Yannis Schumann
| Snapshot Date: 2026-02-15 13:40 -0500 (Sun, 15 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 2026-02-16 11:32 -0500 (Mon, 16 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: 2026-02-15 21:33:33 -0500 (Sun, 15 Feb 2026) |
| EndedAt: 2026-02-15 21:35:09 -0500 (Sun, 15 Feb 2026) |
| EllapsedTime: 96.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 24.245 1.948 17.792
* 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")
2026-02-15 21:34:29.027757 INFO::Formatting Data.
2026-02-15 21:34:29.029246 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:29.040781 INFO::Removing potential empty rows and columns
2026-02-15 21:34:29.282463 INFO::Found 0 missing values.
2026-02-15 21:34:29.285969 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:29.286662 INFO::Done
2026-02-15 21:34:29.287257 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:29.298934 INFO::Starting hierarchical adjustment
2026-02-15 21:34:29.29988 INFO::Found 3 batches.
2026-02-15 21:34:29.300493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:29.301656 INFO::Using default BPPARAM
2026-02-15 21:34:29.302215 INFO::Processing subtree level 1
2026-02-15 21:34:29.424416 INFO::Adjusting the last 1 batches sequentially
2026-02-15 21:34:29.426502 INFO::Done
2026-02-15 21:34:29.427294 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:29.430246 INFO::ASW Batch was 0.022618729834034 prior to batch effect correction and is now 0.022618729834034 .
2026-02-15 21:34:29.431456 INFO::Total function execution time is 0.404382944107056 s and adjustment time is 0.12676215171814 s ( 31.35 )
2026-02-15 21:34:29.447123 INFO::Formatting Data.
2026-02-15 21:34:29.448072 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:29.449147 INFO::Removing potential empty rows and columns
2026-02-15 21:34:29.450496 INFO::Found 0 missing values.
2026-02-15 21:34:29.45159 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.
2026-02-15 21:34:29.463511 INFO::Formatting Data.
2026-02-15 21:34:29.464422 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:29.465472 INFO::Removing potential empty rows and columns
2026-02-15 21:34:29.466635 INFO::Found 0 missing values.
2026-02-15 21:34:29.467641 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.
2026-02-15 21:34:29.48555 INFO::Formatting Data.
2026-02-15 21:34:29.486584 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:29.487725 INFO::Removing potential empty rows and columns
2026-02-15 21:34:29.489116 INFO::Found 0 missing values.
2026-02-15 21:34:29.490336 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.
2026-02-15 21:34:29.496568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:29.497398 INFO::Done
2026-02-15 21:34:29.498044 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:29.500958 INFO::Starting hierarchical adjustment
2026-02-15 21:34:29.501872 INFO::Found 2 batches.
2026-02-15 21:34:29.502569 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:29.503434 INFO::Using default BPPARAM
2026-02-15 21:34:29.504112 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:29.505312 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-15 21:34:29.532472 INFO::Done
2026-02-15 21:34:29.533332 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:29.535933 INFO::ASW Batch was 0.0125328288874072 prior to batch effect correction and is now -0.112489548619189 .
2026-02-15 21:34:29.536896 INFO::Total function execution time is 0.0514466762542725 s and adjustment time is 0.0307276248931885 s ( 59.73 )
2026-02-15 21:34:29.540267 INFO::Formatting Data.
2026-02-15 21:34:29.540995 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:29.550802 INFO::Formatting Data.
2026-02-15 21:34:29.551726 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:29.552752 INFO::Removing potential empty rows and columns
2026-02-15 21:34:29.5539 INFO::Found 0 missing values.
2026-02-15 21:34:29.557238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:29.557837 INFO::Done
2026-02-15 21:34:29.5584 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:29.560718 INFO::Starting hierarchical adjustment
2026-02-15 21:34:29.561486 INFO::Found 2 batches.
2026-02-15 21:34:29.562045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:29.562701 INFO::Using default BPPARAM
2026-02-15 21:34:29.56327 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:29.56431 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-15 21:34:29.609482 INFO::Done
2026-02-15 21:34:29.610304 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:29.612656 INFO::ASW Batch was 0.0403880449572031 prior to batch effect correction and is now -0.110545794564689 .
2026-02-15 21:34:29.613574 INFO::Total function execution time is 0.0628604888916016 s and adjustment time is 0.0481126308441162 s ( 76.54 )
2026-02-15 21:34:29.614714 INFO::Formatting Data.
2026-02-15 21:34:29.615345 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:29.616279 INFO::Removing potential empty rows and columns
2026-02-15 21:34:29.617354 INFO::Found 0 missing values.
2026-02-15 21:34:29.620331 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:29.62091 INFO::Done
2026-02-15 21:34:29.621444 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:29.623644 INFO::Starting hierarchical adjustment
2026-02-15 21:34:29.624382 INFO::Found 2 batches.
2026-02-15 21:34:29.624903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:29.625525 INFO::Using default BPPARAM
2026-02-15 21:34:29.626065 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:29.627054 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-15 21:34:29.643041 INFO::Done
2026-02-15 21:34:29.643832 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:29.6461 INFO::ASW Batch was 0.0403880449572031 prior to batch effect correction and is now -0.110545794564689 .
2026-02-15 21:34:29.646986 INFO::Total function execution time is 0.032271146774292 s and adjustment time is 0.0187785625457764 s ( 58.19 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-15 21:34:33.208839 INFO::Formatting Data.
2026-02-15 21:34:33.209713 INFO::Recognized SummarizedExperiment
2026-02-15 21:34:33.210205 INFO::Typecasting input to dataframe.
2026-02-15 21:34:33.243037 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:33.244568 INFO::Removing potential empty rows and columns
2026-02-15 21:34:33.248861 INFO::Found 0 missing values.
2026-02-15 21:34:33.256853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:33.257614 INFO::Done
2026-02-15 21:34:33.258175 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:33.262173 INFO::Starting hierarchical adjustment
2026-02-15 21:34:33.262956 INFO::Found 2 batches.
2026-02-15 21:34:33.263499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:33.264793 INFO::Using default BPPARAM
2026-02-15 21:34:33.265362 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:33.266411 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-15 21:34:33.327857 INFO::Done
2026-02-15 21:34:33.328639 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:33.332415 INFO::ASW Batch was 0.00248958636061465 prior to batch effect correction and is now -0.0909961833897928 .
2026-02-15 21:34:33.333314 INFO::Total function execution time is 0.124820709228516 s and adjustment time is 0.065035343170166 s ( 52.1 )
Warning: stack imbalance in '{', 73 then 75
2026-02-15 21:34:33.353416 INFO::Formatting Data.
2026-02-15 21:34:33.354209 INFO::Recognized SummarizedExperiment
2026-02-15 21:34:33.35479 INFO::Typecasting input to dataframe.
2026-02-15 21:34:33.364802 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:33.366079 INFO::Removing potential empty rows and columns
2026-02-15 21:34:33.370137 INFO::Found 0 missing values.
2026-02-15 21:34:33.377975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:33.378641 INFO::Done
2026-02-15 21:34:33.379186 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:33.382866 INFO::Starting hierarchical adjustment
2026-02-15 21:34:33.383845 INFO::Found 2 batches.
2026-02-15 21:34:33.384393 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:33.38502 INFO::Using default BPPARAM
2026-02-15 21:34:33.385567 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:33.386576 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-15 21:34:33.413352 INFO::Done
2026-02-15 21:34:33.414158 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:33.417933 INFO::ASW Batch was 0.0110033935046453 prior to batch effect correction and is now 0.0110033935046453 .
2026-02-15 21:34:33.418875 INFO::Total function execution time is 0.0654532909393311 s and adjustment time is 0.0296013355255127 s ( 45.23 )
2026-02-15 21:34:33.438455 INFO::Formatting Data.
2026-02-15 21:34:33.43956 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:33.440505 INFO::Removing potential empty rows and columns
2026-02-15 21:34:33.44158 INFO::Found 0 missing values.
2026-02-15 21:34:33.44464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:33.445187 INFO::Done
2026-02-15 21:34:33.445715 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:33.447847 INFO::Starting hierarchical adjustment
2026-02-15 21:34:33.448564 INFO::Found 3 batches.
2026-02-15 21:34:33.449099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:33.449709 INFO::Using default BPPARAM
2026-02-15 21:34:33.45024 INFO::Processing subtree level 1
2026-02-15 21:34:33.5931 INFO::Adjusting the last 1 batches sequentially
2026-02-15 21:34:33.595006 INFO::Done
2026-02-15 21:34:33.595699 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:33.598249 INFO::ASW Batch was -0.00666832078320516 prior to batch effect correction and is now -0.15327976734155 .
2026-02-15 21:34:33.599478 INFO::Total function execution time is 0.161074161529541 s and adjustment time is 0.146578788757324 s ( 91 )
2026-02-15 21:34:33.614071 INFO::Skipping initial DF formatting
2026-02-15 21:34:33.614801 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:33.618924 INFO::Starting hierarchical adjustment
2026-02-15 21:34:33.619728 INFO::Found 5 batches.
2026-02-15 21:34:33.62029 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:33.620948 INFO::Using default BPPARAM
2026-02-15 21:34:33.621505 INFO::Processing subtree level 1
2026-02-15 21:34:35.010329 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:35.012152 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-15 21:34:35.045618 INFO::Done
2026-02-15 21:34:35.046519 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:35.110988 INFO::ASW Batch was 0.464935746667769 prior to batch effect correction and is now 0.464935746667769 .
2026-02-15 21:34:35.112419 INFO::ASW Label was 0.42332320529792 prior to batch effect correction and is now 0.42332320529792 .
2026-02-15 21:34:35.113356 INFO::Total function execution time is 1.49938201904297 s and adjustment time is 1.42597794532776 s ( 95.1 )
2026-02-15 21:34:35.131987 INFO::Formatting Data.
2026-02-15 21:34:35.132776 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:35.133762 INFO::Removing potential empty rows and columns
2026-02-15 21:34:35.134853 INFO::Found 0 missing values.
2026-02-15 21:34:35.140048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:35.140918 INFO::Done
2026-02-15 21:34:35.141778 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:35.14658 INFO::Starting hierarchical adjustment
2026-02-15 21:34:35.147662 INFO::Found 5 batches.
2026-02-15 21:34:35.148491 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:35.149502 INFO::Using default BPPARAM
2026-02-15 21:34:35.150464 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.
2026-02-15 21:34:35.297994 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:35.300567 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-15 21:34:35.329163 INFO::Done
2026-02-15 21:34:35.330347 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:35.335768 INFO::ASW Batch was 0.166675699825383 prior to batch effect correction and is now -0.0780159563473305 .
2026-02-15 21:34:35.336781 INFO::ASW Label was 0.617988257256002 prior to batch effect correction and is now 0.86425762077927 .
2026-02-15 21:34:35.338143 INFO::Total function execution time is 0.206145048141479 s and adjustment time is 0.181685209274292 s ( 88.13 )
2026-02-15 21:34:35.339521 INFO::Formatting Data.
2026-02-15 21:34:35.340643 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:35.342074 INFO::Removing potential empty rows and columns
2026-02-15 21:34:35.343803 INFO::Found 0 missing values.
2026-02-15 21:34:35.350852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:35.351808 INFO::Done
2026-02-15 21:34:35.352721 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:35.357922 INFO::Starting hierarchical adjustment
2026-02-15 21:34:35.359025 INFO::Found 5 batches.
2026-02-15 21:34:35.359864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:35.360893 INFO::Using default BPPARAM
2026-02-15 21:34:35.361739 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.
2026-02-15 21:34:35.506285 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:35.508024 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-15 21:34:35.525307 INFO::Done
2026-02-15 21:34:35.526066 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:35.529429 INFO::ASW Batch was 0.166675699825383 prior to batch effect correction and is now -0.0780159563473305 .
2026-02-15 21:34:35.530055 INFO::ASW Label was 0.617988257256002 prior to batch effect correction and is now 0.86425762077927 .
2026-02-15 21:34:35.530961 INFO::Total function execution time is 0.191563606262207 s and adjustment time is 0.16650652885437 s ( 86.92 )
2026-02-15 21:34:35.545504 INFO::Formatting Data.
2026-02-15 21:34:35.546346 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:35.547316 INFO::Removing potential empty rows and columns
2026-02-15 21:34:35.548413 INFO::Found 0 missing values.
2026-02-15 21:34:35.552848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:35.553488 INFO::Done
2026-02-15 21:34:35.554072 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:35.557254 INFO::Starting hierarchical adjustment
2026-02-15 21:34:35.558031 INFO::Found 5 batches.
2026-02-15 21:34:35.558591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:35.559247 INFO::Using default BPPARAM
2026-02-15 21:34:35.559845 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.
2026-02-15 21:34:35.697115 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:35.698884 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-15 21:34:35.716065 INFO::Done
2026-02-15 21:34:35.716804 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:35.720136 INFO::ASW Batch was 0.404817736600972 prior to batch effect correction and is now -0.00274253684184093 .
2026-02-15 21:34:35.720838 INFO::ASW Label was 0.391877044926052 prior to batch effect correction and is now 0.777178046679342 .
2026-02-15 21:34:35.72168 INFO::Total function execution time is 0.176286935806274 s and adjustment time is 0.15815281867981 s ( 89.71 )
2026-02-15 21:34:35.722557 INFO::Formatting Data.
2026-02-15 21:34:35.723246 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:35.724189 INFO::Removing potential empty rows and columns
2026-02-15 21:34:35.725282 INFO::Found 0 missing values.
2026-02-15 21:34:35.729766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:35.730426 INFO::Done
2026-02-15 21:34:35.731116 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:35.734204 INFO::Starting hierarchical adjustment
2026-02-15 21:34:35.734946 INFO::Found 5 batches.
2026-02-15 21:34:35.735537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:35.736187 INFO::Using default BPPARAM
2026-02-15 21:34:35.736741 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.
2026-02-15 21:34:35.86353 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:35.865353 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-15 21:34:35.882398 INFO::Done
2026-02-15 21:34:35.883166 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:35.886806 INFO::ASW Batch was 0.404817736600972 prior to batch effect correction and is now -0.00274253684184093 .
2026-02-15 21:34:35.88741 INFO::ASW Label was 0.391877044926052 prior to batch effect correction and is now 0.777178046679342 .
2026-02-15 21:34:35.888249 INFO::Total function execution time is 0.165709018707275 s and adjustment time is 0.147566556930542 s ( 89.05 )
2026-02-15 21:34:35.901264 INFO::Formatting Data.
2026-02-15 21:34:35.902012 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:35.902906 INFO::Removing potential empty rows and columns
2026-02-15 21:34:35.903902 INFO::Found 0 missing values.
2026-02-15 21:34:35.906552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:35.907106 INFO::Done
2026-02-15 21:34:35.907642 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:35.910552 INFO::Starting hierarchical adjustment
2026-02-15 21:34:35.911247 INFO::Found 2 batches.
2026-02-15 21:34:35.911788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:35.912396 INFO::Using default BPPARAM
2026-02-15 21:34:35.912938 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:35.913818 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-15 21:34:35.92798 INFO::Done
2026-02-15 21:34:35.928626 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:35.931452 INFO::ASW Batch was 0.554594587203185 prior to batch effect correction and is now 0.0925886198979145 .
2026-02-15 21:34:35.932031 INFO::ASW Label was 0.507664576596131 prior to batch effect correction and is now 0.80779765578695 .
2026-02-15 21:34:35.93282 INFO::Total function execution time is 0.0316526889801025 s and adjustment time is 0.016864538192749 s ( 53.28 )
2026-02-15 21:34:35.933592 INFO::Formatting Data.
2026-02-15 21:34:35.934192 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:35.935023 INFO::Removing potential empty rows and columns
2026-02-15 21:34:35.935987 INFO::Found 0 missing values.
2026-02-15 21:34:35.938565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:35.939102 INFO::Done
2026-02-15 21:34:35.939623 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:35.942382 INFO::Starting hierarchical adjustment
2026-02-15 21:34:35.943051 INFO::Found 2 batches.
2026-02-15 21:34:35.943573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:35.944153 INFO::Using default BPPARAM
2026-02-15 21:34:35.944691 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:35.945564 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-15 21:34:35.959695 INFO::Done
2026-02-15 21:34:35.960388 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:35.963254 INFO::ASW Batch was 0.554594587203185 prior to batch effect correction and is now 0.0925886198979145 .
2026-02-15 21:34:35.963829 INFO::ASW Label was 0.507664576596131 prior to batch effect correction and is now 0.80779765578695 .
2026-02-15 21:34:35.964636 INFO::Total function execution time is 0.0310616493225098 s and adjustment time is 0.0167553424835205 s ( 53.94 )
2026-02-15 21:34:35.975807 INFO::Formatting Data.
2026-02-15 21:34:35.976626 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:35.97751 INFO::Removing potential empty rows and columns
2026-02-15 21:34:35.978407 INFO::Found 0 missing values.
2026-02-15 21:34:35.98045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:35.980998 INFO::Done
2026-02-15 21:34:35.981506 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:35.983362 INFO::Starting hierarchical adjustment
2026-02-15 21:34:35.98405 INFO::Found 2 batches.
2026-02-15 21:34:35.984574 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:35.985159 INFO::Using default BPPARAM
2026-02-15 21:34:35.985698 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:35.986584 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-15 21:34:36.016784 INFO::Done
2026-02-15 21:34:36.0175 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:36.019419 INFO::ASW Batch was -0.129834849123797 prior to batch effect correction and is now -0.177979507910366 .
2026-02-15 21:34:36.020222 INFO::Total function execution time is 0.0445389747619629 s and adjustment time is 0.0328397750854492 s ( 73.73 )
2026-02-15 21:34:36.03838 INFO::Formatting Data.
2026-02-15 21:34:36.039276 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:36.040242 INFO::Removing potential empty rows and columns
2026-02-15 21:34:36.041356 INFO::Found 0 missing values.
2026-02-15 21:34:36.042672 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.
2026-02-15 21:34:36.047599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:36.048213 INFO::Done
2026-02-15 21:34:36.048786 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:36.0519 INFO::Starting hierarchical adjustment
2026-02-15 21:34:36.052655 INFO::Found 2 batches.
2026-02-15 21:34:36.053221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:36.053867 INFO::Using default BPPARAM
2026-02-15 21:34:36.054446 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:36.055446 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-15 21:34:36.072945 INFO::Done
2026-02-15 21:34:36.073707 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:36.076784 INFO::ASW Batch was 0.552290548376847 prior to batch effect correction and is now -0.0278734062067306 .
2026-02-15 21:34:36.077391 INFO::ASW Label was 0.434376287847347 prior to batch effect correction and is now 0.938417179612871 .
2026-02-15 21:34:36.078221 INFO::Total function execution time is 0.0400118827819824 s and adjustment time is 0.0204033851623535 s ( 50.99 )
2026-02-15 21:34:36.079055 INFO::Formatting Data.
2026-02-15 21:34:36.079715 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:36.080681 INFO::Removing potential empty rows and columns
2026-02-15 21:34:36.081695 INFO::Found 0 missing values.
2026-02-15 21:34:36.082622 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.
2026-02-15 21:34:36.087321 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:36.087889 INFO::Done
2026-02-15 21:34:36.088444 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:36.091427 INFO::Starting hierarchical adjustment
2026-02-15 21:34:36.092143 INFO::Found 2 batches.
2026-02-15 21:34:36.092747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:36.093398 INFO::Using default BPPARAM
2026-02-15 21:34:36.093961 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:36.094942 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-15 21:34:36.111981 INFO::Done
2026-02-15 21:34:36.112701 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:36.115707 INFO::ASW Batch was 0.552290548376847 prior to batch effect correction and is now -0.0278734062067306 .
2026-02-15 21:34:36.116318 INFO::ASW Label was 0.434376287847347 prior to batch effect correction and is now 0.938417179612871 .
2026-02-15 21:34:36.11715 INFO::Total function execution time is 0.0381240844726562 s and adjustment time is 0.0199611186981201 s ( 52.36 )
2026-02-15 21:34:36.3352 INFO::Formatting Data.
2026-02-15 21:34:36.336038 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:36.336961 INFO::Removing potential empty rows and columns
2026-02-15 21:34:36.338046 INFO::Found 0 missing values.
2026-02-15 21:34:36.341266 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:36.341822 INFO::Done
2026-02-15 21:34:36.342355 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:36.344395 INFO::Starting hierarchical adjustment
2026-02-15 21:34:36.345098 INFO::Found 3 batches.
2026-02-15 21:34:36.345643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:36.346274 INFO::Using default BPPARAM
2026-02-15 21:34:36.34683 INFO::Processing subtree level 1
2026-02-15 21:34:36.433567 INFO::Adjusting the last 1 batches sequentially
2026-02-15 21:34:36.43545 INFO::Done
2026-02-15 21:34:36.436102 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:36.438587 INFO::ASW Batch was 0.0905063258216121 prior to batch effect correction and is now 0.0905063258216121 .
2026-02-15 21:34:36.439603 INFO::Total function execution time is 0.1044762134552 s and adjustment time is 0.0904638767242432 s ( 86.59 )
2026-02-15 21:34:36.440773 INFO::Formatting Data.
2026-02-15 21:34:36.441467 INFO::Typecasting input to dataframe.
2026-02-15 21:34:36.442226 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:36.443164 INFO::Removing potential empty rows and columns
2026-02-15 21:34:36.444269 INFO::Found 0 missing values.
2026-02-15 21:34:36.447423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:36.448024 INFO::Done
2026-02-15 21:34:36.448586 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:36.450651 INFO::Starting hierarchical adjustment
2026-02-15 21:34:36.451363 INFO::Found 3 batches.
2026-02-15 21:34:36.451919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:36.45257 INFO::Using default BPPARAM
2026-02-15 21:34:36.453107 INFO::Processing subtree level 1
2026-02-15 21:34:36.538927 INFO::Adjusting the last 1 batches sequentially
2026-02-15 21:34:36.540722 INFO::Done
2026-02-15 21:34:36.541376 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:36.543918 INFO::ASW Batch was 0.0905063258216121 prior to batch effect correction and is now 0.0905063258216121 .
2026-02-15 21:34:36.544904 INFO::Total function execution time is 0.104236841201782 s and adjustment time is 0.0894794464111328 s ( 85.84 )
2026-02-15 21:34:36.557896 INFO::Formatting Data.
2026-02-15 21:34:36.558725 INFO::Typecasting input to dataframe.
2026-02-15 21:34:36.559586 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:36.560502 INFO::Removing potential empty rows and columns
2026-02-15 21:34:36.5616 INFO::Found 0 missing values.
2026-02-15 21:34:36.564654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:36.565201 INFO::Done
2026-02-15 21:34:36.565756 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:36.567856 INFO::Starting hierarchical adjustment
2026-02-15 21:34:36.568581 INFO::Found 3 batches.
2026-02-15 21:34:36.569134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:36.569778 INFO::Using default BPPARAM
2026-02-15 21:34:36.570328 INFO::Processing subtree level 1
2026-02-15 21:34:36.655963 INFO::Adjusting the last 1 batches sequentially
2026-02-15 21:34:36.657951 INFO::Done
2026-02-15 21:34:36.658688 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:36.661303 INFO::ASW Batch was -0.112147842151182 prior to batch effect correction and is now -0.112147842151182 .
2026-02-15 21:34:36.662303 INFO::Total function execution time is 0.104465007781982 s and adjustment time is 0.0894894599914551 s ( 85.66 )
2026-02-15 21:34:36.799843 INFO::Formatting Data.
2026-02-15 21:34:36.800729 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:36.801895 INFO::Removing potential empty rows and columns
2026-02-15 21:34:36.805115 INFO::Found 1000 missing values.
2026-02-15 21:34:36.825639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:36.826497 INFO::Done
2026-02-15 21:34:36.827106 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:36.83285 INFO::Starting hierarchical adjustment
2026-02-15 21:34:36.833693 INFO::Found 10 batches.
2026-02-15 21:34:36.834269 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:36.834962 INFO::Using default BPPARAM
2026-02-15 21:34:36.835547 INFO::Processing subtree level 1
2026-02-15 21:34:36.978659 INFO::Processing subtree level 2
2026-02-15 21:34:37.133987 INFO::Adjusting the last 1 batches sequentially
2026-02-15 21:34:37.137324 INFO::Done
2026-02-15 21:34:37.138565 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:37.148028 INFO::ASW Batch was 0.506406087564424 prior to batch effect correction and is now 0.506406087564424 .
2026-02-15 21:34:37.149225 INFO::ASW Label was 0.356073396587877 prior to batch effect correction and is now 0.356073396587877 .
2026-02-15 21:34:37.150794 INFO::Total function execution time is 0.350955963134766 s and adjustment time is 0.303704977035522 s ( 86.54 )
2026-02-15 21:34:37.151805 INFO::Formatting Data.
2026-02-15 21:34:37.1525 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:37.153782 INFO::Removing potential empty rows and columns
2026-02-15 21:34:37.156849 INFO::Found 1000 missing values.
2026-02-15 21:34:37.177387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:37.178211 INFO::Done
2026-02-15 21:34:37.178808 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:37.184512 INFO::Starting hierarchical adjustment
2026-02-15 21:34:37.185354 INFO::Found 10 batches.
2026-02-15 21:34:38.271558 INFO::Set up parallel execution backend with 2 workers
2026-02-15 21:34:38.273602 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-15 21:34:39.398627 INFO::Adjusting the last 2 batches sequentially
2026-02-15 21:34:39.400732 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-15 21:34:39.418126 INFO::Done
2026-02-15 21:34:39.418896 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:39.423608 INFO::ASW Batch was 0.506406087564424 prior to batch effect correction and is now 0.506406087564424 .
2026-02-15 21:34:39.424258 INFO::ASW Label was 0.356073396587877 prior to batch effect correction and is now 0.356073396587877 .
2026-02-15 21:34:39.425031 INFO::Total function execution time is 2.27327561378479 s and adjustment time is 2.23291683197021 s ( 98.22 )
2026-02-15 21:34:39.588836 INFO::Formatting Data.
2026-02-15 21:34:39.589732 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:39.59077 INFO::Removing potential empty rows and columns
2026-02-15 21:34:39.59202 INFO::Found 0 missing values.
2026-02-15 21:34:39.595943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:39.596526 INFO::Done
2026-02-15 21:34:39.597052 INFO::Acquiring quality metrics before batch effect correction.
2026-02-15 21:34:39.600009 INFO::Starting hierarchical adjustment
2026-02-15 21:34:39.600762 INFO::Found 3 batches.
2026-02-15 21:34:39.6013 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-15 21:34:39.601946 INFO::Using default BPPARAM
2026-02-15 21:34:39.602526 INFO::Processing subtree level 1
2026-02-15 21:34:39.718112 INFO::Adjusting the last 1 batches sequentially
2026-02-15 21:34:39.720074 INFO::Done
2026-02-15 21:34:39.720753 INFO::Acquiring quality metrics after batch effect correction.
2026-02-15 21:34:39.724043 INFO::ASW Batch was 0.166566434504656 prior to batch effect correction and is now -0.135251250589463 .
2026-02-15 21:34:39.724659 INFO::ASW Label was -0.222974872124298 prior to batch effect correction and is now 0.0669608383016572 .
2026-02-15 21:34:39.725605 INFO::Total function execution time is 0.136861085891724 s and adjustment time is 0.119434356689453 s ( 87.27 )
2026-02-15 21:34:39.847615 INFO::Formatting Data.
2026-02-15 21:34:39.848478 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:39.849404 INFO::Removing potential empty rows and columns
2026-02-15 21:34:39.850498 INFO::Found 2 missing values.
2026-02-15 21:34:39.853375 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:39.853916 INFO::Done
2026-02-15 21:34:39.880226 INFO::Found NA in Reference column
2026-02-15 21:34:39.889413 INFO::Require at least two references per batch.
2026-02-15 21:34:39.909564 INFO::Formatting Data.
2026-02-15 21:34:39.910332 INFO::Recognized SummarizedExperiment
2026-02-15 21:34:39.910882 INFO::Typecasting input to dataframe.
2026-02-15 21:34:39.920507 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:39.921645 INFO::Removing potential empty rows and columns
2026-02-15 21:34:39.925153 INFO::Found 0 missing values.
2026-02-15 21:34:39.931956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:39.932515 INFO::Done
2026-02-15 21:34:39.947949 INFO::Formatting Data.
2026-02-15 21:34:39.948743 INFO::Recognized SummarizedExperiment
2026-02-15 21:34:39.949276 INFO::Typecasting input to dataframe.
2026-02-15 21:34:39.96614 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:39.967348 INFO::Removing potential empty rows and columns
2026-02-15 21:34:39.970927 INFO::Found 0 missing values.
2026-02-15 21:34:39.981938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:39.982536 INFO::Done
2026-02-15 21:34:39.997385 INFO::Formatting Data.
2026-02-15 21:34:39.998069 INFO::Recognized SummarizedExperiment
2026-02-15 21:34:39.998582 INFO::Typecasting input to dataframe.
2026-02-15 21:34:40.014228 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:40.015245 INFO::Removing potential empty rows and columns
2026-02-15 21:34:40.016322 INFO::Found 0 missing values.
2026-02-15 21:34:40.02433 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.
2026-02-15 21:34:40.02877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:40.029331 INFO::Done
2026-02-15 21:34:40.039301 INFO::Formatting Data.
2026-02-15 21:34:40.040074 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:40.041038 INFO::Removing potential empty rows and columns
2026-02-15 21:34:40.042133 INFO::Found 0 missing values.
2026-02-15 21:34:40.045233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:40.04579 INFO::Done
2026-02-15 21:34:40.058308 INFO::Formatting Data.
2026-02-15 21:34:40.059095 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:40.060001 INFO::Removing potential empty rows and columns
2026-02-15 21:34:40.061054 INFO::Found 0 missing values.
2026-02-15 21:34:40.064127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:40.064676 INFO::Done
2026-02-15 21:34:40.096404 INFO::Formatting Data.
2026-02-15 21:34:40.097274 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:40.098334 INFO::Removing potential empty rows and columns
2026-02-15 21:34:40.099573 INFO::Found 1 missing values.
2026-02-15 21:34:40.102291 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:40.102916 INFO::Done
2026-02-15 21:34:40.122729 INFO::Formatting Data.
2026-02-15 21:34:40.123596 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:40.124573 INFO::Removing potential empty rows and columns
2026-02-15 21:34:40.125597 INFO::Found 2 missing values.
2026-02-15 21:34:40.12656 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.
2026-02-15 21:34:40.129274 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:40.129835 INFO::Done
2026-02-15 21:34:40.13994 INFO::Formatting Data.
2026-02-15 21:34:40.140685 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:40.14157 INFO::Removing potential empty rows and columns
2026-02-15 21:34:40.142498 INFO::Found 2 missing values.
2026-02-15 21:34:40.14411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:40.144669 INFO::Done
2026-02-15 21:34:40.155004 INFO::Formatting Data.
2026-02-15 21:34:40.155737 INFO::Typecasting input to dataframe.
2026-02-15 21:34:40.156529 INFO::Replacing NaNs with NAs.
2026-02-15 21:34:40.15739 INFO::Removing potential empty rows and columns
2026-02-15 21:34:40.158415 INFO::Found 0 missing values.
2026-02-15 21:34:40.161453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-15 21:34:40.161992 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.522 5.801 26.616
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.245 | 1.948 | 17.792 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.014 | 0.000 | 0.013 | |
| generate_data_covariables | 0.011 | 0.002 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.011 | |