Yannis Schumann
| Snapshot Date: 2025-11-20 15:01 -0500 (Thu, 20 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 2025-11-24 12:04 -0500 (Mon, 24 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" | 4873 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4654 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4600 |
| 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: 2025-11-21 01:45:54 -0500 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 01:48:14 -0500 (Fri, 21 Nov 2025) |
| EllapsedTime: 140.1 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 (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 43.693 2.571 35.131
* 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-x86_64/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 (2025-11-05 r88990) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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")
2025-11-21 01:47:39.207813 INFO::Formatting Data.
2025-11-21 01:47:39.215321 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:39.24808 INFO::Removing potential empty rows and columns
2025-11-21 01:47:39.952372 INFO::Found 0 missing values.
2025-11-21 01:47:39.961419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:39.963303 INFO::Done
2025-11-21 01:47:39.964613 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:39.994907 INFO::Starting hierarchical adjustment
2025-11-21 01:47:39.996922 INFO::Found 3 batches.
2025-11-21 01:47:39.998608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:40.001206 INFO::Using default BPPARAM
2025-11-21 01:47:40.002752 INFO::Processing subtree level 1
2025-11-21 01:47:40.288589 INFO::Adjusting the last 1 batches sequentially
2025-11-21 01:47:40.296606 INFO::Done
2025-11-21 01:47:40.298277 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:40.306573 INFO::ASW Batch was -0.0502253874755889 prior to batch effect correction and is now -0.0502253874755889 .
2025-11-21 01:47:40.310555 INFO::Total function execution time is 1.10365509986877 s and adjustment time is 0.300014019012451 s ( 27.18 )
2025-11-21 01:47:40.354734 INFO::Formatting Data.
2025-11-21 01:47:40.357562 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:40.360762 INFO::Removing potential empty rows and columns
2025-11-21 01:47:40.365214 INFO::Found 0 missing values.
2025-11-21 01:47:40.367974 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.
2025-11-21 01:47:40.401795 INFO::Formatting Data.
2025-11-21 01:47:40.403616 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:40.405897 INFO::Removing potential empty rows and columns
2025-11-21 01:47:40.408885 INFO::Found 0 missing values.
2025-11-21 01:47:40.411497 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.
2025-11-21 01:47:40.458561 INFO::Formatting Data.
2025-11-21 01:47:40.460256 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:40.462866 INFO::Removing potential empty rows and columns
2025-11-21 01:47:40.465921 INFO::Found 0 missing values.
2025-11-21 01:47:40.468721 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.
2025-11-21 01:47:40.481537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:40.483019 INFO::Done
2025-11-21 01:47:40.484384 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:40.489412 INFO::Starting hierarchical adjustment
2025-11-21 01:47:40.491396 INFO::Found 2 batches.
2025-11-21 01:47:40.492866 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:40.494593 INFO::Using default BPPARAM
2025-11-21 01:47:40.496412 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:40.499028 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 01:47:40.558035 INFO::Done
2025-11-21 01:47:40.559556 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:40.564798 INFO::ASW Batch was -0.0413608788303427 prior to batch effect correction and is now -0.128246310541651 .
2025-11-21 01:47:40.567044 INFO::Total function execution time is 0.108445882797241 s and adjustment time is 0.0669970512390137 s ( 61.78 )
2025-11-21 01:47:40.574132 INFO::Formatting Data.
2025-11-21 01:47:40.575755 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:40.600154 INFO::Formatting Data.
2025-11-21 01:47:40.601865 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:40.604073 INFO::Removing potential empty rows and columns
2025-11-21 01:47:40.606729 INFO::Found 0 missing values.
2025-11-21 01:47:40.615881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:40.617405 INFO::Done
2025-11-21 01:47:40.619666 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:40.624827 INFO::Starting hierarchical adjustment
2025-11-21 01:47:40.675654 INFO::Found 2 batches.
2025-11-21 01:47:40.677045 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:40.678464 INFO::Using default BPPARAM
2025-11-21 01:47:40.679744 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:40.681769 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 01:47:40.720694 INFO::Done
2025-11-21 01:47:40.722199 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:40.727362 INFO::ASW Batch was 0.0352024075949237 prior to batch effect correction and is now -0.0804498578306276 .
2025-11-21 01:47:40.729274 INFO::Total function execution time is 0.129189014434814 s and adjustment time is 0.0454039573669434 s ( 35.15 )
2025-11-21 01:47:40.731627 INFO::Formatting Data.
2025-11-21 01:47:40.733071 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:40.73531 INFO::Removing potential empty rows and columns
2025-11-21 01:47:40.737919 INFO::Found 0 missing values.
2025-11-21 01:47:40.745496 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:40.746944 INFO::Done
2025-11-21 01:47:40.748251 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:40.752704 INFO::Starting hierarchical adjustment
2025-11-21 01:47:40.7546 INFO::Found 2 batches.
2025-11-21 01:47:40.756021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:40.757547 INFO::Using default BPPARAM
2025-11-21 01:47:40.758864 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:40.761028 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 01:47:40.798578 INFO::Done
2025-11-21 01:47:40.80003 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:40.804603 INFO::ASW Batch was 0.0352024075949237 prior to batch effect correction and is now -0.0804498578306276 .
2025-11-21 01:47:40.806528 INFO::Total function execution time is 0.0748379230499268 s and adjustment time is 0.0443260669708252 s ( 59.23 )
Warning: stack imbalance in '::', 79 then 80
Warning: stack imbalance in '=', 77 then 78
2025-11-21 01:47:47.307566 INFO::Formatting Data.
2025-11-21 01:47:47.309532 INFO::Recognized SummarizedExperiment
2025-11-21 01:47:47.310706 INFO::Typecasting input to dataframe.
2025-11-21 01:47:47.378894 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:47.381553 INFO::Removing potential empty rows and columns
2025-11-21 01:47:47.393255 INFO::Found 0 missing values.
2025-11-21 01:47:47.416661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:47.418261 INFO::Done
2025-11-21 01:47:47.422087 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:47.43087 INFO::Starting hierarchical adjustment
2025-11-21 01:47:47.432574 INFO::Found 2 batches.
2025-11-21 01:47:47.433882 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:47.436468 INFO::Using default BPPARAM
2025-11-21 01:47:47.438528 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:47.441207 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 01:47:47.598094 INFO::Done
2025-11-21 01:47:47.599675 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:47.609047 INFO::ASW Batch was -0.0174793094922857 prior to batch effect correction and is now -0.0910137330367236 .
2025-11-21 01:47:47.611198 INFO::Total function execution time is 0.304220914840698 s and adjustment time is 0.165847063064575 s ( 54.52 )
Warning: stack imbalance in '{', 73 then 74
2025-11-21 01:47:47.66111 INFO::Formatting Data.
2025-11-21 01:47:47.662539 INFO::Recognized SummarizedExperiment
2025-11-21 01:47:47.663687 INFO::Typecasting input to dataframe.
2025-11-21 01:47:47.688099 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:47.690872 INFO::Removing potential empty rows and columns
2025-11-21 01:47:47.703066 INFO::Found 0 missing values.
2025-11-21 01:47:47.727248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:47.728649 INFO::Done
2025-11-21 01:47:47.729798 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:47.738578 INFO::Starting hierarchical adjustment
2025-11-21 01:47:47.740594 INFO::Found 2 batches.
2025-11-21 01:47:47.742126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:47.743756 INFO::Using default BPPARAM
2025-11-21 01:47:47.745246 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:47.748225 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 01:47:47.824505 INFO::Done
2025-11-21 01:47:47.826127 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:47.835129 INFO::ASW Batch was 0.0110415658825499 prior to batch effect correction and is now 0.0110415658825499 .
2025-11-21 01:47:47.837471 INFO::Total function execution time is 0.176244974136353 s and adjustment time is 0.0843439102172852 s ( 47.86 )
2025-11-21 01:47:47.889207 INFO::Formatting Data.
2025-11-21 01:47:47.890939 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:47.893087 INFO::Removing potential empty rows and columns
2025-11-21 01:47:47.897003 INFO::Found 0 missing values.
2025-11-21 01:47:47.904398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:47.906174 INFO::Done
2025-11-21 01:47:47.907381 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:47.911931 INFO::Starting hierarchical adjustment
2025-11-21 01:47:47.913836 INFO::Found 3 batches.
2025-11-21 01:47:47.915101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:47.917639 INFO::Using default BPPARAM
2025-11-21 01:47:47.918974 INFO::Processing subtree level 1
2025-11-21 01:47:48.28283 INFO::Adjusting the last 1 batches sequentially
2025-11-21 01:47:48.295147 INFO::Done
2025-11-21 01:47:48.297759 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:48.310926 INFO::ASW Batch was -0.0631970656021708 prior to batch effect correction and is now -0.160968204230111 .
2025-11-21 01:47:48.315017 INFO::Total function execution time is 0.42509388923645 s and adjustment time is 0.381645917892456 s ( 89.78 )
2025-11-21 01:47:48.357316 INFO::Skipping initial DF formatting
2025-11-21 01:47:48.359807 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:48.370602 INFO::Starting hierarchical adjustment
2025-11-21 01:47:48.372643 INFO::Found 5 batches.
2025-11-21 01:47:48.374558 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:48.376279 INFO::Using default BPPARAM
2025-11-21 01:47:48.378739 INFO::Processing subtree level 1
2025-11-21 01:47:48.964157 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:48.985574 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 01:47:49.065969 INFO::Done
2025-11-21 01:47:49.069012 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:49.086728 INFO::ASW Batch was 0.539830382171923 prior to batch effect correction and is now 0.539830382171923 .
2025-11-21 01:47:49.088987 INFO::ASW Label was 0.351653117562285 prior to batch effect correction and is now 0.351653117562285 .
2025-11-21 01:47:49.091598 INFO::Total function execution time is 0.734184980392456 s and adjustment time is 0.693712949752808 s ( 94.49 )
2025-11-21 01:47:49.248896 INFO::Formatting Data.
2025-11-21 01:47:49.250691 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:49.252915 INFO::Removing potential empty rows and columns
2025-11-21 01:47:49.255577 INFO::Found 0 missing values.
2025-11-21 01:47:49.266457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:49.267965 INFO::Done
2025-11-21 01:47:49.26928 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:49.276006 INFO::Starting hierarchical adjustment
2025-11-21 01:47:49.277832 INFO::Found 5 batches.
2025-11-21 01:47:49.279317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:49.280916 INFO::Using default BPPARAM
2025-11-21 01:47:49.282353 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.
2025-11-21 01:47:49.620917 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:49.627128 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 01:47:49.709719 INFO::Done
2025-11-21 01:47:49.712162 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:49.725514 INFO::ASW Batch was 0.230953291388973 prior to batch effect correction and is now -0.054317940373937 .
2025-11-21 01:47:49.727852 INFO::ASW Label was 0.566710795626875 prior to batch effect correction and is now 0.8003641236008 .
2025-11-21 01:47:49.731221 INFO::Total function execution time is 0.482123851776123 s and adjustment time is 0.432164907455444 s ( 89.64 )
2025-11-21 01:47:49.735009 INFO::Formatting Data.
2025-11-21 01:47:49.73768 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:49.741243 INFO::Removing potential empty rows and columns
2025-11-21 01:47:49.745675 INFO::Found 0 missing values.
2025-11-21 01:47:49.763341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:49.766162 INFO::Done
2025-11-21 01:47:49.768611 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:49.780137 INFO::Starting hierarchical adjustment
2025-11-21 01:47:49.785417 INFO::Found 5 batches.
2025-11-21 01:47:49.78787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:49.790202 INFO::Using default BPPARAM
2025-11-21 01:47:49.792194 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.
2025-11-21 01:47:50.124158 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:50.130027 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 01:47:50.187451 INFO::Done
2025-11-21 01:47:50.189633 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:50.200417 INFO::ASW Batch was 0.230953291388973 prior to batch effect correction and is now -0.054317940373937 .
2025-11-21 01:47:50.202491 INFO::ASW Label was 0.566710795626875 prior to batch effect correction and is now 0.8003641236008 .
2025-11-21 01:47:50.205178 INFO::Total function execution time is 0.470194816589355 s and adjustment time is 0.402696847915649 s ( 85.64 )
2025-11-21 01:47:50.258245 INFO::Formatting Data.
2025-11-21 01:47:50.260564 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:50.26359 INFO::Removing potential empty rows and columns
2025-11-21 01:47:50.266944 INFO::Found 0 missing values.
2025-11-21 01:47:50.281675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:50.283503 INFO::Done
2025-11-21 01:47:50.285362 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:50.295237 INFO::Starting hierarchical adjustment
2025-11-21 01:47:50.297756 INFO::Found 5 batches.
2025-11-21 01:47:50.299555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:50.30152 INFO::Using default BPPARAM
2025-11-21 01:47:50.303329 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.
2025-11-21 01:47:50.702752 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:50.713986 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 01:47:50.772853 INFO::Done
2025-11-21 01:47:50.774998 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:50.785206 INFO::ASW Batch was 0.688185347156178 prior to batch effect correction and is now -0.100878515174797 .
2025-11-21 01:47:50.787074 INFO::ASW Label was 0.0183714113602183 prior to batch effect correction and is now 0.664930004432625 .
2025-11-21 01:47:50.789144 INFO::Total function execution time is 0.531059980392456 s and adjustment time is 0.475603818893433 s ( 89.56 )
2025-11-21 01:47:50.792162 INFO::Formatting Data.
2025-11-21 01:47:50.793933 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:50.79706 INFO::Removing potential empty rows and columns
2025-11-21 01:47:50.799777 INFO::Found 0 missing values.
2025-11-21 01:47:50.811025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:50.812602 INFO::Done
2025-11-21 01:47:50.814079 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:50.821476 INFO::Starting hierarchical adjustment
2025-11-21 01:47:50.823425 INFO::Found 5 batches.
2025-11-21 01:47:50.824843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:50.826843 INFO::Using default BPPARAM
2025-11-21 01:47:50.828939 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.
2025-11-21 01:47:51.163296 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:51.177378 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 01:47:51.242011 INFO::Done
2025-11-21 01:47:51.244028 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:51.257779 INFO::ASW Batch was 0.688185347156178 prior to batch effect correction and is now -0.100878515174797 .
2025-11-21 01:47:51.259507 INFO::ASW Label was 0.0183714113602183 prior to batch effect correction and is now 0.664930004432625 .
2025-11-21 01:47:51.262093 INFO::Total function execution time is 0.46993613243103 s and adjustment time is 0.418949127197266 s ( 89.15 )
2025-11-21 01:47:51.300737 INFO::Formatting Data.
2025-11-21 01:47:51.302586 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:51.304976 INFO::Removing potential empty rows and columns
2025-11-21 01:47:51.307727 INFO::Found 0 missing values.
2025-11-21 01:47:51.315216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:51.316687 INFO::Done
2025-11-21 01:47:51.317982 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:51.325216 INFO::Starting hierarchical adjustment
2025-11-21 01:47:51.327105 INFO::Found 2 batches.
2025-11-21 01:47:51.328483 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:51.329999 INFO::Using default BPPARAM
2025-11-21 01:47:51.331341 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:51.333507 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 01:47:51.369404 INFO::Done
2025-11-21 01:47:51.370955 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:51.37819 INFO::ASW Batch was 0.734428263861566 prior to batch effect correction and is now 0.0223385189911922 .
2025-11-21 01:47:51.379834 INFO::ASW Label was 0.338802833328366 prior to batch effect correction and is now 0.877900092528032 .
2025-11-21 01:47:51.38179 INFO::Total function execution time is 0.0811691284179688 s and adjustment time is 0.042618989944458 s ( 52.51 )
2025-11-21 01:47:51.383804 INFO::Formatting Data.
2025-11-21 01:47:51.385384 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:51.387556 INFO::Removing potential empty rows and columns
2025-11-21 01:47:51.390073 INFO::Found 0 missing values.
2025-11-21 01:47:51.397391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:51.398885 INFO::Done
2025-11-21 01:47:51.40024 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:51.407204 INFO::Starting hierarchical adjustment
2025-11-21 01:47:51.409136 INFO::Found 2 batches.
2025-11-21 01:47:51.410511 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:51.412041 INFO::Using default BPPARAM
2025-11-21 01:47:51.413365 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:51.415988 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-21 01:47:51.454102 INFO::Done
2025-11-21 01:47:51.455601 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:51.462947 INFO::ASW Batch was 0.734428263861566 prior to batch effect correction and is now 0.0223385189911922 .
2025-11-21 01:47:51.464496 INFO::ASW Label was 0.338802833328366 prior to batch effect correction and is now 0.877900092528032 .
2025-11-21 01:47:51.466427 INFO::Total function execution time is 0.0826740264892578 s and adjustment time is 0.0453410148620605 s ( 54.84 )
2025-11-21 01:47:51.497225 INFO::Formatting Data.
2025-11-21 01:47:51.498918 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:51.501042 INFO::Removing potential empty rows and columns
2025-11-21 01:47:51.503383 INFO::Found 0 missing values.
2025-11-21 01:47:51.509217 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:51.5107 INFO::Done
2025-11-21 01:47:51.512056 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:51.516573 INFO::Starting hierarchical adjustment
2025-11-21 01:47:51.518344 INFO::Found 2 batches.
2025-11-21 01:47:51.519667 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:51.521156 INFO::Using default BPPARAM
2025-11-21 01:47:51.522621 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:51.525057 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 01:47:51.604368 INFO::Done
2025-11-21 01:47:51.605849 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:51.610227 INFO::ASW Batch was -0.0699974361035129 prior to batch effect correction and is now -0.126909523261906 .
2025-11-21 01:47:51.612203 INFO::Total function execution time is 0.115102052688599 s and adjustment time is 0.0863571166992188 s ( 75.03 )
2025-11-21 01:47:51.642314 INFO::Formatting Data.
2025-11-21 01:47:51.644025 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:51.646108 INFO::Removing potential empty rows and columns
2025-11-21 01:47:51.648591 INFO::Found 0 missing values.
2025-11-21 01:47:51.651213 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.
2025-11-21 01:47:51.663179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:51.664683 INFO::Done
2025-11-21 01:47:51.666022 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:51.673129 INFO::Starting hierarchical adjustment
2025-11-21 01:47:51.675075 INFO::Found 2 batches.
2025-11-21 01:47:51.676525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:51.678069 INFO::Using default BPPARAM
2025-11-21 01:47:51.679436 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:51.681855 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 01:47:51.725005 INFO::Done
2025-11-21 01:47:51.726417 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:51.732849 INFO::ASW Batch was 0.540029416289818 prior to batch effect correction and is now 0.0797602869225195 .
2025-11-21 01:47:51.734366 INFO::ASW Label was 0.430179044595038 prior to batch effect correction and is now 0.869845477791266 .
2025-11-21 01:47:51.736218 INFO::Total function execution time is 0.0939948558807373 s and adjustment time is 0.0503108501434326 s ( 53.53 )
2025-11-21 01:47:51.738239 INFO::Formatting Data.
2025-11-21 01:47:51.739944 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:51.742357 INFO::Removing potential empty rows and columns
2025-11-21 01:47:51.745039 INFO::Found 0 missing values.
2025-11-21 01:47:51.747552 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.
2025-11-21 01:47:51.760442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:51.761965 INFO::Done
2025-11-21 01:47:51.763454 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:51.770889 INFO::Starting hierarchical adjustment
2025-11-21 01:47:51.772953 INFO::Found 2 batches.
2025-11-21 01:47:51.77452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:51.776189 INFO::Using default BPPARAM
2025-11-21 01:47:51.777693 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:51.780261 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 01:47:51.825881 INFO::Done
2025-11-21 01:47:51.827478 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:51.836267 INFO::ASW Batch was 0.540029416289818 prior to batch effect correction and is now 0.0797602869225195 .
2025-11-21 01:47:51.837765 INFO::ASW Label was 0.430179044595038 prior to batch effect correction and is now 0.869845477791266 .
2025-11-21 01:47:51.839599 INFO::Total function execution time is 0.101460933685303 s and adjustment time is 0.0533630847930908 s ( 52.59 )
2025-11-21 01:47:52.46912 INFO::Formatting Data.
2025-11-21 01:47:52.470957 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:52.473885 INFO::Removing potential empty rows and columns
2025-11-21 01:47:52.476587 INFO::Found 0 missing values.
2025-11-21 01:47:52.484883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:52.486393 INFO::Done
2025-11-21 01:47:52.4878 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:52.492799 INFO::Starting hierarchical adjustment
2025-11-21 01:47:52.494991 INFO::Found 3 batches.
2025-11-21 01:47:52.496509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:52.498136 INFO::Using default BPPARAM
2025-11-21 01:47:52.499649 INFO::Processing subtree level 1
2025-11-21 01:47:52.735496 INFO::Adjusting the last 1 batches sequentially
2025-11-21 01:47:52.746847 INFO::Done
2025-11-21 01:47:52.748622 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:52.760401 INFO::ASW Batch was -0.143787796339386 prior to batch effect correction and is now -0.143787796339386 .
2025-11-21 01:47:52.764314 INFO::Total function execution time is 0.294471025466919 s and adjustment time is 0.252297163009644 s ( 85.68 )
2025-11-21 01:47:52.767091 INFO::Formatting Data.
2025-11-21 01:47:52.768869 INFO::Typecasting input to dataframe.
2025-11-21 01:47:52.770968 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:52.777473 INFO::Removing potential empty rows and columns
2025-11-21 01:47:52.784006 INFO::Found 0 missing values.
2025-11-21 01:47:52.79323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:52.795072 INFO::Done
2025-11-21 01:47:52.796563 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:52.801591 INFO::Starting hierarchical adjustment
2025-11-21 01:47:52.80405 INFO::Found 3 batches.
2025-11-21 01:47:52.80564 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:52.808062 INFO::Using default BPPARAM
2025-11-21 01:47:52.809689 INFO::Processing subtree level 1
2025-11-21 01:47:53.045646 INFO::Adjusting the last 1 batches sequentially
2025-11-21 01:47:53.057334 INFO::Done
2025-11-21 01:47:53.060611 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:53.072943 INFO::ASW Batch was -0.143787796339386 prior to batch effect correction and is now -0.143787796339386 .
2025-11-21 01:47:53.076158 INFO::Total function execution time is 0.308847904205322 s and adjustment time is 0.254138946533203 s ( 82.29 )
2025-11-21 01:47:53.113413 INFO::Formatting Data.
2025-11-21 01:47:53.115328 INFO::Typecasting input to dataframe.
2025-11-21 01:47:53.117589 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:53.119986 INFO::Removing potential empty rows and columns
2025-11-21 01:47:53.1235 INFO::Found 0 missing values.
2025-11-21 01:47:53.133405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:53.137377 INFO::Done
2025-11-21 01:47:53.139054 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:53.144455 INFO::Starting hierarchical adjustment
2025-11-21 01:47:53.146255 INFO::Found 3 batches.
2025-11-21 01:47:53.14942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:53.150897 INFO::Using default BPPARAM
2025-11-21 01:47:53.153455 INFO::Processing subtree level 1
2025-11-21 01:47:53.394251 INFO::Adjusting the last 1 batches sequentially
2025-11-21 01:47:53.407156 INFO::Done
2025-11-21 01:47:53.409721 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:53.42025 INFO::ASW Batch was 6.72644459352831e-05 prior to batch effect correction and is now 6.72644459352831e-05 .
2025-11-21 01:47:53.423185 INFO::Total function execution time is 0.30978798866272 s and adjustment time is 0.261155128479004 s ( 84.3 )
2025-11-21 01:47:53.811379 INFO::Formatting Data.
2025-11-21 01:47:53.813105 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:53.816493 INFO::Removing potential empty rows and columns
2025-11-21 01:47:53.824357 INFO::Found 1000 missing values.
2025-11-21 01:47:53.884752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:53.886674 INFO::Done
2025-11-21 01:47:53.888854 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:53.905147 INFO::Starting hierarchical adjustment
2025-11-21 01:47:53.907391 INFO::Found 10 batches.
2025-11-21 01:47:53.91191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:53.913747 INFO::Using default BPPARAM
2025-11-21 01:47:53.917031 INFO::Processing subtree level 1
2025-11-21 01:47:54.2345 INFO::Processing subtree level 2
2025-11-21 01:47:54.653715 INFO::Adjusting the last 1 batches sequentially
2025-11-21 01:47:54.670937 INFO::Done
2025-11-21 01:47:54.674689 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:54.693709 INFO::ASW Batch was 0.535894867045085 prior to batch effect correction and is now 0.535894867045085 .
2025-11-21 01:47:54.696598 INFO::ASW Label was 0.298092935243604 prior to batch effect correction and is now 0.298092935243604 .
2025-11-21 01:47:54.700671 INFO::Total function execution time is 0.888700008392334 s and adjustment time is 0.763968229293823 s ( 85.96 )
2025-11-21 01:47:54.703254 INFO::Formatting Data.
2025-11-21 01:47:54.705603 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:54.709511 INFO::Removing potential empty rows and columns
2025-11-21 01:47:54.718152 INFO::Found 1000 missing values.
2025-11-21 01:47:54.777857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:54.779893 INFO::Done
2025-11-21 01:47:54.78226 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:54.799442 INFO::Starting hierarchical adjustment
2025-11-21 01:47:54.801424 INFO::Found 10 batches.
2025-11-21 01:47:56.234732 INFO::Set up parallel execution backend with 2 workers
2025-11-21 01:47:56.236287 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-21 01:47:58.164794 INFO::Adjusting the last 2 batches sequentially
2025-11-21 01:47:58.168384 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-21 01:47:58.220755 INFO::Done
2025-11-21 01:47:58.222099 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:58.235729 INFO::ASW Batch was 0.535894867045085 prior to batch effect correction and is now 0.535894867045085 .
2025-11-21 01:47:58.238552 INFO::ASW Label was 0.298092935243604 prior to batch effect correction and is now 0.298092935243604 .
2025-11-21 01:47:58.240086 INFO::Total function execution time is 3.53709816932678 s and adjustment time is 3.41974496841431 s ( 96.68 )
2025-11-21 01:47:58.647686 INFO::Formatting Data.
2025-11-21 01:47:58.64957 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:58.653126 INFO::Removing potential empty rows and columns
2025-11-21 01:47:58.656747 INFO::Found 0 missing values.
2025-11-21 01:47:58.668745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:58.670345 INFO::Done
2025-11-21 01:47:58.671731 INFO::Acquiring quality metrics before batch effect correction.
2025-11-21 01:47:58.680539 INFO::Starting hierarchical adjustment
2025-11-21 01:47:58.682538 INFO::Found 3 batches.
2025-11-21 01:47:58.683941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-21 01:47:58.68553 INFO::Using default BPPARAM
2025-11-21 01:47:58.686989 INFO::Processing subtree level 1
2025-11-21 01:47:58.993662 INFO::Adjusting the last 1 batches sequentially
2025-11-21 01:47:59.005842 INFO::Done
2025-11-21 01:47:59.00918 INFO::Acquiring quality metrics after batch effect correction.
2025-11-21 01:47:59.024725 INFO::ASW Batch was 0.162747182491147 prior to batch effect correction and is now -0.127285705518388 .
2025-11-21 01:47:59.026658 INFO::ASW Label was -0.205937525660562 prior to batch effect correction and is now -0.0338172166096471 .
2025-11-21 01:47:59.029916 INFO::Total function execution time is 0.382066011428833 s and adjustment time is 0.323672771453857 s ( 84.72 )
2025-11-21 01:47:59.410451 INFO::Formatting Data.
2025-11-21 01:47:59.412413 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:59.41553 INFO::Removing potential empty rows and columns
2025-11-21 01:47:59.418918 INFO::Found 2 missing values.
2025-11-21 01:47:59.426748 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:59.429856 INFO::Done
2025-11-21 01:47:59.521251 INFO::Found NA in Reference column
2025-11-21 01:47:59.55183 INFO::Require at least two references per batch.
2025-11-21 01:47:59.61591 INFO::Formatting Data.
2025-11-21 01:47:59.617347 INFO::Recognized SummarizedExperiment
2025-11-21 01:47:59.618688 INFO::Typecasting input to dataframe.
2025-11-21 01:47:59.648646 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:59.651441 INFO::Removing potential empty rows and columns
2025-11-21 01:47:59.663357 INFO::Found 0 missing values.
2025-11-21 01:47:59.688116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:59.689743 INFO::Done
2025-11-21 01:47:59.735833 INFO::Formatting Data.
2025-11-21 01:47:59.737452 INFO::Recognized SummarizedExperiment
2025-11-21 01:47:59.738829 INFO::Typecasting input to dataframe.
2025-11-21 01:47:59.791528 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:59.79427 INFO::Removing potential empty rows and columns
2025-11-21 01:47:59.806383 INFO::Found 0 missing values.
2025-11-21 01:47:59.845503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:59.847011 INFO::Done
2025-11-21 01:47:59.888312 INFO::Formatting Data.
2025-11-21 01:47:59.889687 INFO::Recognized SummarizedExperiment
2025-11-21 01:47:59.890838 INFO::Typecasting input to dataframe.
2025-11-21 01:47:59.935901 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:59.938401 INFO::Removing potential empty rows and columns
2025-11-21 01:47:59.941058 INFO::Found 0 missing values.
2025-11-21 01:47:59.94332 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.
2025-11-21 01:47:59.955553 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:47:59.957542 INFO::Done
2025-11-21 01:47:59.985382 INFO::Formatting Data.
2025-11-21 01:47:59.987189 INFO::Replacing NaNs with NAs.
2025-11-21 01:47:59.989287 INFO::Removing potential empty rows and columns
2025-11-21 01:47:59.992963 INFO::Found 0 missing values.
2025-11-21 01:48:00.004253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:48:00.00585 INFO::Done
2025-11-21 01:48:00.0392 INFO::Formatting Data.
2025-11-21 01:48:00.041178 INFO::Replacing NaNs with NAs.
2025-11-21 01:48:00.043497 INFO::Removing potential empty rows and columns
2025-11-21 01:48:00.046594 INFO::Found 0 missing values.
2025-11-21 01:48:00.056261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:48:00.058744 INFO::Done
2025-11-21 01:48:00.146916 INFO::Formatting Data.
2025-11-21 01:48:00.148712 INFO::Replacing NaNs with NAs.
2025-11-21 01:48:00.152793 INFO::Removing potential empty rows and columns
2025-11-21 01:48:00.156306 INFO::Found 1 missing values.
2025-11-21 01:48:00.164827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:48:00.16689 INFO::Done
2025-11-21 01:48:00.227286 INFO::Formatting Data.
2025-11-21 01:48:00.229098 INFO::Replacing NaNs with NAs.
2025-11-21 01:48:00.231168 INFO::Removing potential empty rows and columns
2025-11-21 01:48:00.23348 INFO::Found 2 missing values.
2025-11-21 01:48:00.2356 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.
2025-11-21 01:48:00.242706 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:48:00.244249 INFO::Done
2025-11-21 01:48:00.276152 INFO::Formatting Data.
2025-11-21 01:48:00.277937 INFO::Replacing NaNs with NAs.
2025-11-21 01:48:00.281937 INFO::Removing potential empty rows and columns
2025-11-21 01:48:00.285104 INFO::Found 2 missing values.
2025-11-21 01:48:00.289273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:48:00.290725 INFO::Done
2025-11-21 01:48:00.325611 INFO::Formatting Data.
2025-11-21 01:48:00.328073 INFO::Typecasting input to dataframe.
2025-11-21 01:48:00.330775 INFO::Replacing NaNs with NAs.
2025-11-21 01:48:00.3336 INFO::Removing potential empty rows and columns
2025-11-21 01:48:00.336912 INFO::Found 0 missing values.
2025-11-21 01:48:00.346932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-21 01:48:00.349447 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.078 6.786 44.537
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.693 | 2.571 | 35.131 | |
| compute_asw | 0.059 | 0.003 | 0.069 | |
| count_existing | 0.027 | 0.002 | 0.034 | |
| generate_data_covariables | 0.026 | 0.002 | 0.031 | |
| generate_dataset | 0.023 | 0.001 | 0.026 | |