Yannis Schumann
| Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
| 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 163/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 1.5.0 |
| 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_1.5.0.tar.gz |
| StartedAt: 2025-09-22 19:30:44 -0400 (Mon, 22 Sep 2025) |
| EndedAt: 2025-09-22 19:32:10 -0400 (Mon, 22 Sep 2025) |
| EllapsedTime: 86.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘1.5.0’
* 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 26.667 1.448 19.181
* 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 ‘1.5.0’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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")
2025-09-22 19:31:49.17586 INFO::Formatting Data.
2025-09-22 19:31:49.180311 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:49.194571 INFO::Removing potential empty rows and columns
2025-09-22 19:31:49.508665 INFO::Found 0 missing values.
2025-09-22 19:31:49.512681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:49.513504 INFO::Done
2025-09-22 19:31:49.514578 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:49.532045 INFO::Starting hierarchical adjustment
2025-09-22 19:31:49.533344 INFO::Found 3 batches.
2025-09-22 19:31:49.534229 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:49.535811 INFO::Using default BPPARAM
2025-09-22 19:31:49.536665 INFO::Processing subtree level 1
2025-09-22 19:31:49.705644 INFO::Adjusting the last 1 batches sequentially
2025-09-22 19:31:49.710886 INFO::Done
2025-09-22 19:31:49.712651 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:49.719636 INFO::ASW Batch was 0.018024173881602 prior to batch effect correction and is now 0.018024173881602 .
2025-09-22 19:31:49.721413 INFO::Total function execution time is 0.546501159667969 s and adjustment time is 0.177828788757324 s ( 32.54 )
2025-09-22 19:31:49.745841 INFO::Formatting Data.
2025-09-22 19:31:49.747417 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:49.750159 INFO::Removing potential empty rows and columns
2025-09-22 19:31:49.751825 INFO::Found 0 missing values.
2025-09-22 19:31:49.752999 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.
2025-09-22 19:31:49.76811 INFO::Formatting Data.
2025-09-22 19:31:49.769449 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:49.770896 INFO::Removing potential empty rows and columns
2025-09-22 19:31:49.771947 INFO::Found 0 missing values.
2025-09-22 19:31:49.773218 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.
2025-09-22 19:31:49.795643 INFO::Formatting Data.
2025-09-22 19:31:49.796817 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:49.798162 INFO::Removing potential empty rows and columns
2025-09-22 19:31:49.799657 INFO::Found 0 missing values.
2025-09-22 19:31:49.800983 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.
2025-09-22 19:31:49.806983 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:49.80794 INFO::Done
2025-09-22 19:31:49.808823 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:49.811768 INFO::Starting hierarchical adjustment
2025-09-22 19:31:49.81277 INFO::Found 2 batches.
2025-09-22 19:31:49.813384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:49.813971 INFO::Using default BPPARAM
2025-09-22 19:31:49.81447 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:49.815355 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 19:31:49.844518 INFO::Done
2025-09-22 19:31:49.845514 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:49.8483 INFO::ASW Batch was -0.0565629509964803 prior to batch effect correction and is now -0.11944976090971 .
2025-09-22 19:31:49.849093 INFO::Total function execution time is 0.0536210536956787 s and adjustment time is 0.0319089889526367 s ( 59.51 )
2025-09-22 19:31:49.852215 INFO::Formatting Data.
2025-09-22 19:31:49.853078 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:49.863934 INFO::Formatting Data.
2025-09-22 19:31:49.864671 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:49.865666 INFO::Removing potential empty rows and columns
2025-09-22 19:31:49.867097 INFO::Found 0 missing values.
2025-09-22 19:31:49.871353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:49.872035 INFO::Done
2025-09-22 19:31:49.872544 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:49.874569 INFO::Starting hierarchical adjustment
2025-09-22 19:31:49.875224 INFO::Found 2 batches.
2025-09-22 19:31:49.875736 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:49.876419 INFO::Using default BPPARAM
2025-09-22 19:31:49.877136 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:49.878037 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 19:31:49.933446 INFO::Done
2025-09-22 19:31:49.93411 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:49.936077 INFO::ASW Batch was 0.178867586353154 prior to batch effect correction and is now -0.106816321421856 .
2025-09-22 19:31:49.937124 INFO::Total function execution time is 0.0732059478759766 s and adjustment time is 0.0583128929138184 s ( 79.66 )
2025-09-22 19:31:49.93855 INFO::Formatting Data.
2025-09-22 19:31:49.93936 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:49.940498 INFO::Removing potential empty rows and columns
2025-09-22 19:31:49.941824 INFO::Found 0 missing values.
2025-09-22 19:31:49.945525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:49.946238 INFO::Done
2025-09-22 19:31:49.946945 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:49.949485 INFO::Starting hierarchical adjustment
2025-09-22 19:31:49.9501 INFO::Found 2 batches.
2025-09-22 19:31:49.950559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:49.951396 INFO::Using default BPPARAM
2025-09-22 19:31:49.952112 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:49.953341 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 19:31:49.973196 INFO::Done
2025-09-22 19:31:49.974262 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:49.977101 INFO::ASW Batch was 0.178867586353154 prior to batch effect correction and is now -0.106816321421856 .
2025-09-22 19:31:49.978238 INFO::Total function execution time is 0.0396721363067627 s and adjustment time is 0.0231618881225586 s ( 58.38 )
2025-09-22 19:31:53.433389 INFO::Formatting Data.
2025-09-22 19:31:53.434337 INFO::Recognized SummarizedExperiment
2025-09-22 19:31:53.43513 INFO::Typecasting input to dataframe.
2025-09-22 19:31:53.470667 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:53.472338 INFO::Removing potential empty rows and columns
2025-09-22 19:31:53.477711 INFO::Found 0 missing values.
2025-09-22 19:31:53.487429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:53.488629 INFO::Done
2025-09-22 19:31:53.489477 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:53.494736 INFO::Starting hierarchical adjustment
2025-09-22 19:31:53.495861 INFO::Found 2 batches.
2025-09-22 19:31:53.496623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:53.498034 INFO::Using default BPPARAM
2025-09-22 19:31:53.498527 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:53.499489 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 19:31:53.56908 INFO::Done
2025-09-22 19:31:53.570019 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:53.575407 INFO::ASW Batch was 0.00204481339386877 prior to batch effect correction and is now -0.0923698243031387 .
2025-09-22 19:31:53.576775 INFO::Total function execution time is 0.14349102973938 s and adjustment time is 0.0734219551086426 s ( 51.17 )
2025-09-22 19:31:53.600603 INFO::Formatting Data.
2025-09-22 19:31:53.601423 INFO::Recognized SummarizedExperiment
2025-09-22 19:31:53.601974 INFO::Typecasting input to dataframe.
2025-09-22 19:31:53.615025 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:53.616883 INFO::Removing potential empty rows and columns
2025-09-22 19:31:53.62156 INFO::Found 0 missing values.
2025-09-22 19:31:53.630062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:53.630777 INFO::Done
2025-09-22 19:31:53.631312 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:53.635956 INFO::Starting hierarchical adjustment
2025-09-22 19:31:53.637139 INFO::Found 2 batches.
2025-09-22 19:31:53.637947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:53.638787 INFO::Using default BPPARAM
2025-09-22 19:31:53.639495 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:53.640944 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 19:31:53.672287 INFO::Done
2025-09-22 19:31:53.673018 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:53.678046 INFO::ASW Batch was 0.00187471169127347 prior to batch effect correction and is now 0.00187471169127347 .
2025-09-22 19:31:53.679404 INFO::Total function execution time is 0.0787360668182373 s and adjustment time is 0.0354101657867432 s ( 44.97 )
2025-09-22 19:31:53.706381 INFO::Formatting Data.
2025-09-22 19:31:53.707494 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:53.708715 INFO::Removing potential empty rows and columns
2025-09-22 19:31:53.709656 INFO::Found 0 missing values.
2025-09-22 19:31:53.713389 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:53.714373 INFO::Done
2025-09-22 19:31:53.715204 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:53.718004 INFO::Starting hierarchical adjustment
2025-09-22 19:31:53.719084 INFO::Found 3 batches.
2025-09-22 19:31:53.719874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:53.72072 INFO::Using default BPPARAM
2025-09-22 19:31:53.721376 INFO::Processing subtree level 1
2025-09-22 19:31:53.95927 INFO::Adjusting the last 1 batches sequentially
2025-09-22 19:31:53.967721 INFO::Done
2025-09-22 19:31:53.969292 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:53.978011 INFO::ASW Batch was -0.0292816895202123 prior to batch effect correction and is now -0.161163102762998 .
2025-09-22 19:31:53.981066 INFO::Total function execution time is 0.274744987487793 s and adjustment time is 0.248843908309937 s ( 90.57 )
2025-09-22 19:31:54.005022 INFO::Skipping initial DF formatting
2025-09-22 19:31:54.006356 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:54.011163 INFO::Starting hierarchical adjustment
2025-09-22 19:31:54.012599 INFO::Found 5 batches.
2025-09-22 19:31:54.013357 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:54.014039 INFO::Using default BPPARAM
2025-09-22 19:31:54.014668 INFO::Processing subtree level 1
2025-09-22 19:31:54.390928 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:54.394567 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 19:31:54.422285 INFO::Done
2025-09-22 19:31:54.423547 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:54.431183 INFO::ASW Batch was 0.607152505910432 prior to batch effect correction and is now 0.607152505910432 .
2025-09-22 19:31:54.432098 INFO::ASW Label was 0.481977179474208 prior to batch effect correction and is now 0.481977179474208 .
2025-09-22 19:31:54.433308 INFO::Total function execution time is 0.428353071212769 s and adjustment time is 0.409970045089722 s ( 95.71 )
2025-09-22 19:31:54.618476 INFO::Formatting Data.
2025-09-22 19:31:54.619672 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:54.62155 INFO::Removing potential empty rows and columns
2025-09-22 19:31:54.623853 INFO::Found 0 missing values.
2025-09-22 19:31:54.631034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:54.631966 INFO::Done
2025-09-22 19:31:54.632698 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:54.638726 INFO::Starting hierarchical adjustment
2025-09-22 19:31:54.640315 INFO::Found 5 batches.
2025-09-22 19:31:54.641484 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:54.642905 INFO::Using default BPPARAM
2025-09-22 19:31:54.64449 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.
2025-09-22 19:31:54.854202 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:54.858694 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 19:31:54.896693 INFO::Done
2025-09-22 19:31:54.898089 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:54.904463 INFO::ASW Batch was 0.362617575732106 prior to batch effect correction and is now -0.0338830203021699 .
2025-09-22 19:31:54.905792 INFO::ASW Label was 0.395287667759598 prior to batch effect correction and is now 0.824020135679658 .
2025-09-22 19:31:54.9075 INFO::Total function execution time is 0.289005994796753 s and adjustment time is 0.256696224212646 s ( 88.82 )
2025-09-22 19:31:54.909122 INFO::Formatting Data.
2025-09-22 19:31:54.910384 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:54.912095 INFO::Removing potential empty rows and columns
2025-09-22 19:31:54.914055 INFO::Found 0 missing values.
2025-09-22 19:31:54.920503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:54.921386 INFO::Done
2025-09-22 19:31:54.922056 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:54.926793 INFO::Starting hierarchical adjustment
2025-09-22 19:31:54.928273 INFO::Found 5 batches.
2025-09-22 19:31:54.929241 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:54.93036 INFO::Using default BPPARAM
2025-09-22 19:31:54.931291 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.
2025-09-22 19:31:55.122942 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:55.133819 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 19:31:55.164172 INFO::Done
2025-09-22 19:31:55.16535 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:55.17123 INFO::ASW Batch was 0.362617575732106 prior to batch effect correction and is now -0.0338830203021699 .
2025-09-22 19:31:55.172422 INFO::ASW Label was 0.395287667759598 prior to batch effect correction and is now 0.824020135679658 .
2025-09-22 19:31:55.174005 INFO::Total function execution time is 0.264877080917358 s and adjustment time is 0.236231088638306 s ( 89.19 )
2025-09-22 19:31:55.198933 INFO::Formatting Data.
2025-09-22 19:31:55.199983 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:55.201734 INFO::Removing potential empty rows and columns
2025-09-22 19:31:55.203625 INFO::Found 0 missing values.
2025-09-22 19:31:55.209995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:55.211408 INFO::Done
2025-09-22 19:31:55.212447 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:55.217897 INFO::Starting hierarchical adjustment
2025-09-22 19:31:55.21894 INFO::Found 5 batches.
2025-09-22 19:31:55.219715 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:55.220883 INFO::Using default BPPARAM
2025-09-22 19:31:55.221738 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.
2025-09-22 19:31:55.493159 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:55.519149 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 19:31:55.560401 INFO::Done
2025-09-22 19:31:55.56187 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:55.569579 INFO::ASW Batch was 0.541546787809121 prior to batch effect correction and is now -0.0456398168766721 .
2025-09-22 19:31:55.570611 INFO::ASW Label was 0.228505950451476 prior to batch effect correction and is now 0.786034457660376 .
2025-09-22 19:31:55.5725 INFO::Total function execution time is 0.373432874679565 s and adjustment time is 0.341651916503906 s ( 91.49 )
2025-09-22 19:31:55.574068 INFO::Formatting Data.
2025-09-22 19:31:55.574949 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:55.575996 INFO::Removing potential empty rows and columns
2025-09-22 19:31:55.576979 INFO::Found 0 missing values.
2025-09-22 19:31:55.58236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:55.583375 INFO::Done
2025-09-22 19:31:55.584252 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:55.588212 INFO::Starting hierarchical adjustment
2025-09-22 19:31:55.589067 INFO::Found 5 batches.
2025-09-22 19:31:55.589642 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:55.590228 INFO::Using default BPPARAM
2025-09-22 19:31:55.590848 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.
2025-09-22 19:31:55.798895 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:55.81354 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 19:31:55.857391 INFO::Done
2025-09-22 19:31:55.858293 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:55.863453 INFO::ASW Batch was 0.541546787809121 prior to batch effect correction and is now -0.0456398168766721 .
2025-09-22 19:31:55.864299 INFO::ASW Label was 0.228505950451476 prior to batch effect correction and is now 0.786034457660376 .
2025-09-22 19:31:55.866203 INFO::Total function execution time is 0.292130947113037 s and adjustment time is 0.268517017364502 s ( 91.92 )
2025-09-22 19:31:55.889858 INFO::Formatting Data.
2025-09-22 19:31:55.890978 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:55.892361 INFO::Removing potential empty rows and columns
2025-09-22 19:31:55.893864 INFO::Found 0 missing values.
2025-09-22 19:31:55.897984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:55.898607 INFO::Done
2025-09-22 19:31:55.899132 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:55.903164 INFO::Starting hierarchical adjustment
2025-09-22 19:31:55.904332 INFO::Found 2 batches.
2025-09-22 19:31:55.905023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:55.905645 INFO::Using default BPPARAM
2025-09-22 19:31:55.906274 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:55.907212 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 19:31:55.922574 INFO::Done
2025-09-22 19:31:55.923243 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:55.926937 INFO::ASW Batch was 0.581877424594885 prior to batch effect correction and is now 0.00497363252529939 .
2025-09-22 19:31:55.927849 INFO::ASW Label was 0.417841470818336 prior to batch effect correction and is now 0.923349591318819 .
2025-09-22 19:31:55.928937 INFO::Total function execution time is 0.039207935333252 s and adjustment time is 0.0185039043426514 s ( 47.19 )
2025-09-22 19:31:55.929999 INFO::Formatting Data.
2025-09-22 19:31:55.930821 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:55.932018 INFO::Removing potential empty rows and columns
2025-09-22 19:31:55.933432 INFO::Found 0 missing values.
2025-09-22 19:31:55.937605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:55.93852 INFO::Done
2025-09-22 19:31:55.93935 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:55.944241 INFO::Starting hierarchical adjustment
2025-09-22 19:31:55.945387 INFO::Found 2 batches.
2025-09-22 19:31:55.945939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:55.946519 INFO::Using default BPPARAM
2025-09-22 19:31:55.947012 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:55.947887 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-22 19:31:55.96321 INFO::Done
2025-09-22 19:31:55.963901 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:55.966724 INFO::ASW Batch was 0.581877424594885 prior to batch effect correction and is now 0.00497363252529939 .
2025-09-22 19:31:55.96735 INFO::ASW Label was 0.417841470818336 prior to batch effect correction and is now 0.923349591318819 .
2025-09-22 19:31:55.968104 INFO::Total function execution time is 0.0381679534912109 s and adjustment time is 0.0180599689483643 s ( 47.32 )
2025-09-22 19:31:55.985432 INFO::Formatting Data.
2025-09-22 19:31:55.986598 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:55.987574 INFO::Removing potential empty rows and columns
2025-09-22 19:31:55.988503 INFO::Found 0 missing values.
2025-09-22 19:31:55.991483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:55.992056 INFO::Done
2025-09-22 19:31:55.992593 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:55.994387 INFO::Starting hierarchical adjustment
2025-09-22 19:31:55.99508 INFO::Found 2 batches.
2025-09-22 19:31:55.99556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:55.996124 INFO::Using default BPPARAM
2025-09-22 19:31:55.996615 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:55.997624 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 19:31:56.040746 INFO::Done
2025-09-22 19:31:56.041713 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:56.044242 INFO::ASW Batch was -0.166059106329325 prior to batch effect correction and is now -0.168771423227577 .
2025-09-22 19:31:56.04507 INFO::Total function execution time is 0.0598061084747314 s and adjustment time is 0.0457379817962646 s ( 76.48 )
2025-09-22 19:31:56.062581 INFO::Formatting Data.
2025-09-22 19:31:56.063379 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:56.064253 INFO::Removing potential empty rows and columns
2025-09-22 19:31:56.065593 INFO::Found 0 missing values.
2025-09-22 19:31:56.066759 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.
2025-09-22 19:31:56.07228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:56.073307 INFO::Done
2025-09-22 19:31:56.074177 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:56.077896 INFO::Starting hierarchical adjustment
2025-09-22 19:31:56.078947 INFO::Found 2 batches.
2025-09-22 19:31:56.079671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:56.080537 INFO::Using default BPPARAM
2025-09-22 19:31:56.081304 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:56.082786 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 19:31:56.106279 INFO::Done
2025-09-22 19:31:56.10734 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:56.11191 INFO::ASW Batch was 0.512605583723754 prior to batch effect correction and is now 0.00406233935332407 .
2025-09-22 19:31:56.112951 INFO::ASW Label was 0.549880836077966 prior to batch effect correction and is now 0.905897515297342 .
2025-09-22 19:31:56.114223 INFO::Total function execution time is 0.0516269207000732 s and adjustment time is 0.0274310111999512 s ( 53.13 )
2025-09-22 19:31:56.11571 INFO::Formatting Data.
2025-09-22 19:31:56.116713 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:56.118076 INFO::Removing potential empty rows and columns
2025-09-22 19:31:56.119439 INFO::Found 0 missing values.
2025-09-22 19:31:56.120666 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.
2025-09-22 19:31:56.127256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:56.128252 INFO::Done
2025-09-22 19:31:56.129101 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:56.133495 INFO::Starting hierarchical adjustment
2025-09-22 19:31:56.134659 INFO::Found 2 batches.
2025-09-22 19:31:56.13545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:56.136051 INFO::Using default BPPARAM
2025-09-22 19:31:56.136558 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:31:56.137469 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 19:31:56.158543 INFO::Done
2025-09-22 19:31:56.159311 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:56.163501 INFO::ASW Batch was 0.512605583723754 prior to batch effect correction and is now 0.00406233935332407 .
2025-09-22 19:31:56.164549 INFO::ASW Label was 0.549880836077966 prior to batch effect correction and is now 0.905897515297342 .
2025-09-22 19:31:56.165727 INFO::Total function execution time is 0.0502209663391113 s and adjustment time is 0.0241539478302002 s ( 48.1 )
2025-09-22 19:31:56.423213 INFO::Formatting Data.
2025-09-22 19:31:56.423957 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:56.425083 INFO::Removing potential empty rows and columns
2025-09-22 19:31:56.426382 INFO::Found 0 missing values.
2025-09-22 19:31:56.429459 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:56.430275 INFO::Done
2025-09-22 19:31:56.431034 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:56.433918 INFO::Starting hierarchical adjustment
2025-09-22 19:31:56.43488 INFO::Found 3 batches.
2025-09-22 19:31:56.435555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:56.436303 INFO::Using default BPPARAM
2025-09-22 19:31:56.436806 INFO::Processing subtree level 1
2025-09-22 19:31:56.587843 INFO::Adjusting the last 1 batches sequentially
2025-09-22 19:31:56.597896 INFO::Done
2025-09-22 19:31:56.59888 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:56.609858 INFO::ASW Batch was -0.0870179315015594 prior to batch effect correction and is now -0.0870179315015594 .
2025-09-22 19:31:56.6132 INFO::Total function execution time is 0.189015865325928 s and adjustment time is 0.163191080093384 s ( 86.34 )
2025-09-22 19:31:56.61522 INFO::Formatting Data.
2025-09-22 19:31:56.616914 INFO::Typecasting input to dataframe.
2025-09-22 19:31:56.617996 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:56.619631 INFO::Removing potential empty rows and columns
2025-09-22 19:31:56.621378 INFO::Found 0 missing values.
2025-09-22 19:31:56.625369 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:56.626133 INFO::Done
2025-09-22 19:31:56.626854 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:56.629217 INFO::Starting hierarchical adjustment
2025-09-22 19:31:56.630379 INFO::Found 3 batches.
2025-09-22 19:31:56.631092 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:56.631949 INFO::Using default BPPARAM
2025-09-22 19:31:56.632647 INFO::Processing subtree level 1
2025-09-22 19:31:56.785482 INFO::Adjusting the last 1 batches sequentially
2025-09-22 19:31:56.793769 INFO::Done
2025-09-22 19:31:56.795862 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:56.808673 INFO::ASW Batch was -0.0870179315015594 prior to batch effect correction and is now -0.0870179315015594 .
2025-09-22 19:31:56.811277 INFO::Total function execution time is 0.196042060852051 s and adjustment time is 0.163616180419922 s ( 83.46 )
2025-09-22 19:31:56.835328 INFO::Formatting Data.
2025-09-22 19:31:56.836558 INFO::Typecasting input to dataframe.
2025-09-22 19:31:56.837477 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:56.838491 INFO::Removing potential empty rows and columns
2025-09-22 19:31:56.840549 INFO::Found 0 missing values.
2025-09-22 19:31:56.843422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:56.844133 INFO::Done
2025-09-22 19:31:56.844662 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:56.847121 INFO::Starting hierarchical adjustment
2025-09-22 19:31:56.848034 INFO::Found 3 batches.
2025-09-22 19:31:56.849006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:56.850015 INFO::Using default BPPARAM
2025-09-22 19:31:56.851324 INFO::Processing subtree level 1
2025-09-22 19:31:57.001393 INFO::Adjusting the last 1 batches sequentially
2025-09-22 19:31:57.00762 INFO::Done
2025-09-22 19:31:57.008447 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:57.017838 INFO::ASW Batch was -0.111485965803701 prior to batch effect correction and is now -0.111485965803701 .
2025-09-22 19:31:57.021244 INFO::Total function execution time is 0.185472965240479 s and adjustment time is 0.159688949584961 s ( 86.1 )
2025-09-22 19:31:57.262101 INFO::Formatting Data.
2025-09-22 19:31:57.263218 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:57.264769 INFO::Removing potential empty rows and columns
2025-09-22 19:31:57.268608 INFO::Found 1000 missing values.
2025-09-22 19:31:57.295978 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:57.296694 INFO::Done
2025-09-22 19:31:57.297279 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:57.303874 INFO::Starting hierarchical adjustment
2025-09-22 19:31:57.305455 INFO::Found 10 batches.
2025-09-22 19:31:57.306204 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:31:57.30683 INFO::Using default BPPARAM
2025-09-22 19:31:57.307406 INFO::Processing subtree level 1
2025-09-22 19:31:57.4922 INFO::Processing subtree level 2
2025-09-22 19:31:57.726804 INFO::Adjusting the last 1 batches sequentially
2025-09-22 19:31:57.740395 INFO::Done
2025-09-22 19:31:57.741307 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:31:57.757874 INFO::ASW Batch was 0.461469217476973 prior to batch effect correction and is now 0.461469217476973 .
2025-09-22 19:31:57.758572 INFO::ASW Label was 0.369259265826668 prior to batch effect correction and is now 0.369259265826668 .
2025-09-22 19:31:57.76129 INFO::Total function execution time is 0.498854160308838 s and adjustment time is 0.435204029083252 s ( 87.24 )
2025-09-22 19:31:57.764767 INFO::Formatting Data.
2025-09-22 19:31:57.766092 INFO::Replacing NaNs with NAs.
2025-09-22 19:31:57.768143 INFO::Removing potential empty rows and columns
2025-09-22 19:31:57.771098 INFO::Found 1000 missing values.
2025-09-22 19:31:57.793763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:31:57.794478 INFO::Done
2025-09-22 19:31:57.795669 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:31:57.802202 INFO::Starting hierarchical adjustment
2025-09-22 19:31:57.803461 INFO::Found 10 batches.
2025-09-22 19:31:58.876013 INFO::Set up parallel execution backend with 2 workers
2025-09-22 19:31:58.876973 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-22 19:32:00.261943 INFO::Adjusting the last 2 batches sequentially
2025-09-22 19:32:00.263892 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-22 19:32:00.286575 INFO::Done
2025-09-22 19:32:00.287526 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:32:00.294909 INFO::ASW Batch was 0.461469217476973 prior to batch effect correction and is now 0.461469217476973 .
2025-09-22 19:32:00.295684 INFO::ASW Label was 0.369259265826668 prior to batch effect correction and is now 0.369259265826668 .
2025-09-22 19:32:00.296445 INFO::Total function execution time is 2.53182697296143 s and adjustment time is 2.4833550453186 s ( 98.09 )
2025-09-22 19:32:00.554375 INFO::Formatting Data.
2025-09-22 19:32:00.555491 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:00.556758 INFO::Removing potential empty rows and columns
2025-09-22 19:32:00.558184 INFO::Found 0 missing values.
2025-09-22 19:32:00.561696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:00.562262 INFO::Done
2025-09-22 19:32:00.56275 INFO::Acquiring quality metrics before batch effect correction.
2025-09-22 19:32:00.566676 INFO::Starting hierarchical adjustment
2025-09-22 19:32:00.567804 INFO::Found 3 batches.
2025-09-22 19:32:00.568559 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-22 19:32:00.569452 INFO::Using default BPPARAM
2025-09-22 19:32:00.5702 INFO::Processing subtree level 1
2025-09-22 19:32:00.743723 INFO::Adjusting the last 1 batches sequentially
2025-09-22 19:32:00.756549 INFO::Done
2025-09-22 19:32:00.759877 INFO::Acquiring quality metrics after batch effect correction.
2025-09-22 19:32:00.773792 INFO::ASW Batch was 0.219542565482183 prior to batch effect correction and is now -0.132644445432272 .
2025-09-22 19:32:00.775558 INFO::ASW Label was -0.230333377625448 prior to batch effect correction and is now -0.121975446271903 .
2025-09-22 19:32:00.779801 INFO::Total function execution time is 0.224102020263672 s and adjustment time is 0.188915014266968 s ( 84.3 )
2025-09-22 19:32:00.970793 INFO::Formatting Data.
2025-09-22 19:32:00.971962 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:00.973296 INFO::Removing potential empty rows and columns
2025-09-22 19:32:00.974638 INFO::Found 2 missing values.
2025-09-22 19:32:00.97837 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:00.979267 INFO::Done
2025-09-22 19:32:01.02222 INFO::Found NA in Reference column
2025-09-22 19:32:01.037414 INFO::Require at least two references per batch.
2025-09-22 19:32:01.069948 INFO::Formatting Data.
2025-09-22 19:32:01.071017 INFO::Recognized SummarizedExperiment
2025-09-22 19:32:01.071856 INFO::Typecasting input to dataframe.
2025-09-22 19:32:01.085685 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.087397 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.092037 INFO::Found 0 missing values.
2025-09-22 19:32:01.101251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.102204 INFO::Done
2025-09-22 19:32:01.123829 INFO::Formatting Data.
2025-09-22 19:32:01.124878 INFO::Recognized SummarizedExperiment
2025-09-22 19:32:01.125674 INFO::Typecasting input to dataframe.
2025-09-22 19:32:01.150278 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.152009 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.156869 INFO::Found 0 missing values.
2025-09-22 19:32:01.172021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.172912 INFO::Done
2025-09-22 19:32:01.192085 INFO::Formatting Data.
2025-09-22 19:32:01.192766 INFO::Recognized SummarizedExperiment
2025-09-22 19:32:01.193265 INFO::Typecasting input to dataframe.
2025-09-22 19:32:01.215487 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.217057 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.218528 INFO::Found 0 missing values.
2025-09-22 19:32:01.219892 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.
2025-09-22 19:32:01.225894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.226799 INFO::Done
2025-09-22 19:32:01.243959 INFO::Formatting Data.
2025-09-22 19:32:01.245043 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.246214 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.247094 INFO::Found 0 missing values.
2025-09-22 19:32:01.249654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.250167 INFO::Done
2025-09-22 19:32:01.26769 INFO::Formatting Data.
2025-09-22 19:32:01.268789 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.269792 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.271232 INFO::Found 0 missing values.
2025-09-22 19:32:01.274379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.275209 INFO::Done
2025-09-22 19:32:01.324701 INFO::Formatting Data.
2025-09-22 19:32:01.325837 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.327328 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.32905 INFO::Found 1 missing values.
2025-09-22 19:32:01.332804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.333704 INFO::Done
2025-09-22 19:32:01.363575 INFO::Formatting Data.
2025-09-22 19:32:01.364766 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.366018 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.367369 INFO::Found 2 missing values.
2025-09-22 19:32:01.368655 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.
2025-09-22 19:32:01.371904 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.372732 INFO::Done
2025-09-22 19:32:01.387489 INFO::Formatting Data.
2025-09-22 19:32:01.388516 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.389646 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.390832 INFO::Found 2 missing values.
2025-09-22 19:32:01.392807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.393457 INFO::Done
2025-09-22 19:32:01.410321 INFO::Formatting Data.
2025-09-22 19:32:01.41144 INFO::Typecasting input to dataframe.
2025-09-22 19:32:01.412608 INFO::Replacing NaNs with NAs.
2025-09-22 19:32:01.41375 INFO::Removing potential empty rows and columns
2025-09-22 19:32:01.415133 INFO::Found 0 missing values.
2025-09-22 19:32:01.419546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-22 19:32:01.420257 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.863 4.634 25.848
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.667 | 1.448 | 19.181 | |
| compute_asw | 0.030 | 0.001 | 0.032 | |
| count_existing | 0.015 | 0.000 | 0.015 | |
| generate_data_covariables | 0.014 | 0.001 | 0.014 | |
| generate_dataset | 0.014 | 0.001 | 0.015 | |