Yannis Schumann
| Snapshot Date: 2026-02-27 13:40 -0500 (Fri, 27 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 Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-28 11:35 -0500 (Sat, 28 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 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4570 |
| 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz |
| StartedAt: 2026-02-27 18:52:11 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 18:52:48 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 37.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 10.375 0.403 7.727
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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: aarch64-apple-darwin20
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")
2026-02-27 18:52:38.140986 INFO::Formatting Data.
2026-02-27 18:52:38.142597 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:38.147587 INFO::Removing potential empty rows and columns
2026-02-27 18:52:38.261651 INFO::Found 0 missing values.
2026-02-27 18:52:38.262811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:38.263009 INFO::Done
2026-02-27 18:52:38.263193 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:38.272017 INFO::Starting hierarchical adjustment
2026-02-27 18:52:38.272365 INFO::Found 3 batches.
2026-02-27 18:52:38.272573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:38.273081 INFO::Using default BPPARAM
2026-02-27 18:52:38.27333 INFO::Processing subtree level 1
2026-02-27 18:52:38.35892 INFO::Adjusting the last 1 batches sequentially
2026-02-27 18:52:38.359979 INFO::Done
2026-02-27 18:52:38.360255 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:38.361475 INFO::ASW Batch was -0.0593804776886444 prior to batch effect correction and is now -0.0593804776886444 .
2026-02-27 18:52:38.361941 INFO::Total function execution time is 0.221504926681519 s and adjustment time is 0.0876820087432861 s ( 39.58 )
2026-02-27 18:52:38.369518 INFO::Formatting Data.
2026-02-27 18:52:38.369802 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:38.370155 INFO::Removing potential empty rows and columns
2026-02-27 18:52:38.370676 INFO::Found 0 missing values.
2026-02-27 18:52:38.371029 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.
2026-02-27 18:52:38.375818 INFO::Formatting Data.
2026-02-27 18:52:38.37607 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:38.376377 INFO::Removing potential empty rows and columns
2026-02-27 18:52:38.376799 INFO::Found 0 missing values.
2026-02-27 18:52:38.377145 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.
2026-02-27 18:52:38.385291 INFO::Formatting Data.
2026-02-27 18:52:38.385554 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:38.385923 INFO::Removing potential empty rows and columns
2026-02-27 18:52:38.386336 INFO::Found 0 missing values.
2026-02-27 18:52:38.38669 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.
2026-02-27 18:52:38.388512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:38.388729 INFO::Done
2026-02-27 18:52:38.388924 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:38.389705 INFO::Starting hierarchical adjustment
2026-02-27 18:52:38.389945 INFO::Found 2 batches.
2026-02-27 18:52:38.390129 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:38.390754 INFO::Using default BPPARAM
2026-02-27 18:52:38.390915 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:38.391236 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 18:52:38.402105 INFO::Done
2026-02-27 18:52:38.402437 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:38.403267 INFO::ASW Batch was 0.00484332701403374 prior to batch effect correction and is now -0.112593335840398 .
2026-02-27 18:52:38.403566 INFO::Total function execution time is 0.0183091163635254 s and adjustment time is 0.0121839046478271 s ( 66.55 )
2026-02-27 18:52:38.40488 INFO::Formatting Data.
2026-02-27 18:52:38.405228 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:38.411452 INFO::Formatting Data.
2026-02-27 18:52:38.411927 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:38.413161 INFO::Removing potential empty rows and columns
2026-02-27 18:52:38.413617 INFO::Found 0 missing values.
2026-02-27 18:52:38.415473 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:38.41577 INFO::Done
2026-02-27 18:52:38.415967 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:38.416864 INFO::Starting hierarchical adjustment
2026-02-27 18:52:38.417613 INFO::Found 2 batches.
2026-02-27 18:52:38.417805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:38.418044 INFO::Using default BPPARAM
2026-02-27 18:52:38.439648 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:38.440887 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 18:52:38.446435 INFO::Done
2026-02-27 18:52:38.446659 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:38.447286 INFO::ASW Batch was -0.000495518282995479 prior to batch effect correction and is now -0.121661362755181 .
2026-02-27 18:52:38.447517 INFO::Total function execution time is 0.0361249446868896 s and adjustment time is 0.0293540954589844 s ( 81.26 )
2026-02-27 18:52:38.447807 INFO::Formatting Data.
2026-02-27 18:52:38.447978 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:38.448218 INFO::Removing potential empty rows and columns
2026-02-27 18:52:38.448517 INFO::Found 0 missing values.
2026-02-27 18:52:38.449363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:38.449536 INFO::Done
2026-02-27 18:52:38.449687 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:38.450276 INFO::Starting hierarchical adjustment
2026-02-27 18:52:38.450476 INFO::Found 2 batches.
2026-02-27 18:52:38.450626 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:38.450802 INFO::Using default BPPARAM
2026-02-27 18:52:38.450945 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:38.451183 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 18:52:38.456074 INFO::Done
2026-02-27 18:52:38.456258 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:38.456817 INFO::ASW Batch was -0.000495518282995479 prior to batch effect correction and is now -0.121661362755181 .
2026-02-27 18:52:38.457044 INFO::Total function execution time is 0.00923013687133789 s and adjustment time is 0.00563812255859375 s ( 61.08 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-02-27 18:52:39.862878 INFO::Formatting Data.
2026-02-27 18:52:39.86315 INFO::Recognized SummarizedExperiment
2026-02-27 18:52:39.863313 INFO::Typecasting input to dataframe.
2026-02-27 18:52:39.874218 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:39.874658 INFO::Removing potential empty rows and columns
2026-02-27 18:52:39.875935 INFO::Found 0 missing values.
2026-02-27 18:52:39.878197 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:39.87837 INFO::Done
2026-02-27 18:52:39.878529 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:39.879727 INFO::Starting hierarchical adjustment
2026-02-27 18:52:39.87994 INFO::Found 2 batches.
2026-02-27 18:52:39.880087 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:39.880436 INFO::Using default BPPARAM
2026-02-27 18:52:39.880586 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:39.880871 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 18:52:39.900121 INFO::Done
2026-02-27 18:52:39.900358 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:39.901582 INFO::ASW Batch was 0.00541839576439151 prior to batch effect correction and is now -0.0966358679729298 .
2026-02-27 18:52:39.901833 INFO::Total function execution time is 0.0390720367431641 s and adjustment time is 0.0202131271362305 s ( 51.73 )
Warning: stack imbalance in '{', 73 then 75
2026-02-27 18:52:39.909862 INFO::Formatting Data.
2026-02-27 18:52:39.91013 INFO::Recognized SummarizedExperiment
2026-02-27 18:52:39.910295 INFO::Typecasting input to dataframe.
2026-02-27 18:52:39.913446 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:39.91383 INFO::Removing potential empty rows and columns
2026-02-27 18:52:39.915095 INFO::Found 0 missing values.
2026-02-27 18:52:39.917566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:39.917968 INFO::Done
2026-02-27 18:52:39.918147 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:39.919707 INFO::Starting hierarchical adjustment
2026-02-27 18:52:39.919943 INFO::Found 2 batches.
2026-02-27 18:52:39.920126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:39.958341 INFO::Using default BPPARAM
2026-02-27 18:52:39.958668 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:39.959058 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 18:52:39.967302 INFO::Done
2026-02-27 18:52:39.967533 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:39.968769 INFO::ASW Batch was 0.0145438129779109 prior to batch effect correction and is now 0.0145438129779109 .
2026-02-27 18:52:39.969041 INFO::Total function execution time is 0.0591888427734375 s and adjustment time is 0.0473940372467041 s ( 80.07 )
2026-02-27 18:52:39.978665 INFO::Formatting Data.
2026-02-27 18:52:39.978979 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:39.979321 INFO::Removing potential empty rows and columns
2026-02-27 18:52:39.979661 INFO::Found 0 missing values.
2026-02-27 18:52:39.981356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:39.981601 INFO::Done
2026-02-27 18:52:39.981783 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:39.982456 INFO::Starting hierarchical adjustment
2026-02-27 18:52:39.982684 INFO::Found 3 batches.
2026-02-27 18:52:39.982844 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:39.98304 INFO::Using default BPPARAM
2026-02-27 18:52:39.983194 INFO::Processing subtree level 1
2026-02-27 18:52:40.086104 INFO::Adjusting the last 1 batches sequentially
2026-02-27 18:52:40.087079 INFO::Done
2026-02-27 18:52:40.087312 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.088488 INFO::ASW Batch was -0.0987748334848496 prior to batch effect correction and is now -0.199070568685133 .
2026-02-27 18:52:40.088884 INFO::Total function execution time is 0.110233068466187 s and adjustment time is 0.104437112808228 s ( 94.74 )
2026-02-27 18:52:40.09527 INFO::Skipping initial DF formatting
2026-02-27 18:52:40.095491 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.096827 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.097073 INFO::Found 5 batches.
2026-02-27 18:52:40.097239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.097455 INFO::Using default BPPARAM
2026-02-27 18:52:40.097612 INFO::Processing subtree level 1
2026-02-27 18:52:40.289374 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.291052 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 18:52:40.305422 INFO::Done
2026-02-27 18:52:40.305745 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.338275 INFO::ASW Batch was 0.481464694414368 prior to batch effect correction and is now 0.481464694414368 .
2026-02-27 18:52:40.338626 INFO::ASW Label was 0.391924428460807 prior to batch effect correction and is now 0.391924428460807 .
2026-02-27 18:52:40.339059 INFO::Total function execution time is 0.243789196014404 s and adjustment time is 0.20836877822876 s ( 85.47 )
2026-02-27 18:52:40.352117 INFO::Formatting Data.
2026-02-27 18:52:40.352427 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.352857 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.353325 INFO::Found 0 missing values.
2026-02-27 18:52:40.355269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.355706 INFO::Done
2026-02-27 18:52:40.355994 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.357312 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.357604 INFO::Found 5 batches.
2026-02-27 18:52:40.357825 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.358154 INFO::Using default BPPARAM
2026-02-27 18:52:40.358369 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.
2026-02-27 18:52:40.465111 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.466904 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 18:52:40.476502 INFO::Done
2026-02-27 18:52:40.476829 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.478543 INFO::ASW Batch was 0.489633234691268 prior to batch effect correction and is now -0.0507069277849646 .
2026-02-27 18:52:40.47882 INFO::ASW Label was 0.282077737015909 prior to batch effect correction and is now 0.768860348690689 .
2026-02-27 18:52:40.479233 INFO::Total function execution time is 0.127143144607544 s and adjustment time is 0.118923187255859 s ( 93.53 )
2026-02-27 18:52:40.479681 INFO::Formatting Data.
2026-02-27 18:52:40.479936 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.480328 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.480758 INFO::Found 0 missing values.
2026-02-27 18:52:40.482395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.482653 INFO::Done
2026-02-27 18:52:40.48287 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.484348 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.484629 INFO::Found 5 batches.
2026-02-27 18:52:40.484818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.48509 INFO::Using default BPPARAM
2026-02-27 18:52:40.485285 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.
2026-02-27 18:52:40.569129 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.570329 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 18:52:40.579912 INFO::Done
2026-02-27 18:52:40.58029 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.582042 INFO::ASW Batch was 0.489633234691268 prior to batch effect correction and is now -0.0507069277849646 .
2026-02-27 18:52:40.593321 INFO::ASW Label was 0.282077737015909 prior to batch effect correction and is now 0.768860348690689 .
2026-02-27 18:52:40.59403 INFO::Total function execution time is 0.114281177520752 s and adjustment time is 0.0953330993652344 s ( 83.42 )
2026-02-27 18:52:40.615663 INFO::Formatting Data.
2026-02-27 18:52:40.61618 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.616839 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.617367 INFO::Found 0 missing values.
2026-02-27 18:52:40.61946 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.619768 INFO::Done
2026-02-27 18:52:40.61997 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.621456 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.621843 INFO::Found 5 batches.
2026-02-27 18:52:40.622057 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.62235 INFO::Using default BPPARAM
2026-02-27 18:52:40.622561 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.
2026-02-27 18:52:40.725038 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.726932 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 18:52:40.737764 INFO::Done
2026-02-27 18:52:40.738117 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.739947 INFO::ASW Batch was 0.54587338240666 prior to batch effect correction and is now -0.0991794504133496 .
2026-02-27 18:52:40.741725 INFO::ASW Label was 0.123182047800943 prior to batch effect correction and is now 0.7980926359563 .
2026-02-27 18:52:40.742237 INFO::Total function execution time is 0.126621007919312 s and adjustment time is 0.115983009338379 s ( 91.6 )
2026-02-27 18:52:40.742597 INFO::Formatting Data.
2026-02-27 18:52:40.742816 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.743174 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.74358 INFO::Found 0 missing values.
2026-02-27 18:52:40.745309 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.745589 INFO::Done
2026-02-27 18:52:40.745917 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.747203 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.747558 INFO::Found 5 batches.
2026-02-27 18:52:40.747756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.748051 INFO::Using default BPPARAM
2026-02-27 18:52:40.748237 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.
2026-02-27 18:52:40.854755 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.858606 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 18:52:40.868134 INFO::Done
2026-02-27 18:52:40.868392 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.869672 INFO::ASW Batch was 0.54587338240666 prior to batch effect correction and is now -0.0991794504133496 .
2026-02-27 18:52:40.869889 INFO::ASW Label was 0.123182047800943 prior to batch effect correction and is now 0.7980926359563 .
2026-02-27 18:52:40.870222 INFO::Total function execution time is 0.127619981765747 s and adjustment time is 0.120672941207886 s ( 94.56 )
2026-02-27 18:52:40.877361 INFO::Formatting Data.
2026-02-27 18:52:40.877628 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.877949 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.878321 INFO::Found 0 missing values.
2026-02-27 18:52:40.879269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.879452 INFO::Done
2026-02-27 18:52:40.879631 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.8806 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.880857 INFO::Found 2 batches.
2026-02-27 18:52:40.881042 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.881277 INFO::Using default BPPARAM
2026-02-27 18:52:40.881458 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.88175 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 18:52:40.886907 INFO::Done
2026-02-27 18:52:40.887123 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.888061 INFO::ASW Batch was 0.316970270487548 prior to batch effect correction and is now 0.000309175247884596 .
2026-02-27 18:52:40.88827 INFO::ASW Label was 0.694531402969024 prior to batch effect correction and is now 0.913884141478078 .
2026-02-27 18:52:40.888508 INFO::Total function execution time is 0.0111780166625977 s and adjustment time is 0.00609612464904785 s ( 54.54 )
2026-02-27 18:52:40.888735 INFO::Formatting Data.
2026-02-27 18:52:40.888911 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.889181 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.889503 INFO::Found 0 missing values.
2026-02-27 18:52:40.89034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.896376 INFO::Done
2026-02-27 18:52:40.896706 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.897928 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.898202 INFO::Found 2 batches.
2026-02-27 18:52:40.898381 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.898585 INFO::Using default BPPARAM
2026-02-27 18:52:40.899331 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.899856 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-02-27 18:52:40.906162 INFO::Done
2026-02-27 18:52:40.906412 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.908097 INFO::ASW Batch was 0.316970270487548 prior to batch effect correction and is now 0.000309175247884596 .
2026-02-27 18:52:40.908351 INFO::ASW Label was 0.694531402969024 prior to batch effect correction and is now 0.913884141478078 .
2026-02-27 18:52:40.908637 INFO::Total function execution time is 0.0198860168457031 s and adjustment time is 0.00801706314086914 s ( 40.32 )
2026-02-27 18:52:40.915495 INFO::Formatting Data.
2026-02-27 18:52:40.915753 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.916068 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.916391 INFO::Found 0 missing values.
2026-02-27 18:52:40.917149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.91735 INFO::Done
2026-02-27 18:52:40.917574 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.918332 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.91862 INFO::Found 2 batches.
2026-02-27 18:52:40.918813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.919128 INFO::Using default BPPARAM
2026-02-27 18:52:40.919332 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.919701 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 18:52:40.934013 INFO::Done
2026-02-27 18:52:40.934276 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.935023 INFO::ASW Batch was -0.182117748921057 prior to batch effect correction and is now -0.18865017368746 .
2026-02-27 18:52:40.935321 INFO::Total function execution time is 0.0198400020599365 s and adjustment time is 0.0154459476470947 s ( 77.85 )
2026-02-27 18:52:40.941444 INFO::Formatting Data.
2026-02-27 18:52:40.941765 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.942122 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.942507 INFO::Found 0 missing values.
2026-02-27 18:52:40.942954 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.
2026-02-27 18:52:40.944567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.944749 INFO::Done
2026-02-27 18:52:40.944934 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.945952 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.946203 INFO::Found 2 batches.
2026-02-27 18:52:40.947924 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.948184 INFO::Using default BPPARAM
2026-02-27 18:52:40.948362 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.948705 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 18:52:40.955273 INFO::Done
2026-02-27 18:52:40.955497 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.956448 INFO::ASW Batch was 0.626273288337258 prior to batch effect correction and is now 0.368304299623126 .
2026-02-27 18:52:40.9677 INFO::ASW Label was 0.641140116523574 prior to batch effect correction and is now 0.585784478382244 .
2026-02-27 18:52:40.968202 INFO::Total function execution time is 0.0268070697784424 s and adjustment time is 0.00910401344299316 s ( 33.96 )
2026-02-27 18:52:40.968507 INFO::Formatting Data.
2026-02-27 18:52:40.968719 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:40.969109 INFO::Removing potential empty rows and columns
2026-02-27 18:52:40.96952 INFO::Found 0 missing values.
2026-02-27 18:52:40.969848 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.
2026-02-27 18:52:40.97138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:40.97157 INFO::Done
2026-02-27 18:52:40.971741 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:40.972843 INFO::Starting hierarchical adjustment
2026-02-27 18:52:40.973067 INFO::Found 2 batches.
2026-02-27 18:52:40.973221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:40.973411 INFO::Using default BPPARAM
2026-02-27 18:52:40.97356 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:40.973846 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 18:52:40.979603 INFO::Done
2026-02-27 18:52:40.979835 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:40.980812 INFO::ASW Batch was 0.626273288337258 prior to batch effect correction and is now 0.368304299623126 .
2026-02-27 18:52:40.981012 INFO::ASW Label was 0.641140116523574 prior to batch effect correction and is now 0.585784478382244 .
2026-02-27 18:52:40.981277 INFO::Total function execution time is 0.0127720832824707 s and adjustment time is 0.00657415390014648 s ( 51.47 )
2026-02-27 18:52:41.073924 INFO::Formatting Data.
2026-02-27 18:52:41.074221 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:41.07457 INFO::Removing potential empty rows and columns
2026-02-27 18:52:41.074917 INFO::Found 0 missing values.
2026-02-27 18:52:41.075889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:41.076081 INFO::Done
2026-02-27 18:52:41.076251 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:41.07702 INFO::Starting hierarchical adjustment
2026-02-27 18:52:41.077258 INFO::Found 3 batches.
2026-02-27 18:52:41.077423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:41.077622 INFO::Using default BPPARAM
2026-02-27 18:52:41.077781 INFO::Processing subtree level 1
2026-02-27 18:52:41.171438 INFO::Adjusting the last 1 batches sequentially
2026-02-27 18:52:41.172464 INFO::Done
2026-02-27 18:52:41.172674 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:41.173863 INFO::ASW Batch was 0.0067903443036391 prior to batch effect correction and is now 0.0067903443036391 .
2026-02-27 18:52:41.174348 INFO::Total function execution time is 0.100404977798462 s and adjustment time is 0.0952529907226562 s ( 94.87 )
2026-02-27 18:52:41.174738 INFO::Formatting Data.
2026-02-27 18:52:41.174983 INFO::Typecasting input to dataframe.
2026-02-27 18:52:41.175225 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:41.175545 INFO::Removing potential empty rows and columns
2026-02-27 18:52:41.175941 INFO::Found 0 missing values.
2026-02-27 18:52:41.176908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:41.177088 INFO::Done
2026-02-27 18:52:41.177261 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:41.177887 INFO::Starting hierarchical adjustment
2026-02-27 18:52:41.178125 INFO::Found 3 batches.
2026-02-27 18:52:41.178298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:41.178522 INFO::Using default BPPARAM
2026-02-27 18:52:41.178681 INFO::Processing subtree level 1
2026-02-27 18:52:41.247462 INFO::Adjusting the last 1 batches sequentially
2026-02-27 18:52:41.248647 INFO::Done
2026-02-27 18:52:41.248925 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:41.250343 INFO::ASW Batch was 0.0067903443036391 prior to batch effect correction and is now 0.0067903443036391 .
2026-02-27 18:52:41.25094 INFO::Total function execution time is 0.0761651992797852 s and adjustment time is 0.0705578327178955 s ( 92.64 )
2026-02-27 18:52:41.258738 INFO::Formatting Data.
2026-02-27 18:52:41.259016 INFO::Typecasting input to dataframe.
2026-02-27 18:52:41.259319 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:41.259656 INFO::Removing potential empty rows and columns
2026-02-27 18:52:41.260086 INFO::Found 0 missing values.
2026-02-27 18:52:41.261036 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:41.261207 INFO::Done
2026-02-27 18:52:41.261381 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:41.262065 INFO::Starting hierarchical adjustment
2026-02-27 18:52:41.262288 INFO::Found 3 batches.
2026-02-27 18:52:41.262448 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:41.263583 INFO::Using default BPPARAM
2026-02-27 18:52:41.263792 INFO::Processing subtree level 1
2026-02-27 18:52:41.341044 INFO::Adjusting the last 1 batches sequentially
2026-02-27 18:52:41.349231 INFO::Done
2026-02-27 18:52:41.349551 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:41.350666 INFO::ASW Batch was -0.0402153696998219 prior to batch effect correction and is now -0.0402153696998219 .
2026-02-27 18:52:41.351085 INFO::Total function execution time is 0.0923590660095215 s and adjustment time is 0.0869510173797607 s ( 94.14 )
2026-02-27 18:52:41.45455 INFO::Formatting Data.
2026-02-27 18:52:41.454991 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:41.455543 INFO::Removing potential empty rows and columns
2026-02-27 18:52:41.456551 INFO::Found 1000 missing values.
2026-02-27 18:52:41.462556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:41.46281 INFO::Done
2026-02-27 18:52:41.462985 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:41.46504 INFO::Starting hierarchical adjustment
2026-02-27 18:52:41.465297 INFO::Found 10 batches.
2026-02-27 18:52:41.465479 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:41.465701 INFO::Using default BPPARAM
2026-02-27 18:52:41.465871 INFO::Processing subtree level 1
2026-02-27 18:52:41.566759 INFO::Processing subtree level 2
2026-02-27 18:52:41.666888 INFO::Adjusting the last 1 batches sequentially
2026-02-27 18:52:41.669961 INFO::Done
2026-02-27 18:52:41.670318 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:41.673301 INFO::ASW Batch was 0.491193162272435 prior to batch effect correction and is now 0.491193162272435 .
2026-02-27 18:52:41.673582 INFO::ASW Label was 0.318737711095418 prior to batch effect correction and is now 0.318737711095418 .
2026-02-27 18:52:41.67407 INFO::Total function execution time is 0.219577789306641 s and adjustment time is 0.204679012298584 s ( 93.21 )
2026-02-27 18:52:41.67443 INFO::Formatting Data.
2026-02-27 18:52:41.674679 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:41.675288 INFO::Removing potential empty rows and columns
2026-02-27 18:52:41.676672 INFO::Found 1000 missing values.
2026-02-27 18:52:41.683225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:41.683498 INFO::Done
2026-02-27 18:52:41.683675 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:41.685799 INFO::Starting hierarchical adjustment
2026-02-27 18:52:41.686073 INFO::Found 10 batches.
2026-02-27 18:52:42.189253 INFO::Set up parallel execution backend with 2 workers
2026-02-27 18:52:42.189564 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-02-27 18:52:42.942708 INFO::Adjusting the last 2 batches sequentially
2026-02-27 18:52:42.943324 INFO::Adjusting sequential tree level 1 with 2 batches
2026-02-27 18:52:42.949138 INFO::Done
2026-02-27 18:52:42.94954 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:42.951437 INFO::ASW Batch was 0.491193162272435 prior to batch effect correction and is now 0.491193162272435 .
2026-02-27 18:52:42.95162 INFO::ASW Label was 0.318737711095418 prior to batch effect correction and is now 0.318737711095418 .
2026-02-27 18:52:42.951869 INFO::Total function execution time is 1.27745389938354 s and adjustment time is 1.26311802864075 s ( 98.88 )
2026-02-27 18:52:43.106911 INFO::Formatting Data.
2026-02-27 18:52:43.107335 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.107755 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.108287 INFO::Found 0 missing values.
2026-02-27 18:52:43.110233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.110519 INFO::Done
2026-02-27 18:52:43.110754 INFO::Acquiring quality metrics before batch effect correction.
2026-02-27 18:52:43.111908 INFO::Starting hierarchical adjustment
2026-02-27 18:52:43.112224 INFO::Found 3 batches.
2026-02-27 18:52:43.112413 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-02-27 18:52:43.112731 INFO::Using default BPPARAM
2026-02-27 18:52:43.112928 INFO::Processing subtree level 1
2026-02-27 18:52:43.20902 INFO::Adjusting the last 1 batches sequentially
2026-02-27 18:52:43.210059 INFO::Done
2026-02-27 18:52:43.210327 INFO::Acquiring quality metrics after batch effect correction.
2026-02-27 18:52:43.211725 INFO::ASW Batch was 0.138718932845409 prior to batch effect correction and is now -0.157545773476124 .
2026-02-27 18:52:43.211981 INFO::ASW Label was -0.179210009908167 prior to batch effect correction and is now 0.0385129160720222 .
2026-02-27 18:52:43.212378 INFO::Total function execution time is 0.105542182922363 s and adjustment time is 0.0979280471801758 s ( 92.79 )
2026-02-27 18:52:43.280808 INFO::Formatting Data.
2026-02-27 18:52:43.281169 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.281541 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.282049 INFO::Found 2 missing values.
2026-02-27 18:52:43.283298 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.283548 INFO::Done
2026-02-27 18:52:43.297219 INFO::Found NA in Reference column
2026-02-27 18:52:43.302261 INFO::Require at least two references per batch.
2026-02-27 18:52:43.313403 INFO::Formatting Data.
2026-02-27 18:52:43.313843 INFO::Recognized SummarizedExperiment
2026-02-27 18:52:43.314097 INFO::Typecasting input to dataframe.
2026-02-27 18:52:43.320726 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.321355 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.32303 INFO::Found 0 missing values.
2026-02-27 18:52:43.325815 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.326044 INFO::Done
2026-02-27 18:52:43.343893 INFO::Formatting Data.
2026-02-27 18:52:43.344369 INFO::Recognized SummarizedExperiment
2026-02-27 18:52:43.344609 INFO::Typecasting input to dataframe.
2026-02-27 18:52:43.352141 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.35261 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.354291 INFO::Found 0 missing values.
2026-02-27 18:52:43.359262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.359558 INFO::Done
2026-02-27 18:52:43.366725 INFO::Formatting Data.
2026-02-27 18:52:43.366999 INFO::Recognized SummarizedExperiment
2026-02-27 18:52:43.367178 INFO::Typecasting input to dataframe.
2026-02-27 18:52:43.372465 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.372805 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.373164 INFO::Found 0 missing values.
2026-02-27 18:52:43.373465 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.
2026-02-27 18:52:43.374905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.375095 INFO::Done
2026-02-27 18:52:43.381592 INFO::Formatting Data.
2026-02-27 18:52:43.381948 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.382337 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.382743 INFO::Found 0 missing values.
2026-02-27 18:52:43.384259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.384546 INFO::Done
2026-02-27 18:52:43.392155 INFO::Formatting Data.
2026-02-27 18:52:43.392569 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.393 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.393505 INFO::Found 0 missing values.
2026-02-27 18:52:43.395137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.395358 INFO::Done
2026-02-27 18:52:43.420441 INFO::Formatting Data.
2026-02-27 18:52:43.421026 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.421479 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.421942 INFO::Found 1 missing values.
2026-02-27 18:52:43.423092 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.423347 INFO::Done
2026-02-27 18:52:43.432199 INFO::Formatting Data.
2026-02-27 18:52:43.432537 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.432842 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.433272 INFO::Found 2 missing values.
2026-02-27 18:52:43.433585 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.
2026-02-27 18:52:43.434442 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.434611 INFO::Done
2026-02-27 18:52:43.439987 INFO::Formatting Data.
2026-02-27 18:52:43.440374 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.44073 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.441302 INFO::Found 2 missing values.
2026-02-27 18:52:43.442187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.442447 INFO::Done
2026-02-27 18:52:43.449091 INFO::Formatting Data.
2026-02-27 18:52:43.449415 INFO::Typecasting input to dataframe.
2026-02-27 18:52:43.450112 INFO::Replacing NaNs with NAs.
2026-02-27 18:52:43.450592 INFO::Removing potential empty rows and columns
2026-02-27 18:52:43.451023 INFO::Found 0 missing values.
2026-02-27 18:52:43.452438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-02-27 18:52:43.452624 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.537 2.479 10.871
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.375 | 0.403 | 7.727 | |
| compute_asw | 0.010 | 0.000 | 0.011 | |
| count_existing | 0.005 | 0.000 | 0.008 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |