data.
2026-02-16 21:35:29.471973 INFO::Recognized SummarizedExperiment
2026-02-16 21:35:29.472548 INFO::Typecasting input to dataframe.
2026-02-16 21:35:29.481792 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:29.483005 INFO::Removing potential empty rows and columns
2026-02-16 21:35:29.487046 INFO::Found 0 missing values.
2026-02-16 21:35:29.494514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:29.495184 INFO::Done
2026-02-16 21:35:29.495731 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:29.499282 INFO::Starting hierarchical adjustment
2026-02-16 21:35:29.500021 INFO::Found 2 batches.
2026-02-16 21:35:29.500561 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:29.501186 INFO::Using default BPPARAM
2026-02-16 21:35:29.501723 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:29.502713 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:35:29.528478 INFO::Done
2026-02-16 21:35:29.529191 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:29.532746 INFO::ASW Batch was -0.00145904973208246 prior to batch effect correction and is now -0.00145904973208246 .
2026-02-16 21:35:29.533612 INFO::Total function execution time is 0.0623977184295654 s and adjustment time is 0.0285501480102539 s ( 45.76 )
2026-02-16 21:35:29.551803 INFO::Formatting Data.
2026-02-16 21:35:29.552614 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:29.553516 INFO::Removing potential empty rows and columns
2026-02-16 21:35:29.554547 INFO::Found 0 missing values.
2026-02-16 21:35:29.55753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:29.55807 INFO::Done
2026-02-16 21:35:29.558612 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:29.560626 INFO::Starting hierarchical adjustment
2026-02-16 21:35:29.561319 INFO::Found 3 batches.
2026-02-16 21:35:29.561846 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:29.562466 INFO::Using default BPPARAM
2026-02-16 21:35:29.562984 INFO::Processing subtree level 1
2026-02-16 21:35:29.711028 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:35:29.714323 INFO::Done
2026-02-16 21:35:29.715131 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:29.718669 INFO::ASW Batch was -0.0709778978192722 prior to batch effect correction and is now -0.152175844419269 .
2026-02-16 21:35:29.719828 INFO::Total function execution time is 0.168039560317993 s and adjustment time is 0.153109788894653 s ( 91.12 )
2026-02-16 21:35:29.739389 INFO::Skipping initial DF formatting
2026-02-16 21:35:29.740237 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:29.744641 INFO::Starting hierarchical adjustment
2026-02-16 21:35:29.745526 INFO::Found 5 batches.
2026-02-16 21:35:29.746151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:29.746829 INFO::Using default BPPARAM
2026-02-16 21:35:29.747411 INFO::Processing subtree level 1
2026-02-16 21:35:30.002597 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:30.004616 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:35:30.027793 INFO::Done
2026-02-16 21:35:30.028685 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:30.078803 INFO::ASW Batch was 0.544571621176692 prior to batch effect correction and is now 0.544571621176692 .
2026-02-16 21:35:30.079702 INFO::ASW Label was 0.357324548041477 prior to batch effect correction and is now 0.357324548041477 .
2026-02-16 21:35:30.080683 INFO::Total function execution time is 0.341421365737915 s and adjustment time is 0.282411575317383 s ( 82.72 )
2026-02-16 21:35:30.105565 INFO::Formatting Data.
2026-02-16 21:35:30.106457 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:30.107497 INFO::Removing potential empty rows and columns
2026-02-16 21:35:30.10858 INFO::Found 0 missing values.
2026-02-16 21:35:30.113033 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:30.113639 INFO::Done
2026-02-16 21:35:30.11418 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:30.117323 INFO::Starting hierarchical adjustment
2026-02-16 21:35:30.118062 INFO::Found 5 batches.
2026-02-16 21:35:30.118647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:30.119361 INFO::Using default BPPARAM
2026-02-16 21:35:30.1199 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.
2026-02-16 21:35:30.258502 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:30.260679 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:35:30.293725 INFO::Done
2026-02-16 21:35:30.295169 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:30.301209 INFO::ASW Batch was 0.3539862440712 prior to batch effect correction and is now -0.102975634091608 .
2026-02-16 21:35:30.302282 INFO::ASW Label was 0.356102275379057 prior to batch effect correction and is now 0.75411814708292 .
2026-02-16 21:35:30.303818 INFO::Total function execution time is 0.198150396347046 s and adjustment time is 0.17558741569519 s ( 88.61 )
2026-02-16 21:35:30.30558 INFO::Formatting Data.
2026-02-16 21:35:30.306571 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:30.307806 INFO::Removing potential empty rows and columns
2026-02-16 21:35:30.309177 INFO::Found 0 missing values.
2026-02-16 21:35:30.314716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:30.315398 INFO::Done
2026-02-16 21:35:30.316047 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:30.320231 INFO::Starting hierarchical adjustment
2026-02-16 21:35:30.32124 INFO::Found 5 batches.
2026-02-16 21:35:30.321862 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:30.322639 INFO::Using default BPPARAM
2026-02-16 21:35:30.323265 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.
2026-02-16 21:35:30.482453 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:30.484382 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:35:30.501744 INFO::Done
2026-02-16 21:35:30.502593 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:30.506164 INFO::ASW Batch was 0.3539862440712 prior to batch effect correction and is now -0.102975634091608 .
2026-02-16 21:35:30.506817 INFO::ASW Label was 0.356102275379057 prior to batch effect correction and is now 0.75411814708292 .
2026-02-16 21:35:30.507734 INFO::Total function execution time is 0.202363252639771 s and adjustment time is 0.180706024169922 s ( 89.3 )
2026-02-16 21:35:30.523957 INFO::Formatting Data.
2026-02-16 21:35:30.524883 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:30.525946 INFO::Removing potential empty rows and columns
2026-02-16 21:35:30.527128 INFO::Found 0 missing values.
2026-02-16 21:35:30.531504 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:30.532173 INFO::Done
2026-02-16 21:35:30.532746 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:30.536024 INFO::Starting hierarchical adjustment
2026-02-16 21:35:30.53683 INFO::Found 5 batches.
2026-02-16 21:35:30.537423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:30.538126 INFO::Using default BPPARAM
2026-02-16 21:35:30.538793 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.
2026-02-16 21:35:30.676023 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:30.677877 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:35:30.69565 INFO::Done
2026-02-16 21:35:30.696457 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:30.700076 INFO::ASW Batch was 0.240280040706462 prior to batch effect correction and is now -0.0785808357968204 .
2026-02-16 21:35:30.700777 INFO::ASW Label was 0.56729035153082 prior to batch effect correction and is now 0.856188239318587 .
2026-02-16 21:35:30.701691 INFO::Total function execution time is 0.177818059921265 s and adjustment time is 0.158923864364624 s ( 89.37 )
2026-02-16 21:35:30.702654 INFO::Formatting Data.
2026-02-16 21:35:30.703353 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:30.704395 INFO::Removing potential empty rows and columns
2026-02-16 21:35:30.705528 INFO::Found 0 missing values.
2026-02-16 21:35:30.710091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:30.710756 INFO::Done
2026-02-16 21:35:30.711311 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:30.714589 INFO::Starting hierarchical adjustment
2026-02-16 21:35:30.715346 INFO::Found 5 batches.
2026-02-16 21:35:30.715945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:30.716598 INFO::Using default BPPARAM
2026-02-16 21:35:30.717195 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.
2026-02-16 21:35:30.84463 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:30.846337 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:35:30.864146 INFO::Done
2026-02-16 21:35:30.86503 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:30.869031 INFO::ASW Batch was 0.240280040706462 prior to batch effect correction and is now -0.0785808357968204 .
2026-02-16 21:35:30.869721 INFO::ASW Label was 0.56729035153082 prior to batch effect correction and is now 0.856188239318587 .
2026-02-16 21:35:30.870679 INFO::Total function execution time is 0.167995452880859 s and adjustment time is 0.148897171020508 s ( 88.63 )
2026-02-16 21:35:30.885669 INFO::Formatting Data.
2026-02-16 21:35:30.886625 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:30.887663 INFO::Removing potential empty rows and columns
2026-02-16 21:35:30.888815 INFO::Found 0 missing values.
2026-02-16 21:35:30.89173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:30.892344 INFO::Done
2026-02-16 21:35:30.892936 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:30.896084 INFO::Starting hierarchical adjustment
2026-02-16 21:35:30.896849 INFO::Found 2 batches.
2026-02-16 21:35:30.897434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:30.898095 INFO::Using default BPPARAM
2026-02-16 21:35:30.89871 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:30.899715 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:35:30.915044 INFO::Done
2026-02-16 21:35:30.915798 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:30.918952 INFO::ASW Batch was 0.674974240568183 prior to batch effect correction and is now -0.00630811651339854 .
2026-02-16 21:35:30.919628 INFO::ASW Label was 0.394855108290117 prior to batch effect correction and is now 0.894346625593478 .
2026-02-16 21:35:30.920521 INFO::Total function execution time is 0.0349769592285156 s and adjustment time is 0.018336296081543 s ( 52.42 )
2026-02-16 21:35:30.921424 INFO::Formatting Data.
2026-02-16 21:35:30.922089 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:30.923059 INFO::Removing potential empty rows and columns
2026-02-16 21:35:30.924099 INFO::Found 0 missing values.
2026-02-16 21:35:30.926879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:30.927467 INFO::Done
2026-02-16 21:35:30.928023 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:30.931085 INFO::Starting hierarchical adjustment
2026-02-16 21:35:30.931826 INFO::Found 2 batches.
2026-02-16 21:35:30.932381 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:30.93302 INFO::Using default BPPARAM
2026-02-16 21:35:30.933596 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:30.934561 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-16 21:35:30.950679 INFO::Done
2026-02-16 21:35:30.951487 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:30.954802 INFO::ASW Batch was 0.674974240568183 prior to batch effect correction and is now -0.00630811651339854 .
2026-02-16 21:35:30.955485 INFO::ASW Label was 0.394855108290117 prior to batch effect correction and is now 0.894346625593478 .
2026-02-16 21:35:30.95636 INFO::Total function execution time is 0.0349655151367188 s and adjustment time is 0.0189700126647949 s ( 54.25 )
2026-02-16 21:35:30.969136 INFO::Formatting Data.
2026-02-16 21:35:30.970002 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:30.970997 INFO::Removing potential empty rows and columns
2026-02-16 21:35:30.972028 INFO::Found 0 missing values.
2026-02-16 21:35:30.974354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:30.974951 INFO::Done
2026-02-16 21:35:30.975534 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:30.977666 INFO::Starting hierarchical adjustment
2026-02-16 21:35:30.978455 INFO::Found 2 batches.
2026-02-16 21:35:30.979016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:30.979703 INFO::Using default BPPARAM
2026-02-16 21:35:30.980307 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:30.981331 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:35:31.01642 INFO::Done
2026-02-16 21:35:31.017234 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:31.019462 INFO::ASW Batch was -0.0854131587869272 prior to batch effect correction and is now -0.128748616973305 .
2026-02-16 21:35:31.020352 INFO::Total function execution time is 0.0512979030609131 s and adjustment time is 0.0380837917327881 s ( 74.24 )
2026-02-16 21:35:31.034044 INFO::Formatting Data.
2026-02-16 21:35:31.034956 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:31.035947 INFO::Removing potential empty rows and columns
2026-02-16 21:35:31.037028 INFO::Found 0 missing values.
2026-02-16 21:35:31.038256 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.
2026-02-16 21:35:31.043125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:31.043828 INFO::Done
2026-02-16 21:35:31.044409 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:31.047761 INFO::Starting hierarchical adjustment
2026-02-16 21:35:31.048502 INFO::Found 2 batches.
2026-02-16 21:35:31.049054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:31.049758 INFO::Using default BPPARAM
2026-02-16 21:35:31.050334 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:31.051383 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:35:31.068488 INFO::Done
2026-02-16 21:35:31.06921 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:31.072319 INFO::ASW Batch was 0.653579237702031 prior to batch effect correction and is now 0.184274833575593 .
2026-02-16 21:35:31.072946 INFO::ASW Label was 0.461556435300038 prior to batch effect correction and is now 0.785515077732474 .
2026-02-16 21:35:31.073815 INFO::Total function execution time is 0.0399074554443359 s and adjustment time is 0.0200998783111572 s ( 50.37 )
2026-02-16 21:35:31.074638 INFO::Formatting Data.
2026-02-16 21:35:31.075257 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:31.076227 INFO::Removing potential empty rows and columns
2026-02-16 21:35:31.077235 INFO::Found 0 missing values.
2026-02-16 21:35:31.078195 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.
2026-02-16 21:35:31.082878 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:31.083484 INFO::Done
2026-02-16 21:35:31.084014 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:31.08719 INFO::Starting hierarchical adjustment
2026-02-16 21:35:31.08794 INFO::Found 2 batches.
2026-02-16 21:35:31.088511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:31.08911 INFO::Using default BPPARAM
2026-02-16 21:35:31.089656 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:31.090625 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:35:31.113534 INFO::Done
2026-02-16 21:35:31.11446 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:31.117847 INFO::ASW Batch was 0.653579237702031 prior to batch effect correction and is now 0.184274833575593 .
2026-02-16 21:35:31.118555 INFO::ASW Label was 0.461556435300038 prior to batch effect correction and is now 0.785515077732474 .
2026-02-16 21:35:31.119519 INFO::Total function execution time is 0.0448482036590576 s and adjustment time is 0.0256686210632324 s ( 57.23 )
2026-02-16 21:35:31.355559 INFO::Formatting Data.
2026-02-16 21:35:31.356461 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:31.357433 INFO::Removing potential empty rows and columns
2026-02-16 21:35:31.358581 INFO::Found 0 missing values.
2026-02-16 21:35:31.36185 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:31.362419 INFO::Done
2026-02-16 21:35:31.363018 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:31.36519 INFO::Starting hierarchical adjustment
2026-02-16 21:35:31.365932 INFO::Found 3 batches.
2026-02-16 21:35:31.366485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:31.367126 INFO::Using default BPPARAM
2026-02-16 21:35:31.367684 INFO::Processing subtree level 1
2026-02-16 21:35:31.454135 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:35:31.456028 INFO::Done
2026-02-16 21:35:31.456734 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:31.459432 INFO::ASW Batch was -0.109945598785326 prior to batch effect correction and is now -0.109945598785326 .
2026-02-16 21:35:31.460476 INFO::Total function execution time is 0.104982852935791 s and adjustment time is 0.0902247428894043 s ( 85.94 )
2026-02-16 21:35:31.461552 INFO::Formatting Data.
2026-02-16 21:35:31.462221 INFO::Typecasting input to dataframe.
2026-02-16 21:35:31.463041 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:31.46404 INFO::Removing potential empty rows and columns
2026-02-16 21:35:31.465245 INFO::Found 0 missing values.
2026-02-16 21:35:31.468564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:31.469137 INFO::Done
2026-02-16 21:35:31.469693 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:31.471931 INFO::Starting hierarchical adjustment
2026-02-16 21:35:31.472691 INFO::Found 3 batches.
2026-02-16 21:35:31.473228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:31.473882 INFO::Using default BPPARAM
2026-02-16 21:35:31.474472 INFO::Processing subtree level 1
2026-02-16 21:35:31.559674 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:35:31.561584 INFO::Done
2026-02-16 21:35:31.562249 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:31.56479 INFO::ASW Batch was -0.109945598785326 prior to batch effect correction and is now -0.109945598785326 .
2026-02-16 21:35:31.565768 INFO::Total function execution time is 0.104232549667358 s and adjustment time is 0.0890302658081055 s ( 85.42 )
2026-02-16 21:35:31.579501 INFO::Formatting Data.
2026-02-16 21:35:31.580389 INFO::Typecasting input to dataframe.
2026-02-16 21:35:31.581319 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:31.582283 INFO::Removing potential empty rows and columns
2026-02-16 21:35:31.58344 INFO::Found 0 missing values.
2026-02-16 21:35:31.586588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:31.587162 INFO::Done
2026-02-16 21:35:31.587745 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:31.589922 INFO::Starting hierarchical adjustment
2026-02-16 21:35:31.590653 INFO::Found 3 batches.
2026-02-16 21:35:31.59124 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:31.591902 INFO::Using default BPPARAM
2026-02-16 21:35:31.592469 INFO::Processing subtree level 1
2026-02-16 21:35:31.680409 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:35:31.68256 INFO::Done
2026-02-16 21:35:31.683242 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:31.686018 INFO::ASW Batch was -0.102318701217218 prior to batch effect correction and is now -0.102318701217218 .
2026-02-16 21:35:31.687032 INFO::Total function execution time is 0.10761570930481 s and adjustment time is 0.0920493602752686 s ( 85.54 )
2026-02-16 21:35:31.829409 INFO::Formatting Data.
2026-02-16 21:35:31.830282 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:31.831522 INFO::Removing potential empty rows and columns
2026-02-16 21:35:31.834481 INFO::Found 1000 missing values.
2026-02-16 21:35:31.855452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:31.856304 INFO::Done
2026-02-16 21:35:31.856951 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:31.862858 INFO::Starting hierarchical adjustment
2026-02-16 21:35:31.863996 INFO::Found 10 batches.
2026-02-16 21:35:31.864607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:31.865295 INFO::Using default BPPARAM
2026-02-16 21:35:31.865903 INFO::Processing subtree level 1
2026-02-16 21:35:31.999327 INFO::Processing subtree level 2
2026-02-16 21:35:32.147365 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:35:32.151222 INFO::Done
2026-02-16 21:35:32.152093 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:32.158176 INFO::ASW Batch was 0.54629361576266 prior to batch effect correction and is now 0.54629361576266 .
2026-02-16 21:35:32.15903 INFO::ASW Label was 0.327361382813892 prior to batch effect correction and is now 0.327361382813892 .
2026-02-16 21:35:32.160124 INFO::Total function execution time is 0.330801725387573 s and adjustment time is 0.287621021270752 s ( 86.95 )
2026-02-16 21:35:32.161095 INFO::Formatting Data.
2026-02-16 21:35:32.161802 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:32.163218 INFO::Removing potential empty rows and columns
2026-02-16 21:35:32.166287 INFO::Found 1000 missing values.
2026-02-16 21:35:32.198404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:32.200274 INFO::Done
2026-02-16 21:35:32.200935 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:32.20866 INFO::Starting hierarchical adjustment
2026-02-16 21:35:32.209779 INFO::Found 10 batches.
2026-02-16 21:35:33.387774 INFO::Set up parallel execution backend with 2 workers
2026-02-16 21:35:33.389831 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-16 21:35:34.503302 INFO::Adjusting the last 2 batches sequentially
2026-02-16 21:35:34.505273 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-16 21:35:34.521294 INFO::Done
2026-02-16 21:35:34.52195 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:34.526348 INFO::ASW Batch was 0.54629361576266 prior to batch effect correction and is now 0.54629361576266 .
2026-02-16 21:35:34.526953 INFO::ASW Label was 0.327361382813892 prior to batch effect correction and is now 0.327361382813892 .
2026-02-16 21:35:34.527684 INFO::Total function execution time is 2.36666917800903 s and adjustment time is 2.31179547309875 s ( 97.68 )
2026-02-16 21:35:34.662228 INFO::Formatting Data.
2026-02-16 21:35:34.663019 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:34.663921 INFO::Removing potential empty rows and columns
2026-02-16 21:35:34.664978 INFO::Found 0 missing values.
2026-02-16 21:35:34.668582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:34.669104 INFO::Done
2026-02-16 21:35:34.669627 INFO::Acquiring quality metrics before batch effect correction.
2026-02-16 21:35:34.672283 INFO::Starting hierarchical adjustment
2026-02-16 21:35:34.672971 INFO::Found 3 batches.
2026-02-16 21:35:34.673492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-16 21:35:34.674111 INFO::Using default BPPARAM
2026-02-16 21:35:34.674644 INFO::Processing subtree level 1
2026-02-16 21:35:34.773396 INFO::Adjusting the last 1 batches sequentially
2026-02-16 21:35:34.775221 INFO::Done
2026-02-16 21:35:34.775919 INFO::Acquiring quality metrics after batch effect correction.
2026-02-16 21:35:34.779101 INFO::ASW Batch was 0.137523985317789 prior to batch effect correction and is now -0.161487834571761 .
2026-02-16 21:35:34.77972 INFO::ASW Label was -0.174673058577252 prior to batch effect correction and is now -0.0147790624239107 .
2026-02-16 21:35:34.780688 INFO::Total function execution time is 0.118492603302002 s and adjustment time is 0.102360486984253 s ( 86.39 )
2026-02-16 21:35:34.895203 INFO::Formatting Data.
2026-02-16 21:35:34.895988 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:34.896874 INFO::Removing potential empty rows and columns
2026-02-16 21:35:34.897897 INFO::Found 2 missing values.
2026-02-16 21:35:34.90063 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:34.901181 INFO::Done
2026-02-16 21:35:34.927384 INFO::Found NA in Reference column
2026-02-16 21:35:34.93645 INFO::Require at least two references per batch.
2026-02-16 21:35:34.955847 INFO::Formatting Data.
2026-02-16 21:35:34.956603 INFO::Recognized SummarizedExperiment
2026-02-16 21:35:34.957149 INFO::Typecasting input to dataframe.
2026-02-16 21:35:34.966277 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:34.967362 INFO::Removing potential empty rows and columns
2026-02-16 21:35:34.97088 INFO::Found 0 missing values.
2026-02-16 21:35:34.977566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:34.978114 INFO::Done
2026-02-16 21:35:34.992679 INFO::Formatting Data.
2026-02-16 21:35:34.993326 INFO::Recognized SummarizedExperiment
2026-02-16 21:35:34.993837 INFO::Typecasting input to dataframe.
2026-02-16 21:35:35.00992 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:35.011091 INFO::Removing potential empty rows and columns
2026-02-16 21:35:35.014661 INFO::Found 0 missing values.
2026-02-16 21:35:35.025488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:35.02608 INFO::Done
2026-02-16 21:35:35.041117 INFO::Formatting Data.
2026-02-16 21:35:35.041887 INFO::Recognized SummarizedExperiment
2026-02-16 21:35:35.042443 INFO::Typecasting input to dataframe.
2026-02-16 21:35:35.05905 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:35.060141 INFO::Removing potential empty rows and columns
2026-02-16 21:35:35.061262 INFO::Found 0 missing values.
2026-02-16 21:35:35.062169 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.
2026-02-16 21:35:35.0665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:35.06705 INFO::Done
2026-02-16 21:35:35.077293 INFO::Formatting Data.
2026-02-16 21:35:35.078183 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:35.079158 INFO::Removing potential empty rows and columns
2026-02-16 21:35:35.080227 INFO::Found 0 missing values.
2026-02-16 21:35:35.083218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:35.083783 INFO::Done
2026-02-16 21:35:35.096487 INFO::Formatting Data.
2026-02-16 21:35:35.097267 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:35.098171 INFO::Removing potential empty rows and columns
2026-02-16 21:35:35.099203 INFO::Found 0 missing values.
2026-02-16 21:35:35.102094 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:35.102625 INFO::Done
2026-02-16 21:35:35.132235 INFO::Formatting Data.
2026-02-16 21:35:35.133045 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:35.13405 INFO::Removing potential empty rows and columns
2026-02-16 21:35:35.135161 INFO::Found 1 missing values.
2026-02-16 21:35:35.137661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:35.138199 INFO::Done
2026-02-16 21:35:35.156107 INFO::Formatting Data.
2026-02-16 21:35:35.156907 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:35.157793 INFO::Removing potential empty rows and columns
2026-02-16 21:35:35.158726 INFO::Found 2 missing values.
2026-02-16 21:35:35.159613 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.
2026-02-16 21:35:35.161961 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:35.162492 INFO::Done
2026-02-16 21:35:35.171923 INFO::Formatting Data.
2026-02-16 21:35:35.172638 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:35.173492 INFO::Removing potential empty rows and columns
2026-02-16 21:35:35.174364 INFO::Found 2 missing values.
2026-02-16 21:35:35.175893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:35.176435 INFO::Done
2026-02-16 21:35:35.186255 INFO::Formatting Data.
2026-02-16 21:35:35.186985 INFO::Typecasting input to dataframe.
2026-02-16 21:35:35.187758 INFO::Replacing NaNs with NAs.
2026-02-16 21:35:35.188578 INFO::Removing potential empty rows and columns
2026-02-16 21:35:35.189546 INFO::Found 0 missing values.
2026-02-16 21:35:35.192317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-16 21:35:35.192835 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.191 3.473 20.308
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.367 | 1.158 | 17.226 | |
| compute_asw | 0.023 | 0.001 | 0.024 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |