Yannis Schumann
| Snapshot Date: 2026-02-10 13:40 -0500 (Tue, 10 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 2026-02-11 11:32 -0500 (Wed, 11 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" | 4862 |
| 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 169/2351 | 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: 2026-02-10 21:49:22 -0500 (Tue, 10 Feb 2026) |
| EndedAt: 2026-02-10 21:50:52 -0500 (Tue, 10 Feb 2026) |
| EllapsedTime: 90.1 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 23.353 1.117 16.659
* 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")
2026-02-10 21:50:13.35141 INFO::Formatting Data.
2026-02-10 21:50:13.353136 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:13.365623 INFO::Removing potential empty rows and columns
2026-02-10 21:50:13.652638 INFO::Found 0 missing values.
2026-02-10 21:50:13.656583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:13.657389 INFO::Done
2026-02-10 21:50:13.657999 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:13.671375 INFO::Starting hierarchical adjustment
2026-02-10 21:50:13.672404 INFO::Found 3 batches.
2026-02-10 21:50:13.673041 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:13.67433 INFO::Using default BPPARAM
2026-02-10 21:50:13.674957 INFO::Processing subtree level 1
2026-02-10 21:50:13.783809 INFO::Adjusting the last 1 batches sequentially
2026-02-10 21:50:13.785829 INFO::Done
2026-02-10 21:50:13.786617 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:13.789609 INFO::ASW Batch was -0.134778911523048 prior to batch effect correction and is now -0.134778911523048 .
2026-02-10 21:50:13.790862 INFO::Total function execution time is 0.440238237380981 s and adjustment time is 0.113640785217285 s ( 25.81 )
2026-02-10 21:50:13.806209 INFO::Formatting Data.
2026-02-10 21:50:13.807097 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:13.808169 INFO::Removing potential empty rows and columns
2026-02-10 21:50:13.809505 INFO::Found 0 missing values.
2026-02-10 21:50:13.810621 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.
2026-02-10 21:50:13.823182 INFO::Formatting Data.
2026-02-10 21:50:13.824044 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:13.825114 INFO::Removing potential empty rows and columns
2026-02-10 21:50:13.826336 INFO::Found 0 missing values.
2026-02-10 21:50:13.827377 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.
2026-02-10 21:50:13.845782 INFO::Formatting Data.
2026-02-10 21:50:13.846735 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:13.847818 INFO::Removing potential empty rows and columns
2026-02-10 21:50:13.849018 INFO::Found 0 missing values.
2026-02-10 21:50:13.85011 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.
2026-02-10 21:50:13.855351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:13.856075 INFO::Done
2026-02-10 21:50:13.856691 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:13.859078 INFO::Starting hierarchical adjustment
2026-02-10 21:50:13.8599 INFO::Found 2 batches.
2026-02-10 21:50:13.860541 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:13.861269 INFO::Using default BPPARAM
2026-02-10 21:50:13.861893 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:13.862967 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-10 21:50:13.887812 INFO::Done
2026-02-10 21:50:13.888664 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:13.89132 INFO::ASW Batch was -0.00293511710771997 prior to batch effect correction and is now -0.10551861899279 .
2026-02-10 21:50:13.892241 INFO::Total function execution time is 0.0465488433837891 s and adjustment time is 0.0280241966247559 s ( 60.2 )
2026-02-10 21:50:13.895435 INFO::Formatting Data.
2026-02-10 21:50:13.896168 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:13.906097 INFO::Formatting Data.
2026-02-10 21:50:13.907014 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:13.908058 INFO::Removing potential empty rows and columns
2026-02-10 21:50:13.909214 INFO::Found 0 missing values.
2026-02-10 21:50:13.912589 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:13.913203 INFO::Done
2026-02-10 21:50:13.913803 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:13.916229 INFO::Starting hierarchical adjustment
2026-02-10 21:50:13.917077 INFO::Found 2 batches.
2026-02-10 21:50:13.917664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:13.918361 INFO::Using default BPPARAM
2026-02-10 21:50:13.918956 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:13.920023 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-10 21:50:13.975437 INFO::Done
2026-02-10 21:50:13.976346 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:13.978801 INFO::ASW Batch was -0.0264239317260788 prior to batch effect correction and is now -0.114444266145642 .
2026-02-10 21:50:13.979835 INFO::Total function execution time is 0.0737845897674561 s and adjustment time is 0.0584580898284912 s ( 79.23 )
2026-02-10 21:50:13.981051 INFO::Formatting Data.
2026-02-10 21:50:13.98172 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:13.982738 INFO::Removing potential empty rows and columns
2026-02-10 21:50:13.983859 INFO::Found 0 missing values.
2026-02-10 21:50:13.987115 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:13.987719 INFO::Done
2026-02-10 21:50:13.988272 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:13.990535 INFO::Starting hierarchical adjustment
2026-02-10 21:50:13.991312 INFO::Found 2 batches.
2026-02-10 21:50:13.99189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:13.992558 INFO::Using default BPPARAM
2026-02-10 21:50:13.993117 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:13.994165 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-10 21:50:14.011216 INFO::Done
2026-02-10 21:50:14.012113 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:14.01458 INFO::ASW Batch was -0.0264239317260788 prior to batch effect correction and is now -0.114444266145642 .
2026-02-10 21:50:14.015645 INFO::Total function execution time is 0.0345737934112549 s and adjustment time is 0.0200185775756836 s ( 57.9 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-10 21:50:17.276881 INFO::Formatting Data.
2026-02-10 21:50:17.277768 INFO::Recognized SummarizedExperiment
2026-02-10 21:50:17.278313 INFO::Typecasting input to dataframe.
2026-02-10 21:50:17.311394 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:17.312846 INFO::Removing potential empty rows and columns
2026-02-10 21:50:17.317232 INFO::Found 0 missing values.
2026-02-10 21:50:17.325375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:17.326121 INFO::Done
2026-02-10 21:50:17.326726 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:17.330661 INFO::Starting hierarchical adjustment
2026-02-10 21:50:17.331473 INFO::Found 2 batches.
2026-02-10 21:50:17.332047 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:17.333214 INFO::Using default BPPARAM
2026-02-10 21:50:17.333794 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:17.334874 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-10 21:50:17.396238 INFO::Done
2026-02-10 21:50:17.397037 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:17.400841 INFO::ASW Batch was 0.0156598438393661 prior to batch effect correction and is now -0.0913958310726915 .
2026-02-10 21:50:17.401783 INFO::Total function execution time is 0.125338077545166 s and adjustment time is 0.0648984909057617 s ( 51.78 )
Warning: stack imbalance in '{', 73 then 75
2026-02-10 21:50:17.422166 INFO::Formatting Data.
2026-02-10 21:50:17.423022 INFO::Recognized SummarizedExperiment
2026-02-10 21:50:17.423632 INFO::Typecasting input to dataframe.
2026-02-10 21:50:17.433569 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:17.434901 INFO::Removing potential empty rows and columns
2026-02-10 21:50:17.439236 INFO::Found 0 missing values.
2026-02-10 21:50:17.447493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:17.448387 INFO::Done
2026-02-10 21:50:17.449022 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:17.452856 INFO::Starting hierarchical adjustment
2026-02-10 21:50:17.453782 INFO::Found 2 batches.
2026-02-10 21:50:17.454384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:17.455059 INFO::Using default BPPARAM
2026-02-10 21:50:17.455626 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:17.456669 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-10 21:50:17.483956 INFO::Done
2026-02-10 21:50:17.484766 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:17.489071 INFO::ASW Batch was -0.00600423587464224 prior to batch effect correction and is now -0.00600423587464224 .
2026-02-10 21:50:17.490211 INFO::Total function execution time is 0.0679874420166016 s and adjustment time is 0.0303113460540771 s ( 44.58 )
2026-02-10 21:50:17.511326 INFO::Formatting Data.
2026-02-10 21:50:17.512304 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:17.513365 INFO::Removing potential empty rows and columns
2026-02-10 21:50:17.514548 INFO::Found 0 missing values.
2026-02-10 21:50:17.526166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:17.527177 INFO::Done
2026-02-10 21:50:17.527888 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:17.530942 INFO::Starting hierarchical adjustment
2026-02-10 21:50:17.531896 INFO::Found 3 batches.
2026-02-10 21:50:17.532517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:17.533215 INFO::Using default BPPARAM
2026-02-10 21:50:17.533807 INFO::Processing subtree level 1
2026-02-10 21:50:17.692978 INFO::Adjusting the last 1 batches sequentially
2026-02-10 21:50:17.695277 INFO::Done
2026-02-10 21:50:17.696119 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:17.699382 INFO::ASW Batch was -0.132320300127774 prior to batch effect correction and is now -0.170730516798559 .
2026-02-10 21:50:17.700765 INFO::Total function execution time is 0.189460515975952 s and adjustment time is 0.163567781448364 s ( 86.33 )
2026-02-10 21:50:17.719702 INFO::Skipping initial DF formatting
2026-02-10 21:50:17.720641 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:17.725548 INFO::Starting hierarchical adjustment
2026-02-10 21:50:17.726668 INFO::Found 5 batches.
2026-02-10 21:50:17.727391 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:17.728091 INFO::Using default BPPARAM
2026-02-10 21:50:17.728698 INFO::Processing subtree level 1
2026-02-10 21:50:18.013617 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:18.01581 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-10 21:50:18.038108 INFO::Done
2026-02-10 21:50:18.038965 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:18.096759 INFO::ASW Batch was 0.522896853544414 prior to batch effect correction and is now 0.522896853544414 .
2026-02-10 21:50:18.097524 INFO::ASW Label was 0.334295287599826 prior to batch effect correction and is now 0.334295287599826 .
2026-02-10 21:50:18.098448 INFO::Total function execution time is 0.378903388977051 s and adjustment time is 0.311653614044189 s ( 82.25 )
2026-02-10 21:50:18.117413 INFO::Formatting Data.
2026-02-10 21:50:18.118312 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:18.119438 INFO::Removing potential empty rows and columns
2026-02-10 21:50:18.120622 INFO::Found 0 missing values.
2026-02-10 21:50:18.125542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:18.126332 INFO::Done
2026-02-10 21:50:18.127042 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:18.1306 INFO::Starting hierarchical adjustment
2026-02-10 21:50:18.131485 INFO::Found 5 batches.
2026-02-10 21:50:18.13212 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:18.132908 INFO::Using default BPPARAM
2026-02-10 21:50:18.133539 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.
2026-02-10 21:50:18.276119 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:18.277892 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-10 21:50:18.295888 INFO::Done
2026-02-10 21:50:18.296652 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:18.300255 INFO::ASW Batch was 0.112270025111376 prior to batch effect correction and is now -0.0554110793261249 .
2026-02-10 21:50:18.300977 INFO::ASW Label was 0.656446015743937 prior to batch effect correction and is now 0.855704915474179 .
2026-02-10 21:50:18.301872 INFO::Total function execution time is 0.184542417526245 s and adjustment time is 0.164554595947266 s ( 89.17 )
2026-02-10 21:50:18.302839 INFO::Formatting Data.
2026-02-10 21:50:18.303531 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:18.304521 INFO::Removing potential empty rows and columns
2026-02-10 21:50:18.305629 INFO::Found 0 missing values.
2026-02-10 21:50:18.310186 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:18.310881 INFO::Done
2026-02-10 21:50:18.311498 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:18.314881 INFO::Starting hierarchical adjustment
2026-02-10 21:50:18.315688 INFO::Found 5 batches.
2026-02-10 21:50:18.316266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:18.316946 INFO::Using default BPPARAM
2026-02-10 21:50:18.317518 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.
2026-02-10 21:50:18.464165 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:18.466096 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-10 21:50:18.484654 INFO::Done
2026-02-10 21:50:18.48558 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:18.489447 INFO::ASW Batch was 0.112270025111376 prior to batch effect correction and is now -0.0554110793261249 .
2026-02-10 21:50:18.490139 INFO::ASW Label was 0.656446015743937 prior to batch effect correction and is now 0.855704915474179 .
2026-02-10 21:50:18.491089 INFO::Total function execution time is 0.188247680664062 s and adjustment time is 0.169076681137085 s ( 89.82 )
2026-02-10 21:50:18.506912 INFO::Formatting Data.
2026-02-10 21:50:18.507864 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:18.508902 INFO::Removing potential empty rows and columns
2026-02-10 21:50:18.510128 INFO::Found 0 missing values.
2026-02-10 21:50:18.51448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:18.515114 INFO::Done
2026-02-10 21:50:18.515684 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:18.519058 INFO::Starting hierarchical adjustment
2026-02-10 21:50:18.51986 INFO::Found 5 batches.
2026-02-10 21:50:18.520458 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:18.521156 INFO::Using default BPPARAM
2026-02-10 21:50:18.521818 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.
2026-02-10 21:50:18.683137 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:18.684943 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-10 21:50:18.708591 INFO::Done
2026-02-10 21:50:18.709618 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:18.713632 INFO::ASW Batch was 0.310774240791738 prior to batch effect correction and is now -0.0427487790566227 .
2026-02-10 21:50:18.714471 INFO::ASW Label was 0.34797399689472 prior to batch effect correction and is now 0.842640567827492 .
2026-02-10 21:50:18.71548 INFO::Total function execution time is 0.20865797996521 s and adjustment time is 0.188850879669189 s ( 90.51 )
2026-02-10 21:50:18.716543 INFO::Formatting Data.
2026-02-10 21:50:18.717321 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:18.718453 INFO::Removing potential empty rows and columns
2026-02-10 21:50:18.719725 INFO::Found 0 missing values.
2026-02-10 21:50:18.724786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:18.725662 INFO::Done
2026-02-10 21:50:18.726304 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:18.729985 INFO::Starting hierarchical adjustment
2026-02-10 21:50:18.731028 INFO::Found 5 batches.
2026-02-10 21:50:18.731689 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:18.732409 INFO::Using default BPPARAM
2026-02-10 21:50:18.733012 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.
2026-02-10 21:50:18.871444 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:18.873282 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-10 21:50:18.891916 INFO::Done
2026-02-10 21:50:18.892838 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:18.896977 INFO::ASW Batch was 0.310774240791738 prior to batch effect correction and is now -0.0427487790566227 .
2026-02-10 21:50:18.897776 INFO::ASW Label was 0.34797399689472 prior to batch effect correction and is now 0.842640567827492 .
2026-02-10 21:50:18.898736 INFO::Total function execution time is 0.182212114334106 s and adjustment time is 0.161051273345947 s ( 88.39 )
2026-02-10 21:50:18.914531 INFO::Formatting Data.
2026-02-10 21:50:18.915508 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:18.91661 INFO::Removing potential empty rows and columns
2026-02-10 21:50:18.917804 INFO::Found 0 missing values.
2026-02-10 21:50:18.920923 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:18.921664 INFO::Done
2026-02-10 21:50:18.922257 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:18.925551 INFO::Starting hierarchical adjustment
2026-02-10 21:50:18.926443 INFO::Found 2 batches.
2026-02-10 21:50:18.927048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:18.927711 INFO::Using default BPPARAM
2026-02-10 21:50:18.9283 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:18.929303 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-10 21:50:18.945433 INFO::Done
2026-02-10 21:50:18.946305 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:18.949808 INFO::ASW Batch was 0.479901050630153 prior to batch effect correction and is now 0.0750164073764222 .
2026-02-10 21:50:18.950625 INFO::ASW Label was 0.636917137095339 prior to batch effect correction and is now 0.881876954050019 .
2026-02-10 21:50:18.951539 INFO::Total function execution time is 0.0371110439300537 s and adjustment time is 0.0191197395324707 s ( 51.52 )
2026-02-10 21:50:18.95243 INFO::Formatting Data.
2026-02-10 21:50:18.953125 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:18.954133 INFO::Removing potential empty rows and columns
2026-02-10 21:50:18.955254 INFO::Found 0 missing values.
2026-02-10 21:50:18.958117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:18.958743 INFO::Done
2026-02-10 21:50:18.9593 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:18.962348 INFO::Starting hierarchical adjustment
2026-02-10 21:50:18.963155 INFO::Found 2 batches.
2026-02-10 21:50:18.963742 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:18.964378 INFO::Using default BPPARAM
2026-02-10 21:50:18.964962 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:18.965961 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-10 21:50:18.981568 INFO::Done
2026-02-10 21:50:18.982314 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:18.985454 INFO::ASW Batch was 0.479901050630153 prior to batch effect correction and is now 0.0750164073764222 .
2026-02-10 21:50:18.986176 INFO::ASW Label was 0.636917137095339 prior to batch effect correction and is now 0.881876954050019 .
2026-02-10 21:50:18.987035 INFO::Total function execution time is 0.0346395969390869 s and adjustment time is 0.0185451507568359 s ( 53.54 )
2026-02-10 21:50:18.999549 INFO::Formatting Data.
2026-02-10 21:50:19.000475 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:19.00157 INFO::Removing potential empty rows and columns
2026-02-10 21:50:19.002662 INFO::Found 0 missing values.
2026-02-10 21:50:19.005162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:19.005855 INFO::Done
2026-02-10 21:50:19.006439 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:19.008554 INFO::Starting hierarchical adjustment
2026-02-10 21:50:19.009388 INFO::Found 2 batches.
2026-02-10 21:50:19.009972 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:19.010645 INFO::Using default BPPARAM
2026-02-10 21:50:19.011216 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:19.012233 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-10 21:50:19.044556 INFO::Done
2026-02-10 21:50:19.045359 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:19.047572 INFO::ASW Batch was -0.109458297679117 prior to batch effect correction and is now -0.150627087606808 .
2026-02-10 21:50:19.048538 INFO::Total function execution time is 0.049091100692749 s and adjustment time is 0.0353083610534668 s ( 71.92 )
2026-02-10 21:50:19.061469 INFO::Formatting Data.
2026-02-10 21:50:19.062323 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:19.063285 INFO::Removing potential empty rows and columns
2026-02-10 21:50:19.064343 INFO::Found 0 missing values.
2026-02-10 21:50:19.065555 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.
2026-02-10 21:50:19.070424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:19.071136 INFO::Done
2026-02-10 21:50:19.071717 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:19.074853 INFO::Starting hierarchical adjustment
2026-02-10 21:50:19.075748 INFO::Found 2 batches.
2026-02-10 21:50:19.0764 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:19.077102 INFO::Using default BPPARAM
2026-02-10 21:50:19.077687 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:19.078766 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-10 21:50:19.095943 INFO::Done
2026-02-10 21:50:19.096709 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:19.099763 INFO::ASW Batch was 0.754255414732077 prior to batch effect correction and is now 0.0124256155321251 .
2026-02-10 21:50:19.100462 INFO::ASW Label was 0.291810791106803 prior to batch effect correction and is now 0.836497310355667 .
2026-02-10 21:50:19.101304 INFO::Total function execution time is 0.0399460792541504 s and adjustment time is 0.0203442573547363 s ( 50.93 )
2026-02-10 21:50:19.102122 INFO::Formatting Data.
2026-02-10 21:50:19.102764 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:19.103736 INFO::Removing potential empty rows and columns
2026-02-10 21:50:19.104789 INFO::Found 0 missing values.
2026-02-10 21:50:19.105766 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.
2026-02-10 21:50:19.110703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:19.111442 INFO::Done
2026-02-10 21:50:19.112024 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:19.115276 INFO::Starting hierarchical adjustment
2026-02-10 21:50:19.116182 INFO::Found 2 batches.
2026-02-10 21:50:19.11686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:19.117548 INFO::Using default BPPARAM
2026-02-10 21:50:19.118125 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:19.11923 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-10 21:50:19.136318 INFO::Done
2026-02-10 21:50:19.137117 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:19.140585 INFO::ASW Batch was 0.754255414732077 prior to batch effect correction and is now 0.0124256155321251 .
2026-02-10 21:50:19.14131 INFO::ASW Label was 0.291810791106803 prior to batch effect correction and is now 0.836497310355667 .
2026-02-10 21:50:19.142156 INFO::Total function execution time is 0.0400495529174805 s and adjustment time is 0.0202822685241699 s ( 50.64 )
2026-02-10 21:50:19.371543 INFO::Formatting Data.
2026-02-10 21:50:19.372426 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:19.373426 INFO::Removing potential empty rows and columns
2026-02-10 21:50:19.374592 INFO::Found 0 missing values.
2026-02-10 21:50:19.37789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:19.378618 INFO::Done
2026-02-10 21:50:19.379218 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:19.381504 INFO::Starting hierarchical adjustment
2026-02-10 21:50:19.382402 INFO::Found 3 batches.
2026-02-10 21:50:19.383051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:19.383786 INFO::Using default BPPARAM
2026-02-10 21:50:19.384392 INFO::Processing subtree level 1
2026-02-10 21:50:19.476176 INFO::Adjusting the last 1 batches sequentially
2026-02-10 21:50:19.478251 INFO::Done
2026-02-10 21:50:19.479017 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:19.481856 INFO::ASW Batch was -0.00923544754582384 prior to batch effect correction and is now -0.00923544754582384 .
2026-02-10 21:50:19.482971 INFO::Total function execution time is 0.111476421356201 s and adjustment time is 0.0960192680358887 s ( 86.13 )
2026-02-10 21:50:19.484124 INFO::Formatting Data.
2026-02-10 21:50:19.484837 INFO::Typecasting input to dataframe.
2026-02-10 21:50:19.485627 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:19.48663 INFO::Removing potential empty rows and columns
2026-02-10 21:50:19.487808 INFO::Found 0 missing values.
2026-02-10 21:50:19.49113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:19.491748 INFO::Done
2026-02-10 21:50:19.492292 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:19.494568 INFO::Starting hierarchical adjustment
2026-02-10 21:50:19.495314 INFO::Found 3 batches.
2026-02-10 21:50:19.495885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:19.496549 INFO::Using default BPPARAM
2026-02-10 21:50:19.497148 INFO::Processing subtree level 1
2026-02-10 21:50:19.589546 INFO::Adjusting the last 1 batches sequentially
2026-02-10 21:50:19.591645 INFO::Done
2026-02-10 21:50:19.592413 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:19.595178 INFO::ASW Batch was -0.00923544754582384 prior to batch effect correction and is now -0.00923544754582384 .
2026-02-10 21:50:19.596249 INFO::Total function execution time is 0.112100124359131 s and adjustment time is 0.0964486598968506 s ( 86.04 )
2026-02-10 21:50:19.611362 INFO::Formatting Data.
2026-02-10 21:50:19.61235 INFO::Typecasting input to dataframe.
2026-02-10 21:50:19.613321 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:19.614389 INFO::Removing potential empty rows and columns
2026-02-10 21:50:19.615605 INFO::Found 0 missing values.
2026-02-10 21:50:19.618891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:19.61946 INFO::Done
2026-02-10 21:50:19.620006 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:19.622295 INFO::Starting hierarchical adjustment
2026-02-10 21:50:19.623057 INFO::Found 3 batches.
2026-02-10 21:50:19.623631 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:19.624279 INFO::Using default BPPARAM
2026-02-10 21:50:19.624835 INFO::Processing subtree level 1
2026-02-10 21:50:19.724448 INFO::Adjusting the last 1 batches sequentially
2026-02-10 21:50:19.727171 INFO::Done
2026-02-10 21:50:19.727987 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:19.7312 INFO::ASW Batch was -0.00822377996165229 prior to batch effect correction and is now -0.00822377996165229 .
2026-02-10 21:50:19.732292 INFO::Total function execution time is 0.121044158935547 s and adjustment time is 0.104228019714355 s ( 86.11 )
2026-02-10 21:50:19.882048 INFO::Formatting Data.
2026-02-10 21:50:19.883044 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:19.884404 INFO::Removing potential empty rows and columns
2026-02-10 21:50:19.887414 INFO::Found 1000 missing values.
2026-02-10 21:50:19.908527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:19.909437 INFO::Done
2026-02-10 21:50:19.910061 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:19.916018 INFO::Starting hierarchical adjustment
2026-02-10 21:50:19.916848 INFO::Found 10 batches.
2026-02-10 21:50:19.917457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:19.91813 INFO::Using default BPPARAM
2026-02-10 21:50:19.918706 INFO::Processing subtree level 1
2026-02-10 21:50:20.072523 INFO::Processing subtree level 2
2026-02-10 21:50:20.227423 INFO::Adjusting the last 1 batches sequentially
2026-02-10 21:50:20.229639 INFO::Done
2026-02-10 21:50:20.230406 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:20.236447 INFO::ASW Batch was 0.481573626415143 prior to batch effect correction and is now 0.481573626415143 .
2026-02-10 21:50:20.237235 INFO::ASW Label was 0.331374603745769 prior to batch effect correction and is now 0.331374603745769 .
2026-02-10 21:50:20.238244 INFO::Total function execution time is 0.356293678283691 s and adjustment time is 0.312938690185547 s ( 87.83 )
2026-02-10 21:50:20.239141 INFO::Formatting Data.
2026-02-10 21:50:20.239814 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:20.241155 INFO::Removing potential empty rows and columns
2026-02-10 21:50:20.244245 INFO::Found 1000 missing values.
2026-02-10 21:50:20.264743 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:20.265521 INFO::Done
2026-02-10 21:50:20.266094 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:20.271745 INFO::Starting hierarchical adjustment
2026-02-10 21:50:20.272632 INFO::Found 10 batches.
2026-02-10 21:50:21.487797 INFO::Set up parallel execution backend with 2 workers
2026-02-10 21:50:21.489902 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-10 21:50:22.772567 INFO::Adjusting the last 2 batches sequentially
2026-02-10 21:50:22.774328 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-10 21:50:22.790919 INFO::Done
2026-02-10 21:50:22.791601 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:22.796023 INFO::ASW Batch was 0.481573626415143 prior to batch effect correction and is now 0.481573626415143 .
2026-02-10 21:50:22.796606 INFO::ASW Label was 0.331374603745769 prior to batch effect correction and is now 0.331374603745769 .
2026-02-10 21:50:22.797344 INFO::Total function execution time is 2.55822730064392 s and adjustment time is 2.51845264434814 s ( 98.45 )
2026-02-10 21:50:22.967523 INFO::Formatting Data.
2026-02-10 21:50:22.968585 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:22.969721 INFO::Removing potential empty rows and columns
2026-02-10 21:50:22.971012 INFO::Found 0 missing values.
2026-02-10 21:50:22.975506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:22.976182 INFO::Done
2026-02-10 21:50:22.976801 INFO::Acquiring quality metrics before batch effect correction.
2026-02-10 21:50:22.980306 INFO::Starting hierarchical adjustment
2026-02-10 21:50:22.981216 INFO::Found 3 batches.
2026-02-10 21:50:22.981851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-10 21:50:22.982638 INFO::Using default BPPARAM
2026-02-10 21:50:22.983265 INFO::Processing subtree level 1
2026-02-10 21:50:23.118356 INFO::Adjusting the last 1 batches sequentially
2026-02-10 21:50:23.120739 INFO::Done
2026-02-10 21:50:23.121556 INFO::Acquiring quality metrics after batch effect correction.
2026-02-10 21:50:23.125492 INFO::ASW Batch was 0.163905110150915 prior to batch effect correction and is now -0.149664346068143 .
2026-02-10 21:50:23.126209 INFO::ASW Label was -0.22127279120797 prior to batch effect correction and is now -0.175401088578916 .
2026-02-10 21:50:23.127392 INFO::Total function execution time is 0.159978866577148 s and adjustment time is 0.139671325683594 s ( 87.31 )
2026-02-10 21:50:23.275643 INFO::Formatting Data.
2026-02-10 21:50:23.276735 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.277809 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.278993 INFO::Found 2 missing values.
2026-02-10 21:50:23.282046 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.282647 INFO::Done
2026-02-10 21:50:23.313865 INFO::Found NA in Reference column
2026-02-10 21:50:23.325105 INFO::Require at least two references per batch.
2026-02-10 21:50:23.347918 INFO::Formatting Data.
2026-02-10 21:50:23.348773 INFO::Recognized SummarizedExperiment
2026-02-10 21:50:23.349386 INFO::Typecasting input to dataframe.
2026-02-10 21:50:23.360016 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.361386 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.365484 INFO::Found 0 missing values.
2026-02-10 21:50:23.373351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.374173 INFO::Done
2026-02-10 21:50:23.391165 INFO::Formatting Data.
2026-02-10 21:50:23.392014 INFO::Recognized SummarizedExperiment
2026-02-10 21:50:23.392644 INFO::Typecasting input to dataframe.
2026-02-10 21:50:23.412146 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.413625 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.41789 INFO::Found 0 missing values.
2026-02-10 21:50:23.431122 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.431951 INFO::Done
2026-02-10 21:50:23.450964 INFO::Formatting Data.
2026-02-10 21:50:23.451807 INFO::Recognized SummarizedExperiment
2026-02-10 21:50:23.452412 INFO::Typecasting input to dataframe.
2026-02-10 21:50:23.471383 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.47273 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.474066 INFO::Found 0 missing values.
2026-02-10 21:50:23.475172 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.
2026-02-10 21:50:23.480143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.480807 INFO::Done
2026-02-10 21:50:23.492635 INFO::Formatting Data.
2026-02-10 21:50:23.49361 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.494652 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.495752 INFO::Found 0 missing values.
2026-02-10 21:50:23.498906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.499483 INFO::Done
2026-02-10 21:50:23.511946 INFO::Formatting Data.
2026-02-10 21:50:23.512839 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.513849 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.51501 INFO::Found 0 missing values.
2026-02-10 21:50:23.518383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.519014 INFO::Done
2026-02-10 21:50:23.553349 INFO::Formatting Data.
2026-02-10 21:50:23.554413 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.555619 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.556904 INFO::Found 1 missing values.
2026-02-10 21:50:23.559738 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.560362 INFO::Done
2026-02-10 21:50:23.580183 INFO::Formatting Data.
2026-02-10 21:50:23.58104 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.581962 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.582929 INFO::Found 2 missing values.
2026-02-10 21:50:23.583863 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.
2026-02-10 21:50:23.58632 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.586862 INFO::Done
2026-02-10 21:50:23.59678 INFO::Formatting Data.
2026-02-10 21:50:23.597542 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.598443 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.599328 INFO::Found 2 missing values.
2026-02-10 21:50:23.600876 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.601432 INFO::Done
2026-02-10 21:50:23.612127 INFO::Formatting Data.
2026-02-10 21:50:23.61299 INFO::Typecasting input to dataframe.
2026-02-10 21:50:23.613837 INFO::Replacing NaNs with NAs.
2026-02-10 21:50:23.61473 INFO::Removing potential empty rows and columns
2026-02-10 21:50:23.615764 INFO::Found 0 missing values.
2026-02-10 21:50:23.618809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-10 21:50:23.619415 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
18.221 4.214 21.893
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.353 | 1.117 | 16.659 | |
| compute_asw | 0.024 | 0.000 | 0.025 | |
| count_existing | 0.013 | 0.000 | 0.014 | |
| generate_data_covariables | 0.010 | 0.002 | 0.012 | |
| generate_dataset | 0.009 | 0.002 | 0.011 | |