Yannis Schumann
| Snapshot Date: 2026-02-25 13:40 -0500 (Wed, 25 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 2026-02-26 11:32 -0500 (Thu, 26 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" | 4877 |
| 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 169/2357 | 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: 2026-02-25 21:35:07 -0500 (Wed, 25 Feb 2026) |
| EndedAt: 2026-02-25 21:36:37 -0500 (Wed, 25 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 23.611 1.254 16.884
* 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")
2026-02-25 21:35:59.125179 INFO::Formatting Data.
2026-02-25 21:35:59.126795 INFO::Replacing NaNs with NAs.
2026-02-25 21:35:59.154826 INFO::Removing potential empty rows and columns
2026-02-25 21:35:59.429195 INFO::Found 0 missing values.
2026-02-25 21:35:59.43293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:35:59.433664 INFO::Done
2026-02-25 21:35:59.434289 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:35:59.44661 INFO::Starting hierarchical adjustment
2026-02-25 21:35:59.447501 INFO::Found 3 batches.
2026-02-25 21:35:59.448103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:35:59.449307 INFO::Using default BPPARAM
2026-02-25 21:35:59.449925 INFO::Processing subtree level 1
2026-02-25 21:35:59.585591 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:35:59.587776 INFO::Done
2026-02-25 21:35:59.5886 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:35:59.591806 INFO::ASW Batch was -0.129045648291504 prior to batch effect correction and is now -0.129045648291504 .
2026-02-25 21:35:59.593037 INFO::Total function execution time is 0.468577146530151 s and adjustment time is 0.140437602996826 s ( 29.97 )
2026-02-25 21:35:59.609243 INFO::Formatting Data.
2026-02-25 21:35:59.610169 INFO::Replacing NaNs with NAs.
2026-02-25 21:35:59.611234 INFO::Removing potential empty rows and columns
2026-02-25 21:35:59.612552 INFO::Found 0 missing values.
2026-02-25 21:35:59.613672 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.
2026-02-25 21:35:59.626384 INFO::Formatting Data.
2026-02-25 21:35:59.627239 INFO::Replacing NaNs with NAs.
2026-02-25 21:35:59.628253 INFO::Removing potential empty rows and columns
2026-02-25 21:35:59.629431 INFO::Found 0 missing values.
2026-02-25 21:35:59.630457 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.
2026-02-25 21:35:59.648454 INFO::Formatting Data.
2026-02-25 21:35:59.649431 INFO::Replacing NaNs with NAs.
2026-02-25 21:35:59.650681 INFO::Removing potential empty rows and columns
2026-02-25 21:35:59.652154 INFO::Found 0 missing values.
2026-02-25 21:35:59.653402 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.
2026-02-25 21:35:59.659769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:35:59.66064 INFO::Done
2026-02-25 21:35:59.661351 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:35:59.664111 INFO::Starting hierarchical adjustment
2026-02-25 21:35:59.665089 INFO::Found 2 batches.
2026-02-25 21:35:59.666071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:35:59.666929 INFO::Using default BPPARAM
2026-02-25 21:35:59.66764 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:35:59.668866 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:35:59.69714 INFO::Done
2026-02-25 21:35:59.698074 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:35:59.701238 INFO::ASW Batch was 0.106976086344965 prior to batch effect correction and is now -0.10609114656841 .
2026-02-25 21:35:59.702282 INFO::Total function execution time is 0.0539402961730957 s and adjustment time is 0.0321841239929199 s ( 59.67 )
2026-02-25 21:35:59.706012 INFO::Formatting Data.
2026-02-25 21:35:59.7068 INFO::Replacing NaNs with NAs.
2026-02-25 21:35:59.717196 INFO::Formatting Data.
2026-02-25 21:35:59.718137 INFO::Replacing NaNs with NAs.
2026-02-25 21:35:59.719266 INFO::Removing potential empty rows and columns
2026-02-25 21:35:59.720493 INFO::Found 0 missing values.
2026-02-25 21:35:59.724056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:35:59.724695 INFO::Done
2026-02-25 21:35:59.725316 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:35:59.72781 INFO::Starting hierarchical adjustment
2026-02-25 21:35:59.728676 INFO::Found 2 batches.
2026-02-25 21:35:59.729282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:35:59.730005 INFO::Using default BPPARAM
2026-02-25 21:35:59.730603 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:35:59.73174 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:35:59.788276 INFO::Done
2026-02-25 21:35:59.789184 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:35:59.792074 INFO::ASW Batch was 0.0153353322622593 prior to batch effect correction and is now -0.120288350512814 .
2026-02-25 21:35:59.793104 INFO::Total function execution time is 0.0759735107421875 s and adjustment time is 0.0597000122070312 s ( 78.58 )
2026-02-25 21:35:59.794435 INFO::Formatting Data.
2026-02-25 21:35:59.795184 INFO::Replacing NaNs with NAs.
2026-02-25 21:35:59.796231 INFO::Removing potential empty rows and columns
2026-02-25 21:35:59.797494 INFO::Found 0 missing values.
2026-02-25 21:35:59.800884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:35:59.80154 INFO::Done
2026-02-25 21:35:59.802149 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:35:59.804667 INFO::Starting hierarchical adjustment
2026-02-25 21:35:59.805525 INFO::Found 2 batches.
2026-02-25 21:35:59.806148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:35:59.806926 INFO::Using default BPPARAM
2026-02-25 21:35:59.807539 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:35:59.808675 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:35:59.827954 INFO::Done
2026-02-25 21:35:59.82884 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:35:59.831402 INFO::ASW Batch was 0.0153353322622593 prior to batch effect correction and is now -0.120288350512814 .
2026-02-25 21:35:59.832364 INFO::Total function execution time is 0.0379557609558105 s and adjustment time is 0.0225677490234375 s ( 59.46 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-25 21:36:02.934257 INFO::Formatting Data.
2026-02-25 21:36:02.935017 INFO::Recognized SummarizedExperiment
2026-02-25 21:36:02.935537 INFO::Typecasting input to dataframe.
2026-02-25 21:36:02.965762 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:02.967131 INFO::Removing potential empty rows and columns
2026-02-25 21:36:02.971178 INFO::Found 0 missing values.
2026-02-25 21:36:02.978775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:02.97944 INFO::Done
2026-02-25 21:36:02.97998 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:02.983598 INFO::Starting hierarchical adjustment
2026-02-25 21:36:02.984311 INFO::Found 2 batches.
2026-02-25 21:36:02.984849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:02.985965 INFO::Using default BPPARAM
2026-02-25 21:36:02.986515 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:02.987489 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:36:03.044055 INFO::Done
2026-02-25 21:36:03.044832 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:03.048473 INFO::ASW Batch was 0.00417793929582237 prior to batch effect correction and is now -0.0943819318554515 .
2026-02-25 21:36:03.049435 INFO::Total function execution time is 0.115411996841431 s and adjustment time is 0.0598607063293457 s ( 51.87 )
Warning: stack imbalance in '{', 73 then 75
2026-02-25 21:36:03.0686 INFO::Formatting Data.
2026-02-25 21:36:03.069407 INFO::Recognized SummarizedExperiment
2026-02-25 21:36:03.069972 INFO::Typecasting input to dataframe.
2026-02-25 21:36:03.079593 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:03.080784 INFO::Removing potential empty rows and columns
2026-02-25 21:36:03.084762 INFO::Found 0 missing values.
2026-02-25 21:36:03.092449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:03.093116 INFO::Done
2026-02-25 21:36:03.093668 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:03.097331 INFO::Starting hierarchical adjustment
2026-02-25 21:36:03.098101 INFO::Found 2 batches.
2026-02-25 21:36:03.098642 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:03.099271 INFO::Using default BPPARAM
2026-02-25 21:36:03.099809 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:03.100819 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:36:03.127293 INFO::Done
2026-02-25 21:36:03.128089 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:03.13179 INFO::ASW Batch was -0.0175398714504877 prior to batch effect correction and is now -0.0175398714504877 .
2026-02-25 21:36:03.132732 INFO::Total function execution time is 0.0641031265258789 s and adjustment time is 0.0293004512786865 s ( 45.71 )
2026-02-25 21:36:03.152144 INFO::Formatting Data.
2026-02-25 21:36:03.153015 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:03.153961 INFO::Removing potential empty rows and columns
2026-02-25 21:36:03.155016 INFO::Found 0 missing values.
2026-02-25 21:36:03.158064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:03.158609 INFO::Done
2026-02-25 21:36:03.159132 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:03.161274 INFO::Starting hierarchical adjustment
2026-02-25 21:36:03.161987 INFO::Found 3 batches.
2026-02-25 21:36:03.162533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:03.163142 INFO::Using default BPPARAM
2026-02-25 21:36:03.163674 INFO::Processing subtree level 1
2026-02-25 21:36:03.309041 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:36:03.311404 INFO::Done
2026-02-25 21:36:03.312258 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:03.315204 INFO::ASW Batch was -0.0413644838116805 prior to batch effect correction and is now -0.174505911076983 .
2026-02-25 21:36:03.31633 INFO::Total function execution time is 0.164213180541992 s and adjustment time is 0.14947772026062 s ( 91.03 )
2026-02-25 21:36:03.333056 INFO::Skipping initial DF formatting
2026-02-25 21:36:03.334016 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:03.338634 INFO::Starting hierarchical adjustment
2026-02-25 21:36:03.339639 INFO::Found 5 batches.
2026-02-25 21:36:03.340255 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:03.340957 INFO::Using default BPPARAM
2026-02-25 21:36:03.341536 INFO::Processing subtree level 1
2026-02-25 21:36:03.597811 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:03.599711 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:36:03.620919 INFO::Done
2026-02-25 21:36:03.62184 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:03.683813 INFO::ASW Batch was 0.523939172835244 prior to batch effect correction and is now 0.523939172835244 .
2026-02-25 21:36:03.68471 INFO::ASW Label was 0.359814524635549 prior to batch effect correction and is now 0.359814524635549 .
2026-02-25 21:36:03.685694 INFO::Total function execution time is 0.352789878845215 s and adjustment time is 0.281478643417358 s ( 79.79 )
2026-02-25 21:36:03.707497 INFO::Formatting Data.
2026-02-25 21:36:03.708465 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:03.709596 INFO::Removing potential empty rows and columns
2026-02-25 21:36:03.710814 INFO::Found 0 missing values.
2026-02-25 21:36:03.715518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:03.716135 INFO::Done
2026-02-25 21:36:03.716683 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:03.720093 INFO::Starting hierarchical adjustment
2026-02-25 21:36:03.720872 INFO::Found 5 batches.
2026-02-25 21:36:03.721464 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:03.722196 INFO::Using default BPPARAM
2026-02-25 21:36:03.722833 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.
2026-02-25 21:36:03.860485 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:03.869117 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:36:03.889021 INFO::Done
2026-02-25 21:36:03.889802 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:03.893498 INFO::ASW Batch was 0.448707658697249 prior to batch effect correction and is now -0.0187733038276029 .
2026-02-25 21:36:03.894195 INFO::ASW Label was 0.228210190359777 prior to batch effect correction and is now 0.652950637654513 .
2026-02-25 21:36:03.895082 INFO::Total function execution time is 0.187773704528809 s and adjustment time is 0.168287992477417 s ( 89.62 )
2026-02-25 21:36:03.895973 INFO::Formatting Data.
2026-02-25 21:36:03.896687 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:03.897626 INFO::Removing potential empty rows and columns
2026-02-25 21:36:03.898695 INFO::Found 0 missing values.
2026-02-25 21:36:03.903062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:03.903652 INFO::Done
2026-02-25 21:36:03.904197 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:03.907416 INFO::Starting hierarchical adjustment
2026-02-25 21:36:03.908119 INFO::Found 5 batches.
2026-02-25 21:36:03.908677 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:03.909356 INFO::Using default BPPARAM
2026-02-25 21:36:03.909899 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.
2026-02-25 21:36:04.036402 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:04.03807 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:36:04.054521 INFO::Done
2026-02-25 21:36:04.055221 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.058584 INFO::ASW Batch was 0.448707658697249 prior to batch effect correction and is now -0.0187733038276029 .
2026-02-25 21:36:04.059208 INFO::ASW Label was 0.228210190359777 prior to batch effect correction and is now 0.652950637654513 .
2026-02-25 21:36:04.060085 INFO::Total function execution time is 0.164114236831665 s and adjustment time is 0.146513700485229 s ( 89.28 )
2026-02-25 21:36:04.075463 INFO::Formatting Data.
2026-02-25 21:36:04.076282 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.077247 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.078364 INFO::Found 0 missing values.
2026-02-25 21:36:04.082506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.083076 INFO::Done
2026-02-25 21:36:04.083623 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.086676 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.0874 INFO::Found 5 batches.
2026-02-25 21:36:04.087941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.088581 INFO::Using default BPPARAM
2026-02-25 21:36:04.089118 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.
2026-02-25 21:36:04.226098 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:04.229008 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:36:04.248052 INFO::Done
2026-02-25 21:36:04.248902 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.252646 INFO::ASW Batch was 0.325450478331734 prior to batch effect correction and is now 0.0774426039835053 .
2026-02-25 21:36:04.253408 INFO::ASW Label was 0.633104612964845 prior to batch effect correction and is now 0.730149247240399 .
2026-02-25 21:36:04.254414 INFO::Total function execution time is 0.179003238677979 s and adjustment time is 0.16075325012207 s ( 89.8 )
2026-02-25 21:36:04.255373 INFO::Formatting Data.
2026-02-25 21:36:04.256129 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.257201 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.258395 INFO::Found 0 missing values.
2026-02-25 21:36:04.263193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.264006 INFO::Done
2026-02-25 21:36:04.264623 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.268066 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.268885 INFO::Found 5 batches.
2026-02-25 21:36:04.269529 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.270225 INFO::Using default BPPARAM
2026-02-25 21:36:04.270828 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.
2026-02-25 21:36:04.400144 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:04.401954 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:36:04.41992 INFO::Done
2026-02-25 21:36:04.420735 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.424608 INFO::ASW Batch was 0.325450478331734 prior to batch effect correction and is now 0.0774426039835053 .
2026-02-25 21:36:04.425251 INFO::ASW Label was 0.633104612964845 prior to batch effect correction and is now 0.730149247240399 .
2026-02-25 21:36:04.426143 INFO::Total function execution time is 0.170794248580933 s and adjustment time is 0.1511549949646 s ( 88.5 )
2026-02-25 21:36:04.440278 INFO::Formatting Data.
2026-02-25 21:36:04.441062 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.441996 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.443054 INFO::Found 0 missing values.
2026-02-25 21:36:04.445779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.446359 INFO::Done
2026-02-25 21:36:04.446914 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.44989 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.450616 INFO::Found 2 batches.
2026-02-25 21:36:04.451155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.451789 INFO::Using default BPPARAM
2026-02-25 21:36:04.452338 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:04.453249 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:36:04.467783 INFO::Done
2026-02-25 21:36:04.468458 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.471421 INFO::ASW Batch was 0.587740775668573 prior to batch effect correction and is now -0.021412499332994 .
2026-02-25 21:36:04.472025 INFO::ASW Label was 0.517758677861555 prior to batch effect correction and is now 0.925499541468312 .
2026-02-25 21:36:04.472878 INFO::Total function execution time is 0.0326621532440186 s and adjustment time is 0.0173203945159912 s ( 53.03 )
2026-02-25 21:36:04.473682 INFO::Formatting Data.
2026-02-25 21:36:04.474299 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.475174 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.476171 INFO::Found 0 missing values.
2026-02-25 21:36:04.47884 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.479423 INFO::Done
2026-02-25 21:36:04.479945 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.482844 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.483568 INFO::Found 2 batches.
2026-02-25 21:36:04.484097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.484713 INFO::Using default BPPARAM
2026-02-25 21:36:04.485253 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:04.486188 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-25 21:36:04.500579 INFO::Done
2026-02-25 21:36:04.501199 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.504079 INFO::ASW Batch was 0.587740775668573 prior to batch effect correction and is now -0.021412499332994 .
2026-02-25 21:36:04.504694 INFO::ASW Label was 0.517758677861555 prior to batch effect correction and is now 0.925499541468312 .
2026-02-25 21:36:04.505487 INFO::Total function execution time is 0.0318150520324707 s and adjustment time is 0.0171668529510498 s ( 53.96 )
2026-02-25 21:36:04.516688 INFO::Formatting Data.
2026-02-25 21:36:04.517419 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.518263 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.519176 INFO::Found 0 missing values.
2026-02-25 21:36:04.521225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.521771 INFO::Done
2026-02-25 21:36:04.522305 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.524176 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.524885 INFO::Found 2 batches.
2026-02-25 21:36:04.525453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.526044 INFO::Using default BPPARAM
2026-02-25 21:36:04.526618 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:04.527539 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:36:04.558481 INFO::Done
2026-02-25 21:36:04.559208 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.561218 INFO::ASW Batch was 0.162819784694717 prior to batch effect correction and is now -0.173397939454847 .
2026-02-25 21:36:04.562046 INFO::Total function execution time is 0.0454020500183105 s and adjustment time is 0.0336987972259521 s ( 74.22 )
2026-02-25 21:36:04.573846 INFO::Formatting Data.
2026-02-25 21:36:04.574703 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.575646 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.576709 INFO::Found 0 missing values.
2026-02-25 21:36:04.577948 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.
2026-02-25 21:36:04.582757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.583326 INFO::Done
2026-02-25 21:36:04.583879 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.586997 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.587773 INFO::Found 2 batches.
2026-02-25 21:36:04.588315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.589001 INFO::Using default BPPARAM
2026-02-25 21:36:04.589567 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:04.590558 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:36:04.607816 INFO::Done
2026-02-25 21:36:04.608562 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.611647 INFO::ASW Batch was 0.451622180371582 prior to batch effect correction and is now 0.0672313814870254 .
2026-02-25 21:36:04.612265 INFO::ASW Label was 0.652950225431583 prior to batch effect correction and is now 0.891905777161278 .
2026-02-25 21:36:04.613147 INFO::Total function execution time is 0.039395809173584 s and adjustment time is 0.0201842784881592 s ( 51.23 )
2026-02-25 21:36:04.613979 INFO::Formatting Data.
2026-02-25 21:36:04.614662 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.615649 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.616715 INFO::Found 0 missing values.
2026-02-25 21:36:04.617671 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.
2026-02-25 21:36:04.622516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.623095 INFO::Done
2026-02-25 21:36:04.623639 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.62671 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.627476 INFO::Found 2 batches.
2026-02-25 21:36:04.628065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.628689 INFO::Using default BPPARAM
2026-02-25 21:36:04.629236 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:04.6302 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:36:04.656102 INFO::Done
2026-02-25 21:36:04.657002 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.660557 INFO::ASW Batch was 0.451622180371582 prior to batch effect correction and is now 0.0672313814870254 .
2026-02-25 21:36:04.661243 INFO::ASW Label was 0.652950225431583 prior to batch effect correction and is now 0.891905777161278 .
2026-02-25 21:36:04.662166 INFO::Total function execution time is 0.0481777191162109 s and adjustment time is 0.0287175178527832 s ( 59.61 )
2026-02-25 21:36:04.871234 INFO::Formatting Data.
2026-02-25 21:36:04.872075 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.873008 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.874139 INFO::Found 0 missing values.
2026-02-25 21:36:04.87716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.877715 INFO::Done
2026-02-25 21:36:04.87824 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.880261 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.880974 INFO::Found 3 batches.
2026-02-25 21:36:04.881521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.882192 INFO::Using default BPPARAM
2026-02-25 21:36:04.88274 INFO::Processing subtree level 1
2026-02-25 21:36:04.972494 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:36:04.974571 INFO::Done
2026-02-25 21:36:04.975306 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:04.978073 INFO::ASW Batch was -0.0735593952132203 prior to batch effect correction and is now -0.0735593952132203 .
2026-02-25 21:36:04.97923 INFO::Total function execution time is 0.107992172241211 s and adjustment time is 0.0937035083770752 s ( 86.77 )
2026-02-25 21:36:04.980428 INFO::Formatting Data.
2026-02-25 21:36:04.981117 INFO::Typecasting input to dataframe.
2026-02-25 21:36:04.981947 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:04.982985 INFO::Removing potential empty rows and columns
2026-02-25 21:36:04.984182 INFO::Found 0 missing values.
2026-02-25 21:36:04.987509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:04.988167 INFO::Done
2026-02-25 21:36:04.988743 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:04.99102 INFO::Starting hierarchical adjustment
2026-02-25 21:36:04.991796 INFO::Found 3 batches.
2026-02-25 21:36:04.992356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:04.993092 INFO::Using default BPPARAM
2026-02-25 21:36:04.993726 INFO::Processing subtree level 1
2026-02-25 21:36:05.084692 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:36:05.086732 INFO::Done
2026-02-25 21:36:05.087492 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:05.09012 INFO::ASW Batch was -0.0735593952132203 prior to batch effect correction and is now -0.0735593952132203 .
2026-02-25 21:36:05.091163 INFO::Total function execution time is 0.110738039016724 s and adjustment time is 0.095078706741333 s ( 85.86 )
2026-02-25 21:36:05.105863 INFO::Formatting Data.
2026-02-25 21:36:05.106865 INFO::Typecasting input to dataframe.
2026-02-25 21:36:05.107796 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:05.10881 INFO::Removing potential empty rows and columns
2026-02-25 21:36:05.109994 INFO::Found 0 missing values.
2026-02-25 21:36:05.113182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:05.113779 INFO::Done
2026-02-25 21:36:05.114334 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:05.116554 INFO::Starting hierarchical adjustment
2026-02-25 21:36:05.117303 INFO::Found 3 batches.
2026-02-25 21:36:05.117869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:05.118524 INFO::Using default BPPARAM
2026-02-25 21:36:05.119068 INFO::Processing subtree level 1
2026-02-25 21:36:05.212865 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:36:05.214991 INFO::Done
2026-02-25 21:36:05.215707 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:05.218432 INFO::ASW Batch was -0.0920999663628284 prior to batch effect correction and is now -0.0920999663628284 .
2026-02-25 21:36:05.219452 INFO::Total function execution time is 0.11367654800415 s and adjustment time is 0.0978081226348877 s ( 86.04 )
2026-02-25 21:36:05.371321 INFO::Formatting Data.
2026-02-25 21:36:05.372383 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:05.373621 INFO::Removing potential empty rows and columns
2026-02-25 21:36:05.376806 INFO::Found 1000 missing values.
2026-02-25 21:36:05.397721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:05.398631 INFO::Done
2026-02-25 21:36:05.399279 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:05.405197 INFO::Starting hierarchical adjustment
2026-02-25 21:36:05.406168 INFO::Found 10 batches.
2026-02-25 21:36:05.406798 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:05.407531 INFO::Using default BPPARAM
2026-02-25 21:36:05.40812 INFO::Processing subtree level 1
2026-02-25 21:36:05.562664 INFO::Processing subtree level 2
2026-02-25 21:36:05.715835 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:36:05.718103 INFO::Done
2026-02-25 21:36:05.718999 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:05.724952 INFO::ASW Batch was 0.482083995146986 prior to batch effect correction and is now 0.482083995146986 .
2026-02-25 21:36:05.725808 INFO::ASW Label was 0.327462127319042 prior to batch effect correction and is now 0.327462127319042 .
2026-02-25 21:36:05.726995 INFO::Total function execution time is 0.35579252243042 s and adjustment time is 0.312097072601318 s ( 87.72 )
2026-02-25 21:36:05.727918 INFO::Formatting Data.
2026-02-25 21:36:05.728625 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:05.729987 INFO::Removing potential empty rows and columns
2026-02-25 21:36:05.733018 INFO::Found 1000 missing values.
2026-02-25 21:36:05.753811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:05.754847 INFO::Done
2026-02-25 21:36:05.75556 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:05.761812 INFO::Starting hierarchical adjustment
2026-02-25 21:36:05.763123 INFO::Found 10 batches.
2026-02-25 21:36:07.300697 INFO::Set up parallel execution backend with 2 workers
2026-02-25 21:36:07.302903 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-25 21:36:08.674731 INFO::Adjusting the last 2 batches sequentially
2026-02-25 21:36:08.676771 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-25 21:36:08.693582 INFO::Done
2026-02-25 21:36:08.694283 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:08.698851 INFO::ASW Batch was 0.482083995146986 prior to batch effect correction and is now 0.482083995146986 .
2026-02-25 21:36:08.699471 INFO::ASW Label was 0.327462127319042 prior to batch effect correction and is now 0.327462127319042 .
2026-02-25 21:36:08.700216 INFO::Total function execution time is 2.97235560417175 s and adjustment time is 2.9309561252594 s ( 98.61 )
2026-02-25 21:36:08.841743 INFO::Formatting Data.
2026-02-25 21:36:08.842568 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:08.843507 INFO::Removing potential empty rows and columns
2026-02-25 21:36:08.844591 INFO::Found 0 missing values.
2026-02-25 21:36:08.848275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:08.848828 INFO::Done
2026-02-25 21:36:08.849333 INFO::Acquiring quality metrics before batch effect correction.
2026-02-25 21:36:08.852103 INFO::Starting hierarchical adjustment
2026-02-25 21:36:08.852808 INFO::Found 3 batches.
2026-02-25 21:36:08.853327 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-25 21:36:08.853978 INFO::Using default BPPARAM
2026-02-25 21:36:08.854505 INFO::Processing subtree level 1
2026-02-25 21:36:08.95816 INFO::Adjusting the last 1 batches sequentially
2026-02-25 21:36:08.963498 INFO::Done
2026-02-25 21:36:08.964281 INFO::Acquiring quality metrics after batch effect correction.
2026-02-25 21:36:08.967815 INFO::ASW Batch was 0.17168073053348 prior to batch effect correction and is now -0.182946294926242 .
2026-02-25 21:36:08.96855 INFO::ASW Label was -0.171324865633152 prior to batch effect correction and is now 0.136068959555527 .
2026-02-25 21:36:08.9696 INFO::Total function execution time is 0.127900838851929 s and adjustment time is 0.110759258270264 s ( 86.6 )
2026-02-25 21:36:09.10886 INFO::Formatting Data.
2026-02-25 21:36:09.109779 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.110726 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.111803 INFO::Found 2 missing values.
2026-02-25 21:36:09.114707 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.115284 INFO::Done
2026-02-25 21:36:09.142233 INFO::Found NA in Reference column
2026-02-25 21:36:09.151315 INFO::Require at least two references per batch.
2026-02-25 21:36:09.170835 INFO::Formatting Data.
2026-02-25 21:36:09.171572 INFO::Recognized SummarizedExperiment
2026-02-25 21:36:09.172104 INFO::Typecasting input to dataframe.
2026-02-25 21:36:09.181217 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.182318 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.185858 INFO::Found 0 missing values.
2026-02-25 21:36:09.192651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.193268 INFO::Done
2026-02-25 21:36:09.208298 INFO::Formatting Data.
2026-02-25 21:36:09.209027 INFO::Recognized SummarizedExperiment
2026-02-25 21:36:09.209558 INFO::Typecasting input to dataframe.
2026-02-25 21:36:09.22578 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.226989 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.230572 INFO::Found 0 missing values.
2026-02-25 21:36:09.241531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.242179 INFO::Done
2026-02-25 21:36:09.257025 INFO::Formatting Data.
2026-02-25 21:36:09.257764 INFO::Recognized SummarizedExperiment
2026-02-25 21:36:09.258285 INFO::Typecasting input to dataframe.
2026-02-25 21:36:09.274203 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.275219 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.276297 INFO::Found 0 missing values.
2026-02-25 21:36:09.277188 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.
2026-02-25 21:36:09.281394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.281926 INFO::Done
2026-02-25 21:36:09.291703 INFO::Formatting Data.
2026-02-25 21:36:09.292485 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.293358 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.294384 INFO::Found 0 missing values.
2026-02-25 21:36:09.297205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.297739 INFO::Done
2026-02-25 21:36:09.309122 INFO::Formatting Data.
2026-02-25 21:36:09.309884 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.310735 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.311786 INFO::Found 0 missing values.
2026-02-25 21:36:09.314614 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.315127 INFO::Done
2026-02-25 21:36:09.343927 INFO::Formatting Data.
2026-02-25 21:36:09.34474 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.345725 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.346855 INFO::Found 1 missing values.
2026-02-25 21:36:09.349335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.349885 INFO::Done
2026-02-25 21:36:09.368049 INFO::Formatting Data.
2026-02-25 21:36:09.368861 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.369726 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.370677 INFO::Found 2 missing values.
2026-02-25 21:36:09.371545 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.
2026-02-25 21:36:09.373929 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.374457 INFO::Done
2026-02-25 21:36:09.384053 INFO::Formatting Data.
2026-02-25 21:36:09.384812 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.385644 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.386549 INFO::Found 2 missing values.
2026-02-25 21:36:09.388057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.388614 INFO::Done
2026-02-25 21:36:09.398427 INFO::Formatting Data.
2026-02-25 21:36:09.399155 INFO::Typecasting input to dataframe.
2026-02-25 21:36:09.399915 INFO::Replacing NaNs with NAs.
2026-02-25 21:36:09.400741 INFO::Removing potential empty rows and columns
2026-02-25 21:36:09.401708 INFO::Found 0 missing values.
2026-02-25 21:36:09.404485 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-25 21:36:09.404993 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
17.711 4.980 22.183
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.611 | 1.254 | 16.884 | |
| compute_asw | 0.024 | 0.001 | 0.025 | |
| count_existing | 0.012 | 0.002 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |