Yannis Schumann
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_22 |
| git_last_commit: 49dbe48 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-27 12:04 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 166/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.6.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-11-25 16:29:20 -0500 (Tue, 25 Nov 2025) |
| EndedAt: 2025-11-25 16:31:22 -0500 (Tue, 25 Nov 2025) |
| EllapsedTime: 122.4 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.6.0’
* 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 29.871 1.149 32.94
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.6.0’ ** 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 version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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")
2025-11-25 16:30:52.062469 INFO::Formatting Data.
2025-11-25 16:30:52.066856 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:52.086338 INFO::Removing potential empty rows and columns
2025-11-25 16:30:52.565605 INFO::Found 0 missing values.
2025-11-25 16:30:52.580851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:52.58198 INFO::Done
2025-11-25 16:30:52.582731 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:52.622707 INFO::Starting hierarchical adjustment
2025-11-25 16:30:52.623728 INFO::Found 3 batches.
2025-11-25 16:30:52.624292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:52.625593 INFO::Using default BPPARAM
2025-11-25 16:30:52.626134 INFO::Processing subtree level 1
2025-11-25 16:30:52.77461 INFO::Adjusting the last 1 batches sequentially
2025-11-25 16:30:52.778081 INFO::Done
2025-11-25 16:30:52.778746 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:52.790908 INFO::ASW Batch was -0.0895014042943763 prior to batch effect correction and is now -0.0895014042943763 .
2025-11-25 16:30:52.794448 INFO::Total function execution time is 0.731703996658325 s and adjustment time is 0.154529094696045 s ( 21.12 )
2025-11-25 16:30:52.819932 INFO::Formatting Data.
2025-11-25 16:30:52.821059 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:52.82231 INFO::Removing potential empty rows and columns
2025-11-25 16:30:52.824066 INFO::Found 0 missing values.
2025-11-25 16:30:52.825282 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.
2025-11-25 16:30:52.840739 INFO::Formatting Data.
2025-11-25 16:30:52.841839 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:52.843189 INFO::Removing potential empty rows and columns
2025-11-25 16:30:52.844496 INFO::Found 0 missing values.
2025-11-25 16:30:52.845532 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.
2025-11-25 16:30:52.864805 INFO::Formatting Data.
2025-11-25 16:30:52.865659 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:52.866578 INFO::Removing potential empty rows and columns
2025-11-25 16:30:52.867804 INFO::Found 0 missing values.
2025-11-25 16:30:52.868794 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.
2025-11-25 16:30:52.873636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:52.874247 INFO::Done
2025-11-25 16:30:52.874802 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:52.877042 INFO::Starting hierarchical adjustment
2025-11-25 16:30:52.877758 INFO::Found 2 batches.
2025-11-25 16:30:52.878276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:52.87894 INFO::Using default BPPARAM
2025-11-25 16:30:52.879428 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:30:52.880335 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 16:30:52.938069 INFO::Done
2025-11-25 16:30:52.939081 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:52.94215 INFO::ASW Batch was -0.0242122192378554 prior to batch effect correction and is now -0.114945011386808 .
2025-11-25 16:30:52.943635 INFO::Total function execution time is 0.0788249969482422 s and adjustment time is 0.0603349208831787 s ( 76.54 )
2025-11-25 16:30:52.948039 INFO::Formatting Data.
2025-11-25 16:30:52.948877 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:52.96117 INFO::Formatting Data.
2025-11-25 16:30:52.964589 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:52.966096 INFO::Removing potential empty rows and columns
2025-11-25 16:30:52.967916 INFO::Found 0 missing values.
2025-11-25 16:30:52.971721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:52.972518 INFO::Done
2025-11-25 16:30:52.973109 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:52.976054 INFO::Starting hierarchical adjustment
2025-11-25 16:30:53.040714 INFO::Found 2 batches.
2025-11-25 16:30:53.041627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:53.043732 INFO::Using default BPPARAM
2025-11-25 16:30:53.04466 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:30:53.045709 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 16:30:53.06278 INFO::Done
2025-11-25 16:30:53.063617 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:53.069032 INFO::ASW Batch was 0.00856821130584311 prior to batch effect correction and is now -0.125335053342106 .
2025-11-25 16:30:53.069936 INFO::Total function execution time is 0.108909845352173 s and adjustment time is 0.0223989486694336 s ( 20.57 )
2025-11-25 16:30:53.070999 INFO::Formatting Data.
2025-11-25 16:30:53.071571 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:53.072454 INFO::Removing potential empty rows and columns
2025-11-25 16:30:53.074852 INFO::Found 0 missing values.
2025-11-25 16:30:53.082039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:53.083134 INFO::Done
2025-11-25 16:30:53.083775 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:53.08658 INFO::Starting hierarchical adjustment
2025-11-25 16:30:53.0876 INFO::Found 2 batches.
2025-11-25 16:30:53.088225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:53.088875 INFO::Using default BPPARAM
2025-11-25 16:30:53.089428 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:30:53.090362 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 16:30:53.123588 INFO::Done
2025-11-25 16:30:53.124448 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:53.130118 INFO::ASW Batch was 0.00856821130584311 prior to batch effect correction and is now -0.125335053342106 .
2025-11-25 16:30:53.131303 INFO::Total function execution time is 0.060234785079956 s and adjustment time is 0.0360958576202393 s ( 59.93 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-25 16:30:58.466925 INFO::Formatting Data.
2025-11-25 16:30:58.467724 INFO::Recognized SummarizedExperiment
2025-11-25 16:30:58.468253 INFO::Typecasting input to dataframe.
2025-11-25 16:30:58.510955 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:58.512415 INFO::Removing potential empty rows and columns
2025-11-25 16:30:58.519689 INFO::Found 0 missing values.
2025-11-25 16:30:58.535592 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:58.536934 INFO::Done
2025-11-25 16:30:58.538037 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:58.545206 INFO::Starting hierarchical adjustment
2025-11-25 16:30:58.546226 INFO::Found 2 batches.
2025-11-25 16:30:58.546772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:58.551457 INFO::Using default BPPARAM
2025-11-25 16:30:58.552149 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:30:58.553279 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 16:30:58.665458 INFO::Done
2025-11-25 16:30:58.666308 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:58.670564 INFO::ASW Batch was 0.00160487737736091 prior to batch effect correction and is now -0.0916165410582029 .
2025-11-25 16:30:58.671557 INFO::Total function execution time is 0.204975843429565 s and adjustment time is 0.119354963302612 s ( 58.23 )
Warning: stack imbalance in '{', 73 then 75
2025-11-25 16:30:58.691026 INFO::Formatting Data.
2025-11-25 16:30:58.691863 INFO::Recognized SummarizedExperiment
2025-11-25 16:30:58.692355 INFO::Typecasting input to dataframe.
2025-11-25 16:30:58.70171 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:58.70291 INFO::Removing potential empty rows and columns
2025-11-25 16:30:58.719518 INFO::Found 0 missing values.
2025-11-25 16:30:58.726629 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:58.727351 INFO::Done
2025-11-25 16:30:58.727855 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:58.731704 INFO::Starting hierarchical adjustment
2025-11-25 16:30:58.740658 INFO::Found 2 batches.
2025-11-25 16:30:58.741574 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:58.753077 INFO::Using default BPPARAM
2025-11-25 16:30:58.75695 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:30:58.758298 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 16:30:58.810108 INFO::Done
2025-11-25 16:30:58.810907 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:58.819284 INFO::ASW Batch was 0.00356714807957373 prior to batch effect correction and is now 0.00356714807957373 .
2025-11-25 16:30:58.82036 INFO::Total function execution time is 0.12935209274292 s and adjustment time is 0.0699329376220703 s ( 54.06 )
2025-11-25 16:30:58.85617 INFO::Formatting Data.
2025-11-25 16:30:58.857059 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:58.858069 INFO::Removing potential empty rows and columns
2025-11-25 16:30:58.859073 INFO::Found 0 missing values.
2025-11-25 16:30:58.861762 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:58.862419 INFO::Done
2025-11-25 16:30:58.862904 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:58.865037 INFO::Starting hierarchical adjustment
2025-11-25 16:30:58.86578 INFO::Found 3 batches.
2025-11-25 16:30:58.866256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:58.876325 INFO::Using default BPPARAM
2025-11-25 16:30:58.881973 INFO::Processing subtree level 1
2025-11-25 16:30:59.092472 INFO::Adjusting the last 1 batches sequentially
2025-11-25 16:30:59.097929 INFO::Done
2025-11-25 16:30:59.098863 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:59.104186 INFO::ASW Batch was -0.11782906392678 prior to batch effect correction and is now -0.191709334631423 .
2025-11-25 16:30:59.105878 INFO::Total function execution time is 0.249441862106323 s and adjustment time is 0.232197999954224 s ( 93.09 )
2025-11-25 16:30:59.125845 INFO::Skipping initial DF formatting
2025-11-25 16:30:59.126675 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:59.131 INFO::Starting hierarchical adjustment
2025-11-25 16:30:59.13192 INFO::Found 5 batches.
2025-11-25 16:30:59.132465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:59.133169 INFO::Using default BPPARAM
2025-11-25 16:30:59.133693 INFO::Processing subtree level 1
2025-11-25 16:30:59.489263 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:30:59.492546 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 16:30:59.517649 INFO::Done
2025-11-25 16:30:59.518625 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:59.524377 INFO::ASW Batch was 0.542012859567658 prior to batch effect correction and is now 0.542012859567658 .
2025-11-25 16:30:59.52519 INFO::ASW Label was 0.357013244092214 prior to batch effect correction and is now 0.357013244092214 .
2025-11-25 16:30:59.526448 INFO::Total function execution time is 0.400619983673096 s and adjustment time is 0.385853052139282 s ( 96.31 )
2025-11-25 16:30:59.667835 INFO::Formatting Data.
2025-11-25 16:30:59.668761 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:59.66971 INFO::Removing potential empty rows and columns
2025-11-25 16:30:59.670708 INFO::Found 0 missing values.
2025-11-25 16:30:59.674533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:59.675089 INFO::Done
2025-11-25 16:30:59.675598 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:59.678659 INFO::Starting hierarchical adjustment
2025-11-25 16:30:59.679402 INFO::Found 5 batches.
2025-11-25 16:30:59.679902 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:59.680498 INFO::Using default BPPARAM
2025-11-25 16:30:59.68097 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.
2025-11-25 16:30:59.85151 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:30:59.862188 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 16:30:59.891143 INFO::Done
2025-11-25 16:30:59.892578 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:30:59.898144 INFO::ASW Batch was 0.555316178693086 prior to batch effect correction and is now -0.107165970566039 .
2025-11-25 16:30:59.899089 INFO::ASW Label was 0.177687231766084 prior to batch effect correction and is now 0.882380375109457 .
2025-11-25 16:30:59.900163 INFO::Total function execution time is 0.232400894165039 s and adjustment time is 0.21170711517334 s ( 91.1 )
2025-11-25 16:30:59.901148 INFO::Formatting Data.
2025-11-25 16:30:59.904115 INFO::Replacing NaNs with NAs.
2025-11-25 16:30:59.906382 INFO::Removing potential empty rows and columns
2025-11-25 16:30:59.908071 INFO::Found 0 missing values.
2025-11-25 16:30:59.914206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:30:59.915227 INFO::Done
2025-11-25 16:30:59.918167 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:30:59.923173 INFO::Starting hierarchical adjustment
2025-11-25 16:30:59.924126 INFO::Found 5 batches.
2025-11-25 16:30:59.924725 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:30:59.925419 INFO::Using default BPPARAM
2025-11-25 16:30:59.927537 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.
2025-11-25 16:31:00.132906 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:00.147606 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 16:31:00.191806 INFO::Done
2025-11-25 16:31:00.192856 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:00.197499 INFO::ASW Batch was 0.555316178693086 prior to batch effect correction and is now -0.107165970566039 .
2025-11-25 16:31:00.198472 INFO::ASW Label was 0.177687231766084 prior to batch effect correction and is now 0.882380375109457 .
2025-11-25 16:31:00.200794 INFO::Total function execution time is 0.299417018890381 s and adjustment time is 0.267771005630493 s ( 89.43 )
2025-11-25 16:31:00.224268 INFO::Formatting Data.
2025-11-25 16:31:00.225683 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:00.226853 INFO::Removing potential empty rows and columns
2025-11-25 16:31:00.228065 INFO::Found 0 missing values.
2025-11-25 16:31:00.232407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:00.23313 INFO::Done
2025-11-25 16:31:00.233725 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:00.237104 INFO::Starting hierarchical adjustment
2025-11-25 16:31:00.238027 INFO::Found 5 batches.
2025-11-25 16:31:00.238649 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:00.239312 INFO::Using default BPPARAM
2025-11-25 16:31:00.239827 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.
2025-11-25 16:31:00.455139 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:00.460468 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 16:31:00.525341 INFO::Done
2025-11-25 16:31:00.52841 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:00.534669 INFO::ASW Batch was 0.330709770173339 prior to batch effect correction and is now -0.109267799900853 .
2025-11-25 16:31:00.535523 INFO::ASW Label was 0.317352043861077 prior to batch effect correction and is now 0.79865017646346 .
2025-11-25 16:31:00.537067 INFO::Total function execution time is 0.312844038009644 s and adjustment time is 0.285926818847656 s ( 91.4 )
2025-11-25 16:31:00.538101 INFO::Formatting Data.
2025-11-25 16:31:00.538781 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:00.539855 INFO::Removing potential empty rows and columns
2025-11-25 16:31:00.541 INFO::Found 0 missing values.
2025-11-25 16:31:00.545251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:00.546014 INFO::Done
2025-11-25 16:31:00.546564 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:00.550023 INFO::Starting hierarchical adjustment
2025-11-25 16:31:00.550936 INFO::Found 5 batches.
2025-11-25 16:31:00.552425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:00.553227 INFO::Using default BPPARAM
2025-11-25 16:31:00.55385 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.
2025-11-25 16:31:00.74755 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:00.757205 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 16:31:00.78511 INFO::Done
2025-11-25 16:31:00.789563 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:00.797292 INFO::ASW Batch was 0.330709770173339 prior to batch effect correction and is now -0.109267799900853 .
2025-11-25 16:31:00.798477 INFO::ASW Label was 0.317352043861077 prior to batch effect correction and is now 0.79865017646346 .
2025-11-25 16:31:00.800139 INFO::Total function execution time is 0.261826992034912 s and adjustment time is 0.234318017959595 s ( 89.49 )
2025-11-25 16:31:00.822577 INFO::Formatting Data.
2025-11-25 16:31:00.823502 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:00.824495 INFO::Removing potential empty rows and columns
2025-11-25 16:31:00.825612 INFO::Found 0 missing values.
2025-11-25 16:31:00.828375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:00.828966 INFO::Done
2025-11-25 16:31:00.829473 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:00.832566 INFO::Starting hierarchical adjustment
2025-11-25 16:31:00.833455 INFO::Found 2 batches.
2025-11-25 16:31:00.834067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:00.83483 INFO::Using default BPPARAM
2025-11-25 16:31:00.83531 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:00.836179 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 16:31:00.858382 INFO::Done
2025-11-25 16:31:00.859457 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:00.867375 INFO::ASW Batch was 0.516571838159376 prior to batch effect correction and is now 0.100413458310556 .
2025-11-25 16:31:00.868155 INFO::ASW Label was 0.611949394683546 prior to batch effect correction and is now 0.866551417648884 .
2025-11-25 16:31:00.869008 INFO::Total function execution time is 0.0465800762176514 s and adjustment time is 0.0249631404876709 s ( 53.59 )
2025-11-25 16:31:00.869926 INFO::Formatting Data.
2025-11-25 16:31:00.870588 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:00.87152 INFO::Removing potential empty rows and columns
2025-11-25 16:31:00.872637 INFO::Found 0 missing values.
2025-11-25 16:31:00.875387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:00.875961 INFO::Done
2025-11-25 16:31:00.876452 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:00.879531 INFO::Starting hierarchical adjustment
2025-11-25 16:31:00.880327 INFO::Found 2 batches.
2025-11-25 16:31:00.880873 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:00.881476 INFO::Using default BPPARAM
2025-11-25 16:31:00.881948 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:00.882856 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-25 16:31:00.907256 INFO::Done
2025-11-25 16:31:00.908532 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:00.912015 INFO::ASW Batch was 0.516571838159376 prior to batch effect correction and is now 0.100413458310556 .
2025-11-25 16:31:00.91282 INFO::ASW Label was 0.611949394683546 prior to batch effect correction and is now 0.866551417648884 .
2025-11-25 16:31:00.913636 INFO::Total function execution time is 0.0437028408050537 s and adjustment time is 0.0268290042877197 s ( 61.39 )
2025-11-25 16:31:00.927623 INFO::Formatting Data.
2025-11-25 16:31:00.92862 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:00.929567 INFO::Removing potential empty rows and columns
2025-11-25 16:31:00.930508 INFO::Found 0 missing values.
2025-11-25 16:31:00.93604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:00.936797 INFO::Done
2025-11-25 16:31:00.937344 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:00.939367 INFO::Starting hierarchical adjustment
2025-11-25 16:31:00.940162 INFO::Found 2 batches.
2025-11-25 16:31:00.940693 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:00.941298 INFO::Using default BPPARAM
2025-11-25 16:31:00.941836 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:00.942744 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 16:31:00.979438 INFO::Done
2025-11-25 16:31:00.980623 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:00.983002 INFO::ASW Batch was -0.00566921970773934 prior to batch effect correction and is now -0.1646299144512 .
2025-11-25 16:31:00.983892 INFO::Total function execution time is 0.056394100189209 s and adjustment time is 0.0392839908599854 s ( 69.66 )
2025-11-25 16:31:01.002163 INFO::Formatting Data.
2025-11-25 16:31:01.003043 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:01.003947 INFO::Removing potential empty rows and columns
2025-11-25 16:31:01.004898 INFO::Found 0 missing values.
2025-11-25 16:31:01.006138 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.
2025-11-25 16:31:01.013871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:01.014907 INFO::Done
2025-11-25 16:31:01.01553 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:01.019023 INFO::Starting hierarchical adjustment
2025-11-25 16:31:01.019952 INFO::Found 2 batches.
2025-11-25 16:31:01.020468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:01.021071 INFO::Using default BPPARAM
2025-11-25 16:31:01.021549 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:01.023305 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 16:31:01.045369 INFO::Done
2025-11-25 16:31:01.048087 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:01.05145 INFO::ASW Batch was 0.549955735089568 prior to batch effect correction and is now 0.0301850691366837 .
2025-11-25 16:31:01.052149 INFO::ASW Label was 0.323406377901323 prior to batch effect correction and is now 0.89252055557749 .
2025-11-25 16:31:01.052986 INFO::Total function execution time is 0.0509669780731201 s and adjustment time is 0.0255579948425293 s ( 50.15 )
2025-11-25 16:31:01.053755 INFO::Formatting Data.
2025-11-25 16:31:01.054313 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:01.055251 INFO::Removing potential empty rows and columns
2025-11-25 16:31:01.056295 INFO::Found 0 missing values.
2025-11-25 16:31:01.057307 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.
2025-11-25 16:31:01.063636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:01.06497 INFO::Done
2025-11-25 16:31:01.065542 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:01.069174 INFO::Starting hierarchical adjustment
2025-11-25 16:31:01.070512 INFO::Found 2 batches.
2025-11-25 16:31:01.071077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:01.071904 INFO::Using default BPPARAM
2025-11-25 16:31:01.072471 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:01.074251 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 16:31:01.092347 INFO::Done
2025-11-25 16:31:01.093187 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:01.103926 INFO::ASW Batch was 0.549955735089568 prior to batch effect correction and is now 0.0301850691366837 .
2025-11-25 16:31:01.105416 INFO::ASW Label was 0.323406377901323 prior to batch effect correction and is now 0.89252055557749 .
2025-11-25 16:31:01.110725 INFO::Total function execution time is 0.0568621158599854 s and adjustment time is 0.0220041275024414 s ( 38.7 )
2025-11-25 16:31:01.43535 INFO::Formatting Data.
2025-11-25 16:31:01.445768 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:01.447215 INFO::Removing potential empty rows and columns
2025-11-25 16:31:01.448929 INFO::Found 0 missing values.
2025-11-25 16:31:01.455162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:01.455834 INFO::Done
2025-11-25 16:31:01.456446 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:01.458666 INFO::Starting hierarchical adjustment
2025-11-25 16:31:01.459416 INFO::Found 3 batches.
2025-11-25 16:31:01.459922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:01.460524 INFO::Using default BPPARAM
2025-11-25 16:31:01.460988 INFO::Processing subtree level 1
2025-11-25 16:31:01.569809 INFO::Adjusting the last 1 batches sequentially
2025-11-25 16:31:01.574934 INFO::Done
2025-11-25 16:31:01.575897 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:01.580377 INFO::ASW Batch was 0.0191876457071012 prior to batch effect correction and is now 0.0191876457071012 .
2025-11-25 16:31:01.581645 INFO::Total function execution time is 0.147714138031006 s and adjustment time is 0.115592956542969 s ( 78.25 )
2025-11-25 16:31:01.583696 INFO::Formatting Data.
2025-11-25 16:31:01.584316 INFO::Typecasting input to dataframe.
2025-11-25 16:31:01.585355 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:01.586328 INFO::Removing potential empty rows and columns
2025-11-25 16:31:01.587483 INFO::Found 0 missing values.
2025-11-25 16:31:01.590319 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:01.590983 INFO::Done
2025-11-25 16:31:01.591484 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:01.593701 INFO::Starting hierarchical adjustment
2025-11-25 16:31:01.594445 INFO::Found 3 batches.
2025-11-25 16:31:01.594758 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:01.595286 INFO::Using default BPPARAM
2025-11-25 16:31:01.595585 INFO::Processing subtree level 1
2025-11-25 16:31:01.687231 INFO::Adjusting the last 1 batches sequentially
2025-11-25 16:31:01.692335 INFO::Done
2025-11-25 16:31:01.693415 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:01.697446 INFO::ASW Batch was 0.0191876457071012 prior to batch effect correction and is now 0.0191876457071012 .
2025-11-25 16:31:01.698713 INFO::Total function execution time is 0.114957809448242 s and adjustment time is 0.0974118709564209 s ( 84.74 )
2025-11-25 16:31:01.718065 INFO::Formatting Data.
2025-11-25 16:31:01.718658 INFO::Typecasting input to dataframe.
2025-11-25 16:31:01.719119 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:01.719749 INFO::Removing potential empty rows and columns
2025-11-25 16:31:01.721026 INFO::Found 0 missing values.
2025-11-25 16:31:01.72262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:01.722914 INFO::Done
2025-11-25 16:31:01.723131 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:01.724192 INFO::Starting hierarchical adjustment
2025-11-25 16:31:01.724536 INFO::Found 3 batches.
2025-11-25 16:31:01.724865 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:01.725206 INFO::Using default BPPARAM
2025-11-25 16:31:01.725455 INFO::Processing subtree level 1
2025-11-25 16:31:01.809908 INFO::Adjusting the last 1 batches sequentially
2025-11-25 16:31:01.81445 INFO::Done
2025-11-25 16:31:01.815243 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:01.820175 INFO::ASW Batch was -0.0844564658691212 prior to batch effect correction and is now -0.0844564658691212 .
2025-11-25 16:31:01.822016 INFO::Total function execution time is 0.103739976882935 s and adjustment time is 0.0896761417388916 s ( 86.44 )
2025-11-25 16:31:01.946246 INFO::Formatting Data.
2025-11-25 16:31:01.946862 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:01.947482 INFO::Removing potential empty rows and columns
2025-11-25 16:31:01.948905 INFO::Found 1000 missing values.
2025-11-25 16:31:01.956954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:01.95771 INFO::Done
2025-11-25 16:31:01.957973 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:01.961606 INFO::Starting hierarchical adjustment
2025-11-25 16:31:01.962189 INFO::Found 10 batches.
2025-11-25 16:31:01.962472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:01.963428 INFO::Using default BPPARAM
2025-11-25 16:31:01.964441 INFO::Processing subtree level 1
2025-11-25 16:31:02.10018 INFO::Processing subtree level 2
2025-11-25 16:31:02.271264 INFO::Adjusting the last 1 batches sequentially
2025-11-25 16:31:02.276353 INFO::Done
2025-11-25 16:31:02.278162 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:02.284785 INFO::ASW Batch was 0.473975643277958 prior to batch effect correction and is now 0.473975643277958 .
2025-11-25 16:31:02.285546 INFO::ASW Label was 0.358248207255117 prior to batch effect correction and is now 0.358248207255117 .
2025-11-25 16:31:02.286573 INFO::Total function execution time is 0.340430974960327 s and adjustment time is 0.314052820205688 s ( 92.25 )
2025-11-25 16:31:02.287228 INFO::Formatting Data.
2025-11-25 16:31:02.287505 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:02.288415 INFO::Removing potential empty rows and columns
2025-11-25 16:31:02.289682 INFO::Found 1000 missing values.
2025-11-25 16:31:02.297421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:02.298019 INFO::Done
2025-11-25 16:31:02.298292 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:02.301314 INFO::Starting hierarchical adjustment
2025-11-25 16:31:02.301815 INFO::Found 10 batches.
2025-11-25 16:31:04.131726 INFO::Set up parallel execution backend with 2 workers
2025-11-25 16:31:04.133225 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-25 16:31:06.049953 INFO::Adjusting the last 2 batches sequentially
2025-11-25 16:31:06.075267 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-25 16:31:06.098449 INFO::Done
2025-11-25 16:31:06.099326 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:06.105012 INFO::ASW Batch was 0.473975643277958 prior to batch effect correction and is now 0.473975643277958 .
2025-11-25 16:31:06.105692 INFO::ASW Label was 0.358248207255117 prior to batch effect correction and is now 0.358248207255117 .
2025-11-25 16:31:06.106446 INFO::Total function execution time is 3.81913185119629 s and adjustment time is 3.79660391807556 s ( 99.41 )
2025-11-25 16:31:06.356247 INFO::Formatting Data.
2025-11-25 16:31:06.357296 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:06.35844 INFO::Removing potential empty rows and columns
2025-11-25 16:31:06.359646 INFO::Found 0 missing values.
2025-11-25 16:31:06.364568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:06.365979 INFO::Done
2025-11-25 16:31:06.36657 INFO::Acquiring quality metrics before batch effect correction.
2025-11-25 16:31:06.37059 INFO::Starting hierarchical adjustment
2025-11-25 16:31:06.371541 INFO::Found 3 batches.
2025-11-25 16:31:06.372127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-25 16:31:06.381338 INFO::Using default BPPARAM
2025-11-25 16:31:06.382359 INFO::Processing subtree level 1
2025-11-25 16:31:06.510755 INFO::Adjusting the last 1 batches sequentially
2025-11-25 16:31:06.520561 INFO::Done
2025-11-25 16:31:06.522662 INFO::Acquiring quality metrics after batch effect correction.
2025-11-25 16:31:06.533458 INFO::ASW Batch was 0.110675852876367 prior to batch effect correction and is now -0.182499091718132 .
2025-11-25 16:31:06.534722 INFO::ASW Label was -0.181945979806327 prior to batch effect correction and is now -0.075496290071573 .
2025-11-25 16:31:06.536811 INFO::Total function execution time is 0.180063009262085 s and adjustment time is 0.149134874343872 s ( 82.82 )
2025-11-25 16:31:06.753803 INFO::Formatting Data.
2025-11-25 16:31:06.754845 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:06.7559 INFO::Removing potential empty rows and columns
2025-11-25 16:31:06.761177 INFO::Found 2 missing values.
2025-11-25 16:31:06.76544 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:06.766177 INFO::Done
2025-11-25 16:31:06.834245 INFO::Found NA in Reference column
2025-11-25 16:31:06.847083 INFO::Require at least two references per batch.
2025-11-25 16:31:06.88252 INFO::Formatting Data.
2025-11-25 16:31:06.883621 INFO::Recognized SummarizedExperiment
2025-11-25 16:31:06.884212 INFO::Typecasting input to dataframe.
2025-11-25 16:31:06.910882 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:06.914953 INFO::Removing potential empty rows and columns
2025-11-25 16:31:06.928327 INFO::Found 0 missing values.
2025-11-25 16:31:06.946577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:06.94739 INFO::Done
2025-11-25 16:31:06.968042 INFO::Formatting Data.
2025-11-25 16:31:06.969038 INFO::Recognized SummarizedExperiment
2025-11-25 16:31:06.96959 INFO::Typecasting input to dataframe.
2025-11-25 16:31:06.987849 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:06.989259 INFO::Removing potential empty rows and columns
2025-11-25 16:31:06.993045 INFO::Found 0 missing values.
2025-11-25 16:31:07.004028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:07.004777 INFO::Done
2025-11-25 16:31:07.065425 INFO::Formatting Data.
2025-11-25 16:31:07.066429 INFO::Recognized SummarizedExperiment
2025-11-25 16:31:07.067007 INFO::Typecasting input to dataframe.
2025-11-25 16:31:07.085433 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:07.086824 INFO::Removing potential empty rows and columns
2025-11-25 16:31:07.087964 INFO::Found 0 missing values.
2025-11-25 16:31:07.088959 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.
2025-11-25 16:31:07.093705 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:07.094444 INFO::Done
2025-11-25 16:31:07.13342 INFO::Formatting Data.
2025-11-25 16:31:07.138562 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:07.139622 INFO::Removing potential empty rows and columns
2025-11-25 16:31:07.140658 INFO::Found 0 missing values.
2025-11-25 16:31:07.14404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:07.14473 INFO::Done
2025-11-25 16:31:07.193751 INFO::Formatting Data.
2025-11-25 16:31:07.19551 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:07.200696 INFO::Removing potential empty rows and columns
2025-11-25 16:31:07.202226 INFO::Found 0 missing values.
2025-11-25 16:31:07.205642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:07.20633 INFO::Done
2025-11-25 16:31:07.254384 INFO::Formatting Data.
2025-11-25 16:31:07.255488 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:07.256696 INFO::Removing potential empty rows and columns
2025-11-25 16:31:07.258099 INFO::Found 1 missing values.
2025-11-25 16:31:07.261096 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:07.261903 INFO::Done
2025-11-25 16:31:07.299346 INFO::Formatting Data.
2025-11-25 16:31:07.300383 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:07.301297 INFO::Removing potential empty rows and columns
2025-11-25 16:31:07.302399 INFO::Found 2 missing values.
2025-11-25 16:31:07.303425 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.
2025-11-25 16:31:07.305933 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:07.306562 INFO::Done
2025-11-25 16:31:07.320249 INFO::Formatting Data.
2025-11-25 16:31:07.321751 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:07.324093 INFO::Removing potential empty rows and columns
2025-11-25 16:31:07.325496 INFO::Found 2 missing values.
2025-11-25 16:31:07.32765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:07.33117 INFO::Done
2025-11-25 16:31:07.355272 INFO::Formatting Data.
2025-11-25 16:31:07.356291 INFO::Typecasting input to dataframe.
2025-11-25 16:31:07.357075 INFO::Replacing NaNs with NAs.
2025-11-25 16:31:07.357945 INFO::Removing potential empty rows and columns
2025-11-25 16:31:07.358926 INFO::Found 0 missing values.
2025-11-25 16:31:07.366455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-25 16:31:07.367313 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.204 3.883 36.919
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.871 | 1.149 | 32.940 | |
| compute_asw | 0.030 | 0.001 | 0.031 | |
| count_existing | 0.017 | 0.001 | 0.031 | |
| generate_data_covariables | 0.015 | 0.001 | 0.032 | |
| generate_dataset | 0.015 | 0.000 | 0.023 | |