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This page was generated on 2025-03-20 12:09 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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 159/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.2.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_20
git_last_commit: 9764e3f
git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on kjohnson1

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.

raw results


Summary

Package: BERT
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2025-03-18 12:31:01 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 12:32:15 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 74.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* 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 27.116  1.481  20.198
* 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

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘BERT’ ...
** 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)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-03-18 12:31:59.856696 INFO::Formatting Data.
2025-03-18 12:31:59.860337 INFO::Replacing NaNs with NAs.
2025-03-18 12:31:59.865574 INFO::Removing potential empty rows and columns
2025-03-18 12:32:00.059242 INFO::Found  0  missing values.
2025-03-18 12:32:00.060454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:00.060702 INFO::Done
2025-03-18 12:32:00.06088 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:00.068821 INFO::Starting hierarchical adjustment
2025-03-18 12:32:00.069191 INFO::Found  3  batches.
2025-03-18 12:32:00.06938 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:00.069811 INFO::Using default BPPARAM
2025-03-18 12:32:00.069983 INFO::Processing subtree level 1
2025-03-18 12:32:00.126623 INFO::Adjusting the last 1 batches sequentially
2025-03-18 12:32:00.128367 INFO::Done
2025-03-18 12:32:00.128737 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:00.130546 INFO::ASW Batch was -0.0850173303661533 prior to batch effect correction and is now -0.0850173303661533 .
2025-03-18 12:32:00.131085 INFO::Total function execution time is  0.274781942367554  s and adjustment time is  0.0592350959777832 s ( 21.56 )
2025-03-18 12:32:00.137134 INFO::Formatting Data.
2025-03-18 12:32:00.137809 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:00.138146 INFO::Removing potential empty rows and columns
2025-03-18 12:32:00.138734 INFO::Found  0  missing values.
2025-03-18 12:32:00.139147 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.
2025-03-18 12:32:00.143465 INFO::Formatting Data.
2025-03-18 12:32:00.143715 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:00.144018 INFO::Removing potential empty rows and columns
2025-03-18 12:32:00.14504 INFO::Found  0  missing values.
2025-03-18 12:32:00.145445 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.
2025-03-18 12:32:00.153949 INFO::Formatting Data.
2025-03-18 12:32:00.154311 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:00.154723 INFO::Removing potential empty rows and columns
2025-03-18 12:32:00.155196 INFO::Found  0  missing values.
2025-03-18 12:32:00.155552 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.
2025-03-18 12:32:00.16009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:00.160457 INFO::Done
2025-03-18 12:32:00.160655 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:00.161503 INFO::Starting hierarchical adjustment
2025-03-18 12:32:00.161758 INFO::Found  2  batches.
2025-03-18 12:32:00.16193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:00.162165 INFO::Using default BPPARAM
2025-03-18 12:32:00.162324 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:00.162631 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:00.178308 INFO::Done
2025-03-18 12:32:00.178984 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:00.181177 INFO::ASW Batch was -0.0342444346825364 prior to batch effect correction and is now -0.120198443174036 .
2025-03-18 12:32:00.182133 INFO::Total function execution time is  0.0281369686126709  s and adjustment time is  0.0165238380432129 s ( 58.73 )
2025-03-18 12:32:00.188188 INFO::Formatting Data.
2025-03-18 12:32:00.188487 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:00.192067 INFO::Formatting Data.
2025-03-18 12:32:00.192342 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:00.192645 INFO::Removing potential empty rows and columns
2025-03-18 12:32:00.193018 INFO::Found  0  missing values.
2025-03-18 12:32:00.194003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:00.194204 INFO::Done
2025-03-18 12:32:00.19438 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:00.195108 INFO::Starting hierarchical adjustment
2025-03-18 12:32:00.195371 INFO::Found  2  batches.
2025-03-18 12:32:00.195543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:00.195817 INFO::Using default BPPARAM
2025-03-18 12:32:00.196058 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:00.196426 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:00.201713 INFO::Done
2025-03-18 12:32:00.201979 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:00.202721 INFO::ASW Batch was 0.00691139997446761 prior to batch effect correction and is now -0.10510143295798 .
2025-03-18 12:32:00.203011 INFO::Total function execution time is  0.0109748840332031  s and adjustment time is  0.00638198852539062 s ( 58.15 )
2025-03-18 12:32:00.203354 INFO::Formatting Data.
2025-03-18 12:32:00.203528 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:00.203795 INFO::Removing potential empty rows and columns
2025-03-18 12:32:00.204117 INFO::Found  0  missing values.
2025-03-18 12:32:00.205033 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:00.20525 INFO::Done
2025-03-18 12:32:00.205413 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:00.206128 INFO::Starting hierarchical adjustment
2025-03-18 12:32:00.206406 INFO::Found  2  batches.
2025-03-18 12:32:00.206605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:00.206817 INFO::Using default BPPARAM
2025-03-18 12:32:00.206981 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:00.207273 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:00.21793 INFO::Done
2025-03-18 12:32:00.218713 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:00.220755 INFO::ASW Batch was 0.00691139997446761 prior to batch effect correction and is now -0.10510143295798 .
2025-03-18 12:32:00.221628 INFO::Total function execution time is  0.0181100368499756  s and adjustment time is  0.00962209701538086 s ( 53.13 )
2025-03-18 12:32:03.106871 INFO::Formatting Data.
2025-03-18 12:32:03.107762 INFO::Recognized SummarizedExperiment
2025-03-18 12:32:03.108218 INFO::Typecasting input to dataframe.
2025-03-18 12:32:03.140974 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:03.142209 INFO::Removing potential empty rows and columns
2025-03-18 12:32:03.145473 INFO::Found  0  missing values.
2025-03-18 12:32:03.151311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:03.152226 INFO::Done
2025-03-18 12:32:03.152871 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:03.156828 INFO::Starting hierarchical adjustment
2025-03-18 12:32:03.157551 INFO::Found  2  batches.
2025-03-18 12:32:03.157983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:03.159007 INFO::Using default BPPARAM
2025-03-18 12:32:03.15944 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:03.160289 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:03.211559 INFO::Done
2025-03-18 12:32:03.212336 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:03.215959 INFO::ASW Batch was -0.0233312744416401 prior to batch effect correction and is now -0.0906479379244618 .
2025-03-18 12:32:03.216738 INFO::Total function execution time is  0.11052393913269  s and adjustment time is  0.054091215133667 s ( 48.94 )
2025-03-18 12:32:03.23703 INFO::Formatting Data.
2025-03-18 12:32:03.237893 INFO::Recognized SummarizedExperiment
2025-03-18 12:32:03.238382 INFO::Typecasting input to dataframe.
2025-03-18 12:32:03.247827 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:03.249033 INFO::Removing potential empty rows and columns
2025-03-18 12:32:03.252212 INFO::Found  0  missing values.
2025-03-18 12:32:03.259299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:03.260396 INFO::Done
2025-03-18 12:32:03.260935 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:03.265249 INFO::Starting hierarchical adjustment
2025-03-18 12:32:03.266119 INFO::Found  2  batches.
2025-03-18 12:32:03.266616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:03.267167 INFO::Using default BPPARAM
2025-03-18 12:32:03.267611 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:03.26852 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:03.294663 INFO::Done
2025-03-18 12:32:03.295556 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:03.299647 INFO::ASW Batch was -0.0269260567966461 prior to batch effect correction and is now -0.0269260567966461 .
2025-03-18 12:32:03.300713 INFO::Total function execution time is  0.0636899471282959  s and adjustment time is  0.0286209583282471 s ( 44.94 )
2025-03-18 12:32:03.321694 INFO::Formatting Data.
2025-03-18 12:32:03.322482 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:03.323307 INFO::Removing potential empty rows and columns
2025-03-18 12:32:03.324258 INFO::Found  0  missing values.
2025-03-18 12:32:03.327014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:03.327548 INFO::Done
2025-03-18 12:32:03.328001 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:03.33004 INFO::Starting hierarchical adjustment
2025-03-18 12:32:03.330744 INFO::Found  3  batches.
2025-03-18 12:32:03.331209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:03.331737 INFO::Using default BPPARAM
2025-03-18 12:32:03.332154 INFO::Processing subtree level 1
2025-03-18 12:32:03.52424 INFO::Adjusting the last 1 batches sequentially
2025-03-18 12:32:03.527385 INFO::Done
2025-03-18 12:32:03.527849 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:03.530338 INFO::ASW Batch was -0.0889010150402954 prior to batch effect correction and is now -0.160310633973526 .
2025-03-18 12:32:03.530988 INFO::Total function execution time is  0.209445953369141  s and adjustment time is  0.196737051010132 s ( 93.93 )
2025-03-18 12:32:03.553781 INFO::Skipping initial DF formatting
2025-03-18 12:32:03.554579 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:03.558672 INFO::Starting hierarchical adjustment
2025-03-18 12:32:03.559506 INFO::Found  5  batches.
2025-03-18 12:32:03.560032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:03.560666 INFO::Using default BPPARAM
2025-03-18 12:32:03.561144 INFO::Processing subtree level 1
2025-03-18 12:32:03.641695 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:03.643033 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:03.660125 INFO::Done
2025-03-18 12:32:03.660883 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:03.66561 INFO::ASW Batch was 0.558857223077348 prior to batch effect correction and is now 0.558857223077348 .
2025-03-18 12:32:03.666242 INFO::ASW Label was 0.328676210573949 prior to batch effect correction and is now 0.328676210573949 .
2025-03-18 12:32:03.667148 INFO::Total function execution time is  0.113458156585693  s and adjustment time is  0.100752115249634 s ( 88.8 )
2025-03-18 12:32:03.687486 INFO::Formatting Data.
2025-03-18 12:32:03.688337 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:03.689248 INFO::Removing potential empty rows and columns
2025-03-18 12:32:03.690314 INFO::Found  0  missing values.
2025-03-18 12:32:03.693886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:03.694429 INFO::Done
2025-03-18 12:32:03.694921 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:03.697673 INFO::Starting hierarchical adjustment
2025-03-18 12:32:03.698347 INFO::Found  5  batches.
2025-03-18 12:32:03.698827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:03.699402 INFO::Using default BPPARAM
2025-03-18 12:32:03.700462 INFO::Processing subtree level 1
2025-03-18 12:32:03.775897 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:03.7773 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:03.788037 INFO::Done
2025-03-18 12:32:03.788736 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:03.792002 INFO::ASW Batch was 0.388139212792773 prior to batch effect correction and is now -0.0847674259239977 .
2025-03-18 12:32:03.792582 INFO::ASW Label was 0.434953355816686 prior to batch effect correction and is now 0.887177331563773 .
2025-03-18 12:32:03.793359 INFO::Total function execution time is  0.105921030044556  s and adjustment time is  0.0898151397705078 s ( 84.79 )
2025-03-18 12:32:03.794157 INFO::Formatting Data.
2025-03-18 12:32:03.794697 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:03.795517 INFO::Removing potential empty rows and columns
2025-03-18 12:32:03.796448 INFO::Found  0  missing values.
2025-03-18 12:32:03.79979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:03.80032 INFO::Done
2025-03-18 12:32:03.800776 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:03.80331 INFO::Starting hierarchical adjustment
2025-03-18 12:32:03.803983 INFO::Found  5  batches.
2025-03-18 12:32:03.804453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:03.805036 INFO::Using default BPPARAM
2025-03-18 12:32:03.805543 INFO::Processing subtree level 1
2025-03-18 12:32:03.885984 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:03.887105 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:03.899063 INFO::Done
2025-03-18 12:32:03.899748 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:03.904485 INFO::ASW Batch was 0.388139212792773 prior to batch effect correction and is now -0.0847674259239977 .
2025-03-18 12:32:03.905186 INFO::ASW Label was 0.434953355816686 prior to batch effect correction and is now 0.887177331563773 .
2025-03-18 12:32:03.906001 INFO::Total function execution time is  0.111809968948364  s and adjustment time is  0.0951781272888184 s ( 85.12 )
2025-03-18 12:32:03.926398 INFO::Formatting Data.
2025-03-18 12:32:03.92711 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:03.92795 INFO::Removing potential empty rows and columns
2025-03-18 12:32:03.929561 INFO::Found  0  missing values.
2025-03-18 12:32:03.933023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:03.933581 INFO::Done
2025-03-18 12:32:03.934126 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:03.939263 INFO::Starting hierarchical adjustment
2025-03-18 12:32:03.94069 INFO::Found  5  batches.
2025-03-18 12:32:03.941462 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:03.942178 INFO::Using default BPPARAM
2025-03-18 12:32:03.942724 INFO::Processing subtree level 1
2025-03-18 12:32:04.027864 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:04.029055 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:04.036666 INFO::Done
2025-03-18 12:32:04.036946 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.038309 INFO::ASW Batch was 0.290368267669014 prior to batch effect correction and is now -0.0603109980412117 .
2025-03-18 12:32:04.038517 INFO::ASW Label was 0.400571881560491 prior to batch effect correction and is now 0.870432841723166 .
2025-03-18 12:32:04.038952 INFO::Total function execution time is  0.112588882446289  s and adjustment time is  0.096458911895752 s ( 85.67 )
2025-03-18 12:32:04.039266 INFO::Formatting Data.
2025-03-18 12:32:04.039458 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.039766 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.040145 INFO::Found  0  missing values.
2025-03-18 12:32:04.041394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.041594 INFO::Done
2025-03-18 12:32:04.041765 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.042685 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.042934 INFO::Found  5  batches.
2025-03-18 12:32:04.043102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.04332 INFO::Using default BPPARAM
2025-03-18 12:32:04.043516 INFO::Processing subtree level 1
2025-03-18 12:32:04.13743 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:04.138685 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:04.147356 INFO::Done
2025-03-18 12:32:04.147704 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.151414 INFO::ASW Batch was 0.290368267669014 prior to batch effect correction and is now -0.0603109980412117 .
2025-03-18 12:32:04.152209 INFO::ASW Label was 0.400571881560491 prior to batch effect correction and is now 0.870432841723166 .
2025-03-18 12:32:04.153562 INFO::Total function execution time is  0.114207983016968  s and adjustment time is  0.104444026947021 s ( 91.45 )
2025-03-18 12:32:04.166194 INFO::Formatting Data.
2025-03-18 12:32:04.166578 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.166951 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.168179 INFO::Found  0  missing values.
2025-03-18 12:32:04.170636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.170921 INFO::Done
2025-03-18 12:32:04.17111 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.173283 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.174074 INFO::Found  2  batches.
2025-03-18 12:32:04.174554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.175177 INFO::Using default BPPARAM
2025-03-18 12:32:04.175703 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:04.176848 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:04.19029 INFO::Done
2025-03-18 12:32:04.190929 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.193709 INFO::ASW Batch was 0.700835622161588 prior to batch effect correction and is now 0.0157327449038028 .
2025-03-18 12:32:04.194297 INFO::ASW Label was 0.30940037869931 prior to batch effect correction and is now 0.862405001842913 .
2025-03-18 12:32:04.195064 INFO::Total function execution time is  0.0303339958190918  s and adjustment time is  0.0163421630859375 s ( 53.87 )
2025-03-18 12:32:04.195777 INFO::Formatting Data.
2025-03-18 12:32:04.196322 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.197124 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.198027 INFO::Found  0  missing values.
2025-03-18 12:32:04.200439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.200947 INFO::Done
2025-03-18 12:32:04.201403 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.204457 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.205192 INFO::Found  2  batches.
2025-03-18 12:32:04.205657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.206172 INFO::Using default BPPARAM
2025-03-18 12:32:04.207418 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:04.207799 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:04.215682 INFO::Done
2025-03-18 12:32:04.215935 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.218587 INFO::ASW Batch was 0.700835622161588 prior to batch effect correction and is now 0.0157327449038028 .
2025-03-18 12:32:04.219143 INFO::ASW Label was 0.30940037869931 prior to batch effect correction and is now 0.862405001842913 .
2025-03-18 12:32:04.219834 INFO::Total function execution time is  0.0240538120269775  s and adjustment time is  0.0106651782989502 s ( 44.34 )
2025-03-18 12:32:04.231136 INFO::Formatting Data.
2025-03-18 12:32:04.231815 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.232585 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.233392 INFO::Found  0  missing values.
2025-03-18 12:32:04.235274 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.235806 INFO::Done
2025-03-18 12:32:04.236259 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.237967 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.238664 INFO::Found  2  batches.
2025-03-18 12:32:04.23916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.239716 INFO::Using default BPPARAM
2025-03-18 12:32:04.240176 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:04.240958 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:04.255259 INFO::Done
2025-03-18 12:32:04.255544 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.256231 INFO::ASW Batch was 0.056884357181194 prior to batch effect correction and is now -0.0286335604687422 .
2025-03-18 12:32:04.256559 INFO::Total function execution time is  0.0255599021911621  s and adjustment time is  0.0167670249938965 s ( 65.6 )
2025-03-18 12:32:04.260862 INFO::Formatting Data.
2025-03-18 12:32:04.261113 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.261397 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.261774 INFO::Found  0  missing values.
2025-03-18 12:32:04.262212 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.
2025-03-18 12:32:04.26366 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.263871 INFO::Done
2025-03-18 12:32:04.264034 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.265007 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.265246 INFO::Found  2  batches.
2025-03-18 12:32:04.265424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.265622 INFO::Using default BPPARAM
2025-03-18 12:32:04.26577 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:04.266062 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:04.274845 INFO::Done
2025-03-18 12:32:04.275515 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.278241 INFO::ASW Batch was 0.49695768765657 prior to batch effect correction and is now 0.18705839357875 .
2025-03-18 12:32:04.278814 INFO::ASW Label was 0.5761848770276 prior to batch effect correction and is now 0.788310015949583 .
2025-03-18 12:32:04.279526 INFO::Total function execution time is  0.0185980796813965  s and adjustment time is  0.0095679759979248 s ( 51.45 )
2025-03-18 12:32:04.280219 INFO::Formatting Data.
2025-03-18 12:32:04.28075 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.28153 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.282393 INFO::Found  0  missing values.
2025-03-18 12:32:04.283172 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.
2025-03-18 12:32:04.287118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.287536 INFO::Done
2025-03-18 12:32:04.287959 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.289858 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.290139 INFO::Found  2  batches.
2025-03-18 12:32:04.290319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.290516 INFO::Using default BPPARAM
2025-03-18 12:32:04.290674 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:04.290986 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:04.29881 INFO::Done
2025-03-18 12:32:04.299487 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.30279 INFO::ASW Batch was 0.49695768765657 prior to batch effect correction and is now 0.18705839357875 .
2025-03-18 12:32:04.30352 INFO::ASW Label was 0.5761848770276 prior to batch effect correction and is now 0.788310015949583 .
2025-03-18 12:32:04.304329 INFO::Total function execution time is  0.0240809917449951  s and adjustment time is  0.00864005088806152 s ( 35.88 )
2025-03-18 12:32:04.467356 INFO::Formatting Data.
2025-03-18 12:32:04.468054 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.468817 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.46974 INFO::Found  0  missing values.
2025-03-18 12:32:04.472272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.472804 INFO::Done
2025-03-18 12:32:04.473229 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.474978 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.475605 INFO::Found  3  batches.
2025-03-18 12:32:04.476042 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.476534 INFO::Using default BPPARAM
2025-03-18 12:32:04.477075 INFO::Processing subtree level 1
2025-03-18 12:32:04.536489 INFO::Adjusting the last 1 batches sequentially
2025-03-18 12:32:04.537743 INFO::Done
2025-03-18 12:32:04.53805 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.5394 INFO::ASW Batch was -0.117850621361668 prior to batch effect correction and is now -0.117850621361668 .
2025-03-18 12:32:04.539916 INFO::Total function execution time is  0.0726580619812012  s and adjustment time is  0.0623171329498291 s ( 85.77 )
2025-03-18 12:32:04.540351 INFO::Formatting Data.
2025-03-18 12:32:04.540561 INFO::Typecasting input to dataframe.
2025-03-18 12:32:04.540987 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.541346 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.541779 INFO::Found  0  missing values.
2025-03-18 12:32:04.542859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.543487 INFO::Done
2025-03-18 12:32:04.544407 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.546517 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.547366 INFO::Found  3  batches.
2025-03-18 12:32:04.547856 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.548481 INFO::Using default BPPARAM
2025-03-18 12:32:04.54896 INFO::Processing subtree level 1
2025-03-18 12:32:04.719944 INFO::Adjusting the last 1 batches sequentially
2025-03-18 12:32:04.721146 INFO::Done
2025-03-18 12:32:04.721398 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.730246 INFO::ASW Batch was -0.117850621361668 prior to batch effect correction and is now -0.117850621361668 .
2025-03-18 12:32:04.731525 INFO::Total function execution time is  0.190943002700806  s and adjustment time is  0.174012899398804 s ( 91.13 )
2025-03-18 12:32:04.738093 INFO::Formatting Data.
2025-03-18 12:32:04.738391 INFO::Typecasting input to dataframe.
2025-03-18 12:32:04.738821 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:04.739262 INFO::Removing potential empty rows and columns
2025-03-18 12:32:04.739768 INFO::Found  0  missing values.
2025-03-18 12:32:04.74071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:04.74089 INFO::Done
2025-03-18 12:32:04.741045 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:04.741705 INFO::Starting hierarchical adjustment
2025-03-18 12:32:04.74194 INFO::Found  3  batches.
2025-03-18 12:32:04.742107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:04.742489 INFO::Using default BPPARAM
2025-03-18 12:32:04.742653 INFO::Processing subtree level 1
2025-03-18 12:32:04.87627 INFO::Adjusting the last 1 batches sequentially
2025-03-18 12:32:04.877398 INFO::Done
2025-03-18 12:32:04.877625 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:04.879591 INFO::ASW Batch was 0.0192811774955629 prior to batch effect correction and is now 0.0192811774955629 .
2025-03-18 12:32:04.88262 INFO::Total function execution time is  0.144099950790405  s and adjustment time is  0.135503053665161 s ( 94.03 )
2025-03-18 12:32:05.060049 INFO::Formatting Data.
2025-03-18 12:32:05.06055 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:05.061143 INFO::Removing potential empty rows and columns
2025-03-18 12:32:05.062608 INFO::Found  1000  missing values.
2025-03-18 12:32:05.073233 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:05.073674 INFO::Done
2025-03-18 12:32:05.074059 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:05.079074 INFO::Starting hierarchical adjustment
2025-03-18 12:32:05.079814 INFO::Found  10  batches.
2025-03-18 12:32:05.080272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:05.080861 INFO::Using default BPPARAM
2025-03-18 12:32:05.081352 INFO::Processing subtree level 1
2025-03-18 12:32:05.199068 INFO::Processing subtree level 2
2025-03-18 12:32:05.328095 INFO::Adjusting the last 1 batches sequentially
2025-03-18 12:32:05.331638 INFO::Done
2025-03-18 12:32:05.332189 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:05.339551 INFO::ASW Batch was 0.535570555865114 prior to batch effect correction and is now 0.535570555865114 .
2025-03-18 12:32:05.339913 INFO::ASW Label was 0.275819049118872 prior to batch effect correction and is now 0.275819049118872 .
2025-03-18 12:32:05.340775 INFO::Total function execution time is  0.280524015426636  s and adjustment time is  0.251871109008789 s ( 89.79 )
2025-03-18 12:32:05.342064 INFO::Formatting Data.
2025-03-18 12:32:05.342409 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:05.343255 INFO::Removing potential empty rows and columns
2025-03-18 12:32:05.346647 INFO::Found  1000  missing values.
2025-03-18 12:32:05.365611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:05.366517 INFO::Done
2025-03-18 12:32:05.367122 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:05.373723 INFO::Starting hierarchical adjustment
2025-03-18 12:32:05.374671 INFO::Found  10  batches.
2025-03-18 12:32:06.087055 INFO::Set up parallel execution backend with 2 workers
2025-03-18 12:32:06.087768 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-18 12:32:06.761311 INFO::Adjusting the last 2 batches sequentially
2025-03-18 12:32:06.763054 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 12:32:06.779986 INFO::Done
2025-03-18 12:32:06.780277 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:06.78235 INFO::ASW Batch was 0.535570555865114 prior to batch effect correction and is now 0.535570555865114 .
2025-03-18 12:32:06.782583 INFO::ASW Label was 0.275819049118872 prior to batch effect correction and is now 0.275819049118872 .
2025-03-18 12:32:06.782832 INFO::Total function execution time is  1.44086384773254  s and adjustment time is  1.40551900863647 s ( 97.55 )
2025-03-18 12:32:06.893945 INFO::Formatting Data.
2025-03-18 12:32:06.894273 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:06.894621 INFO::Removing potential empty rows and columns
2025-03-18 12:32:06.895062 INFO::Found  0  missing values.
2025-03-18 12:32:06.896375 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:06.896603 INFO::Done
2025-03-18 12:32:06.896784 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 12:32:06.897836 INFO::Starting hierarchical adjustment
2025-03-18 12:32:06.898095 INFO::Found  3  batches.
2025-03-18 12:32:06.898272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 12:32:06.898513 INFO::Using default BPPARAM
2025-03-18 12:32:06.898692 INFO::Processing subtree level 1
2025-03-18 12:32:06.975832 INFO::Adjusting the last 1 batches sequentially
2025-03-18 12:32:06.977676 INFO::Done
2025-03-18 12:32:06.978114 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 12:32:06.980013 INFO::ASW Batch was 0.167760908501434 prior to batch effect correction and is now -0.136425495565697 .
2025-03-18 12:32:06.981109 INFO::ASW Label was -0.205936323961864 prior to batch effect correction and is now 0.00348751307409813 .
2025-03-18 12:32:06.981808 INFO::Total function execution time is  0.0878889560699463  s and adjustment time is  0.0796058177947998 s ( 90.58 )
2025-03-18 12:32:07.076199 INFO::Formatting Data.
2025-03-18 12:32:07.076633 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.077065 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.077622 INFO::Found  2  missing values.
2025-03-18 12:32:07.080274 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.080916 INFO::Done
2025-03-18 12:32:07.108943 INFO::Found NA in Reference column
2025-03-18 12:32:07.118827 INFO::Require at least two references per batch.
2025-03-18 12:32:07.134227 INFO::Formatting Data.
2025-03-18 12:32:07.134572 INFO::Recognized SummarizedExperiment
2025-03-18 12:32:07.134753 INFO::Typecasting input to dataframe.
2025-03-18 12:32:07.140584 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.141089 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.14248 INFO::Found  0  missing values.
2025-03-18 12:32:07.145226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.146052 INFO::Done
2025-03-18 12:32:07.158012 INFO::Formatting Data.
2025-03-18 12:32:07.158416 INFO::Recognized SummarizedExperiment
2025-03-18 12:32:07.158624 INFO::Typecasting input to dataframe.
2025-03-18 12:32:07.173536 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.174708 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.17827 INFO::Found  0  missing values.
2025-03-18 12:32:07.190467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.190825 INFO::Done
2025-03-18 12:32:07.197164 INFO::Formatting Data.
2025-03-18 12:32:07.197495 INFO::Recognized SummarizedExperiment
2025-03-18 12:32:07.197714 INFO::Typecasting input to dataframe.
2025-03-18 12:32:07.207947 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.208942 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.209978 INFO::Found  0  missing values.
2025-03-18 12:32:07.210859 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.
2025-03-18 12:32:07.214986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.215518 INFO::Done
2025-03-18 12:32:07.225424 INFO::Formatting Data.
2025-03-18 12:32:07.226184 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.227018 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.227982 INFO::Found  0  missing values.
2025-03-18 12:32:07.230644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.231164 INFO::Done
2025-03-18 12:32:07.243227 INFO::Formatting Data.
2025-03-18 12:32:07.244054 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.244963 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.24665 INFO::Found  0  missing values.
2025-03-18 12:32:07.24973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.250336 INFO::Done
2025-03-18 12:32:07.271057 INFO::Formatting Data.
2025-03-18 12:32:07.271782 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.272722 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.27374 INFO::Found  1  missing values.
2025-03-18 12:32:07.275951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.276461 INFO::Done
2025-03-18 12:32:07.296867 INFO::Formatting Data.
2025-03-18 12:32:07.297573 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.298307 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.299094 INFO::Found  2  missing values.
2025-03-18 12:32:07.299857 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.
2025-03-18 12:32:07.301754 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.302247 INFO::Done
2025-03-18 12:32:07.311807 INFO::Formatting Data.
2025-03-18 12:32:07.312476 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.313224 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.31443 INFO::Found  2  missing values.
2025-03-18 12:32:07.316364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.316997 INFO::Done
2025-03-18 12:32:07.322394 INFO::Formatting Data.
2025-03-18 12:32:07.322737 INFO::Typecasting input to dataframe.
2025-03-18 12:32:07.323034 INFO::Replacing NaNs with NAs.
2025-03-18 12:32:07.323353 INFO::Removing potential empty rows and columns
2025-03-18 12:32:07.323705 INFO::Found  0  missing values.
2025-03-18 12:32:07.324697 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 12:32:07.324924 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 15.702   2.569  19.692

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT27.116 1.48120.198
compute_asw0.0300.0010.032
count_existing0.0150.0020.017
generate_data_covariables0.0140.0010.016
generate_dataset0.0140.0010.016