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This page was generated on 2025-03-20 12:08 -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 merida1

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 00:37:23 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 00:39:44 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 141.2 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: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* 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 43.953  2.546  34.069
* 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-x86_64/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: 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")
2025-03-18 00:39:07.80863 INFO::Formatting Data.
2025-03-18 00:39:07.814694 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:07.849783 INFO::Removing potential empty rows and columns
2025-03-18 00:39:08.604421 INFO::Found  0  missing values.
2025-03-18 00:39:08.615243 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:08.616629 INFO::Done
2025-03-18 00:39:08.617872 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:08.648729 INFO::Starting hierarchical adjustment
2025-03-18 00:39:08.650522 INFO::Found  3  batches.
2025-03-18 00:39:08.651745 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:08.65417 INFO::Using default BPPARAM
2025-03-18 00:39:08.655455 INFO::Processing subtree level 1
2025-03-18 00:39:08.919734 INFO::Adjusting the last 1 batches sequentially
2025-03-18 00:39:08.926994 INFO::Done
2025-03-18 00:39:08.928597 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:08.93605 INFO::ASW Batch was -0.101444435991748 prior to batch effect correction and is now -0.101444435991748 .
2025-03-18 00:39:08.93852 INFO::Total function execution time is  1.13103199005127  s and adjustment time is  0.276751041412354 s ( 24.47 )
2025-03-18 00:39:08.973448 INFO::Formatting Data.
2025-03-18 00:39:08.975062 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:08.977199 INFO::Removing potential empty rows and columns
2025-03-18 00:39:08.979953 INFO::Found  0  missing values.
2025-03-18 00:39:08.982247 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 00:39:09.011033 INFO::Formatting Data.
2025-03-18 00:39:09.012471 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:09.014386 INFO::Removing potential empty rows and columns
2025-03-18 00:39:09.016917 INFO::Found  0  missing values.
2025-03-18 00:39:09.021506 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 00:39:09.06823 INFO::Formatting Data.
2025-03-18 00:39:09.069955 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:09.072447 INFO::Removing potential empty rows and columns
2025-03-18 00:39:09.075365 INFO::Found  0  missing values.
2025-03-18 00:39:09.077666 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 00:39:09.090073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:09.091539 INFO::Done
2025-03-18 00:39:09.092801 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:09.098889 INFO::Starting hierarchical adjustment
2025-03-18 00:39:09.100749 INFO::Found  2  batches.
2025-03-18 00:39:09.102483 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:09.104172 INFO::Using default BPPARAM
2025-03-18 00:39:09.10559 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:09.10849 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:09.176138 INFO::Done
2025-03-18 00:39:09.177567 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:09.182539 INFO::ASW Batch was -0.0189999837782188 prior to batch effect correction and is now -0.113318211827973 .
2025-03-18 00:39:09.185016 INFO::Total function execution time is  0.116782188415527  s and adjustment time is  0.0757429599761963 s ( 64.86 )
2025-03-18 00:39:09.19202 INFO::Formatting Data.
2025-03-18 00:39:09.193738 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:09.223701 INFO::Formatting Data.
2025-03-18 00:39:09.225473 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:09.227701 INFO::Removing potential empty rows and columns
2025-03-18 00:39:09.23043 INFO::Found  0  missing values.
2025-03-18 00:39:09.239564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:09.241039 INFO::Done
2025-03-18 00:39:09.2423 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:09.24778 INFO::Starting hierarchical adjustment
2025-03-18 00:39:09.249452 INFO::Found  2  batches.
2025-03-18 00:39:09.250589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:09.252093 INFO::Using default BPPARAM
2025-03-18 00:39:09.253414 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:09.257439 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:09.300773 INFO::Done
2025-03-18 00:39:09.302772 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:09.307514 INFO::ASW Batch was -0.0700044193059183 prior to batch effect correction and is now -0.126482666462831 .
2025-03-18 00:39:09.30944 INFO::Total function execution time is  0.0858500003814697  s and adjustment time is  0.0516049861907959 s ( 60.11 )
2025-03-18 00:39:09.312585 INFO::Formatting Data.
2025-03-18 00:39:09.314109 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:09.316182 INFO::Removing potential empty rows and columns
2025-03-18 00:39:09.318796 INFO::Found  0  missing values.
2025-03-18 00:39:09.326976 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:09.328401 INFO::Done
2025-03-18 00:39:09.329668 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:09.335686 INFO::Starting hierarchical adjustment
2025-03-18 00:39:09.337541 INFO::Found  2  batches.
2025-03-18 00:39:09.338874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:09.340388 INFO::Using default BPPARAM
2025-03-18 00:39:09.341653 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:09.344252 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:09.385966 INFO::Done
2025-03-18 00:39:09.387648 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:09.392165 INFO::ASW Batch was -0.0700044193059183 prior to batch effect correction and is now -0.126482666462831 .
2025-03-18 00:39:09.393899 INFO::Total function execution time is  0.0814089775085449  s and adjustment time is  0.048799991607666 s ( 59.94 )
2025-03-18 00:39:15.926368 INFO::Formatting Data.
2025-03-18 00:39:15.927897 INFO::Recognized SummarizedExperiment
2025-03-18 00:39:15.929527 INFO::Typecasting input to dataframe.
2025-03-18 00:39:16.002227 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:16.00452 INFO::Removing potential empty rows and columns
2025-03-18 00:39:16.013721 INFO::Found  0  missing values.
2025-03-18 00:39:16.033134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:16.034361 INFO::Done
2025-03-18 00:39:16.035435 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:16.043779 INFO::Starting hierarchical adjustment
2025-03-18 00:39:16.04538 INFO::Found  2  batches.
2025-03-18 00:39:16.046457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:16.048773 INFO::Using default BPPARAM
2025-03-18 00:39:16.049984 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:16.052129 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:16.189677 INFO::Done
2025-03-18 00:39:16.191052 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:16.199342 INFO::ASW Batch was -0.0043415612027256 prior to batch effect correction and is now -0.0897885462604068 .
2025-03-18 00:39:16.201154 INFO::Total function execution time is  0.275527000427246  s and adjustment time is  0.144541025161743 s ( 52.46 )
2025-03-18 00:39:16.248949 INFO::Formatting Data.
2025-03-18 00:39:16.250499 INFO::Recognized SummarizedExperiment
2025-03-18 00:39:16.251924 INFO::Typecasting input to dataframe.
2025-03-18 00:39:16.27821 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:16.280846 INFO::Removing potential empty rows and columns
2025-03-18 00:39:16.292847 INFO::Found  0  missing values.
2025-03-18 00:39:16.317005 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:16.318481 INFO::Done
2025-03-18 00:39:16.319788 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:16.329579 INFO::Starting hierarchical adjustment
2025-03-18 00:39:16.331578 INFO::Found  2  batches.
2025-03-18 00:39:16.333006 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:16.334532 INFO::Using default BPPARAM
2025-03-18 00:39:16.335782 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:16.338366 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:16.424407 INFO::Done
2025-03-18 00:39:16.425909 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:16.435897 INFO::ASW Batch was 0.0130929745482262 prior to batch effect correction and is now 0.0130929745482262 .
2025-03-18 00:39:16.438066 INFO::Total function execution time is  0.189011812210083  s and adjustment time is  0.0932369232177734 s ( 49.33 )
2025-03-18 00:39:16.486589 INFO::Formatting Data.
2025-03-18 00:39:16.48823 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:16.490275 INFO::Removing potential empty rows and columns
2025-03-18 00:39:16.492895 INFO::Found  0  missing values.
2025-03-18 00:39:16.500268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:16.501719 INFO::Done
2025-03-18 00:39:16.502946 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:16.507829 INFO::Starting hierarchical adjustment
2025-03-18 00:39:16.509686 INFO::Found  3  batches.
2025-03-18 00:39:16.511039 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:16.512561 INFO::Using default BPPARAM
2025-03-18 00:39:16.513831 INFO::Processing subtree level 1
2025-03-18 00:39:16.884584 INFO::Adjusting the last 1 batches sequentially
2025-03-18 00:39:16.890891 INFO::Done
2025-03-18 00:39:16.896598 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:16.909621 INFO::ASW Batch was 0.0100382765193515 prior to batch effect correction and is now -0.187014173804345 .
2025-03-18 00:39:16.912966 INFO::Total function execution time is  0.426275014877319  s and adjustment time is  0.381573915481567 s ( 89.51 )
2025-03-18 00:39:16.956943 INFO::Skipping initial DF formatting
2025-03-18 00:39:16.958386 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:16.968157 INFO::Starting hierarchical adjustment
2025-03-18 00:39:16.970098 INFO::Found  5  batches.
2025-03-18 00:39:16.971419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:16.972964 INFO::Using default BPPARAM
2025-03-18 00:39:16.97432 INFO::Processing subtree level 1
2025-03-18 00:39:17.273761 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:17.282321 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:17.351307 INFO::Done
2025-03-18 00:39:17.353029 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:17.368019 INFO::ASW Batch was 0.479797766030943 prior to batch effect correction and is now 0.479797766030943 .
2025-03-18 00:39:17.369946 INFO::ASW Label was 0.40121286596628 prior to batch effect correction and is now 0.40121286596628 .
2025-03-18 00:39:17.373362 INFO::Total function execution time is  0.416414022445679  s and adjustment time is  0.381569147109985 s ( 91.63 )
2025-03-18 00:39:17.424664 INFO::Formatting Data.
2025-03-18 00:39:17.426592 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:17.428811 INFO::Removing potential empty rows and columns
2025-03-18 00:39:17.431737 INFO::Found  0  missing values.
2025-03-18 00:39:17.443241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:17.444718 INFO::Done
2025-03-18 00:39:17.448817 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:17.455909 INFO::Starting hierarchical adjustment
2025-03-18 00:39:17.457609 INFO::Found  5  batches.
2025-03-18 00:39:17.458814 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:17.46018 INFO::Using default BPPARAM
2025-03-18 00:39:17.461516 INFO::Processing subtree level 1
2025-03-18 00:39:17.723644 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:17.737171 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:17.794416 INFO::Done
2025-03-18 00:39:17.796154 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:17.806132 INFO::ASW Batch was 0.40237639466648 prior to batch effect correction and is now -0.0902959132933998 .
2025-03-18 00:39:17.808379 INFO::ASW Label was 0.351085447046835 prior to batch effect correction and is now 0.88332489859547 .
2025-03-18 00:39:17.810535 INFO::Total function execution time is  0.385838031768799  s and adjustment time is  0.337128877639771 s ( 87.38 )
2025-03-18 00:39:17.813152 INFO::Formatting Data.
2025-03-18 00:39:17.815308 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:17.818857 INFO::Removing potential empty rows and columns
2025-03-18 00:39:17.821437 INFO::Found  0  missing values.
2025-03-18 00:39:17.832494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:17.833913 INFO::Done
2025-03-18 00:39:17.835563 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:17.842259 INFO::Starting hierarchical adjustment
2025-03-18 00:39:17.844078 INFO::Found  5  batches.
2025-03-18 00:39:17.845353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:17.846859 INFO::Using default BPPARAM
2025-03-18 00:39:17.848251 INFO::Processing subtree level 1
2025-03-18 00:39:18.099844 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:18.112008 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:18.170239 INFO::Done
2025-03-18 00:39:18.171856 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:18.180398 INFO::ASW Batch was 0.40237639466648 prior to batch effect correction and is now -0.0902959132933998 .
2025-03-18 00:39:18.181931 INFO::ASW Label was 0.351085447046835 prior to batch effect correction and is now 0.88332489859547 .
2025-03-18 00:39:18.184541 INFO::Total function execution time is  0.371425151824951  s and adjustment time is  0.326503038406372 s ( 87.91 )
2025-03-18 00:39:18.222754 INFO::Formatting Data.
2025-03-18 00:39:18.224458 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:18.226675 INFO::Removing potential empty rows and columns
2025-03-18 00:39:18.229131 INFO::Found  0  missing values.
2025-03-18 00:39:18.239953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:18.241385 INFO::Done
2025-03-18 00:39:18.243232 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:18.250209 INFO::Starting hierarchical adjustment
2025-03-18 00:39:18.252019 INFO::Found  5  batches.
2025-03-18 00:39:18.253356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:18.255058 INFO::Using default BPPARAM
2025-03-18 00:39:18.257897 INFO::Processing subtree level 1
2025-03-18 00:39:18.507713 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:18.522112 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:18.579098 INFO::Done
2025-03-18 00:39:18.581453 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:18.592038 INFO::ASW Batch was 0.494193147100475 prior to batch effect correction and is now -0.0849480728732315 .
2025-03-18 00:39:18.593698 INFO::ASW Label was 0.182847110635516 prior to batch effect correction and is now 0.826364475765361 .
2025-03-18 00:39:18.595741 INFO::Total function execution time is  0.373013019561768  s and adjustment time is  0.327315092086792 s ( 87.75 )
2025-03-18 00:39:18.598339 INFO::Formatting Data.
2025-03-18 00:39:18.600706 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:18.60304 INFO::Removing potential empty rows and columns
2025-03-18 00:39:18.605582 INFO::Found  0  missing values.
2025-03-18 00:39:18.619675 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:18.621825 INFO::Done
2025-03-18 00:39:18.623694 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:18.631389 INFO::Starting hierarchical adjustment
2025-03-18 00:39:18.634118 INFO::Found  5  batches.
2025-03-18 00:39:18.635532 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:18.637132 INFO::Using default BPPARAM
2025-03-18 00:39:18.638579 INFO::Processing subtree level 1
2025-03-18 00:39:18.898018 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:18.907658 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:18.965247 INFO::Done
2025-03-18 00:39:18.967577 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:18.976262 INFO::ASW Batch was 0.494193147100475 prior to batch effect correction and is now -0.0849480728732315 .
2025-03-18 00:39:18.977818 INFO::ASW Label was 0.182847110635516 prior to batch effect correction and is now 0.826364475765361 .
2025-03-18 00:39:18.979812 INFO::Total function execution time is  0.38162088394165  s and adjustment time is  0.331551074981689 s ( 86.88 )
2025-03-18 00:39:19.016733 INFO::Formatting Data.
2025-03-18 00:39:19.018442 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:19.020692 INFO::Removing potential empty rows and columns
2025-03-18 00:39:19.023316 INFO::Found  0  missing values.
2025-03-18 00:39:19.030723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:19.032174 INFO::Done
2025-03-18 00:39:19.033952 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:19.040979 INFO::Starting hierarchical adjustment
2025-03-18 00:39:19.042828 INFO::Found  2  batches.
2025-03-18 00:39:19.04409 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:19.045554 INFO::Using default BPPARAM
2025-03-18 00:39:19.046699 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:19.048689 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:19.088367 INFO::Done
2025-03-18 00:39:19.089837 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:19.096799 INFO::ASW Batch was 0.643496271989578 prior to batch effect correction and is now 0.0367760285104475 .
2025-03-18 00:39:19.098329 INFO::ASW Label was 0.459294875677262 prior to batch effect correction and is now 0.905309292852285 .
2025-03-18 00:39:19.10022 INFO::Total function execution time is  0.0836069583892822  s and adjustment time is  0.0458841323852539 s ( 54.88 )
2025-03-18 00:39:19.102183 INFO::Formatting Data.
2025-03-18 00:39:19.103648 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:19.105765 INFO::Removing potential empty rows and columns
2025-03-18 00:39:19.108167 INFO::Found  0  missing values.
2025-03-18 00:39:19.115547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:19.117074 INFO::Done
2025-03-18 00:39:19.118536 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:19.127934 INFO::Starting hierarchical adjustment
2025-03-18 00:39:19.129635 INFO::Found  2  batches.
2025-03-18 00:39:19.130876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:19.132198 INFO::Using default BPPARAM
2025-03-18 00:39:19.133384 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:19.136185 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:19.176637 INFO::Done
2025-03-18 00:39:19.178191 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:19.185193 INFO::ASW Batch was 0.643496271989578 prior to batch effect correction and is now 0.0367760285104475 .
2025-03-18 00:39:19.187079 INFO::ASW Label was 0.459294875677262 prior to batch effect correction and is now 0.905309292852285 .
2025-03-18 00:39:19.189215 INFO::Total function execution time is  0.0870258808135986  s and adjustment time is  0.0472750663757324 s ( 54.32 )
2025-03-18 00:39:19.218149 INFO::Formatting Data.
2025-03-18 00:39:19.219779 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:19.221814 INFO::Removing potential empty rows and columns
2025-03-18 00:39:19.22453 INFO::Found  0  missing values.
2025-03-18 00:39:19.230429 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:19.231833 INFO::Done
2025-03-18 00:39:19.234137 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:19.238773 INFO::Starting hierarchical adjustment
2025-03-18 00:39:19.240581 INFO::Found  2  batches.
2025-03-18 00:39:19.242462 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:19.244053 INFO::Using default BPPARAM
2025-03-18 00:39:19.245649 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:19.247864 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:19.339085 INFO::Done
2025-03-18 00:39:19.340399 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:19.345413 INFO::ASW Batch was -0.0579372758593293 prior to batch effect correction and is now -0.115953512262512 .
2025-03-18 00:39:19.347426 INFO::Total function execution time is  0.129374980926514  s and adjustment time is  0.0988240242004395 s ( 76.39 )
2025-03-18 00:39:19.378277 INFO::Formatting Data.
2025-03-18 00:39:19.379999 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:19.382103 INFO::Removing potential empty rows and columns
2025-03-18 00:39:19.385115 INFO::Found  0  missing values.
2025-03-18 00:39:19.388054 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 00:39:19.403095 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:19.404635 INFO::Done
2025-03-18 00:39:19.406496 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:19.413655 INFO::Starting hierarchical adjustment
2025-03-18 00:39:19.416478 INFO::Found  2  batches.
2025-03-18 00:39:19.417939 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:19.419453 INFO::Using default BPPARAM
2025-03-18 00:39:19.42081 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:19.423211 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:19.471526 INFO::Done
2025-03-18 00:39:19.473041 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:19.4805 INFO::ASW Batch was 0.674433046355327 prior to batch effect correction and is now 0.0482701109571511 .
2025-03-18 00:39:19.482155 INFO::ASW Label was 0.425953479671894 prior to batch effect correction and is now 0.896230441329486 .
2025-03-18 00:39:19.484126 INFO::Total function execution time is  0.105932950973511  s and adjustment time is  0.0563609600067139 s ( 53.2 )
2025-03-18 00:39:19.48606 INFO::Formatting Data.
2025-03-18 00:39:19.487524 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:19.490419 INFO::Removing potential empty rows and columns
2025-03-18 00:39:19.493232 INFO::Found  0  missing values.
2025-03-18 00:39:19.495789 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 00:39:19.508995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:19.510511 INFO::Done
2025-03-18 00:39:19.512239 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:19.521043 INFO::Starting hierarchical adjustment
2025-03-18 00:39:19.523354 INFO::Found  2  batches.
2025-03-18 00:39:19.524879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:19.526401 INFO::Using default BPPARAM
2025-03-18 00:39:19.52852 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:19.530953 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:19.575726 INFO::Done
2025-03-18 00:39:19.577254 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:19.583966 INFO::ASW Batch was 0.674433046355327 prior to batch effect correction and is now 0.0482701109571511 .
2025-03-18 00:39:19.585518 INFO::ASW Label was 0.425953479671894 prior to batch effect correction and is now 0.896230441329486 .
2025-03-18 00:39:19.587716 INFO::Total function execution time is  0.101688146591187  s and adjustment time is  0.0531690120697021 s ( 52.29 )
2025-03-18 00:39:20.174878 INFO::Formatting Data.
2025-03-18 00:39:20.176624 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:20.178667 INFO::Removing potential empty rows and columns
2025-03-18 00:39:20.181202 INFO::Found  0  missing values.
2025-03-18 00:39:20.189122 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:20.190541 INFO::Done
2025-03-18 00:39:20.191777 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:20.196384 INFO::Starting hierarchical adjustment
2025-03-18 00:39:20.198235 INFO::Found  3  batches.
2025-03-18 00:39:20.199487 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:20.200867 INFO::Using default BPPARAM
2025-03-18 00:39:20.202092 INFO::Processing subtree level 1
2025-03-18 00:39:20.435864 INFO::Adjusting the last 1 batches sequentially
2025-03-18 00:39:20.442995 INFO::Done
2025-03-18 00:39:20.445207 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:20.460568 INFO::ASW Batch was -0.077285932012531 prior to batch effect correction and is now -0.077285932012531 .
2025-03-18 00:39:20.463855 INFO::Total function execution time is  0.288593053817749  s and adjustment time is  0.24508810043335 s ( 84.93 )
2025-03-18 00:39:20.466284 INFO::Formatting Data.
2025-03-18 00:39:20.469649 INFO::Typecasting input to dataframe.
2025-03-18 00:39:20.471256 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:20.47369 INFO::Removing potential empty rows and columns
2025-03-18 00:39:20.476005 INFO::Found  0  missing values.
2025-03-18 00:39:20.483715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:20.48512 INFO::Done
2025-03-18 00:39:20.486481 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:20.491826 INFO::Starting hierarchical adjustment
2025-03-18 00:39:20.493784 INFO::Found  3  batches.
2025-03-18 00:39:20.495092 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:20.498045 INFO::Using default BPPARAM
2025-03-18 00:39:20.500593 INFO::Processing subtree level 1
2025-03-18 00:39:20.741468 INFO::Adjusting the last 1 batches sequentially
2025-03-18 00:39:20.749178 INFO::Done
2025-03-18 00:39:20.754499 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:20.766475 INFO::ASW Batch was -0.077285932012531 prior to batch effect correction and is now -0.077285932012531 .
2025-03-18 00:39:20.769209 INFO::Total function execution time is  0.30285906791687  s and adjustment time is  0.255753993988037 s ( 84.45 )
2025-03-18 00:39:20.811449 INFO::Formatting Data.
2025-03-18 00:39:20.813302 INFO::Typecasting input to dataframe.
2025-03-18 00:39:20.815489 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:20.81808 INFO::Removing potential empty rows and columns
2025-03-18 00:39:20.821839 INFO::Found  0  missing values.
2025-03-18 00:39:20.830764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:20.832337 INFO::Done
2025-03-18 00:39:20.833716 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:20.838451 INFO::Starting hierarchical adjustment
2025-03-18 00:39:20.840806 INFO::Found  3  batches.
2025-03-18 00:39:20.842147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:20.843632 INFO::Using default BPPARAM
2025-03-18 00:39:20.845055 INFO::Processing subtree level 1
2025-03-18 00:39:21.317116 INFO::Adjusting the last 1 batches sequentially
2025-03-18 00:39:21.323005 INFO::Done
2025-03-18 00:39:21.324715 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:21.367475 INFO::ASW Batch was -0.00723238083916684 prior to batch effect correction and is now -0.00723238083916684 .
2025-03-18 00:39:21.376978 INFO::Total function execution time is  0.563630104064941  s and adjustment time is  0.482506990432739 s ( 85.61 )
2025-03-18 00:39:21.982016 INFO::Formatting Data.
2025-03-18 00:39:21.983962 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:21.986901 INFO::Removing potential empty rows and columns
2025-03-18 00:39:21.995236 INFO::Found  1000  missing values.
2025-03-18 00:39:22.067531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:22.070295 INFO::Done
2025-03-18 00:39:22.074267 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:22.092261 INFO::Starting hierarchical adjustment
2025-03-18 00:39:22.094219 INFO::Found  10  batches.
2025-03-18 00:39:22.095571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:22.097062 INFO::Using default BPPARAM
2025-03-18 00:39:22.104677 INFO::Processing subtree level 1
2025-03-18 00:39:22.51427 INFO::Processing subtree level 2
2025-03-18 00:39:23.071047 INFO::Adjusting the last 1 batches sequentially
2025-03-18 00:39:23.083274 INFO::Done
2025-03-18 00:39:23.087215 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:23.10942 INFO::ASW Batch was 0.522227128950135 prior to batch effect correction and is now 0.522227128950135 .
2025-03-18 00:39:23.112089 INFO::ASW Label was 0.319017760346387 prior to batch effect correction and is now 0.319017760346387 .
2025-03-18 00:39:23.114563 INFO::Total function execution time is  1.13258790969849  s and adjustment time is  0.989401817321777 s ( 87.36 )
2025-03-18 00:39:23.116675 INFO::Formatting Data.
2025-03-18 00:39:23.118303 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:23.121077 INFO::Removing potential empty rows and columns
2025-03-18 00:39:23.129192 INFO::Found  1000  missing values.
2025-03-18 00:39:23.195104 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:23.198149 INFO::Done
2025-03-18 00:39:23.199509 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:23.212785 INFO::Starting hierarchical adjustment
2025-03-18 00:39:23.215901 INFO::Found  10  batches.
2025-03-18 00:39:24.553035 INFO::Set up parallel execution backend with 2 workers
2025-03-18 00:39:24.554369 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-18 00:39:26.397566 INFO::Adjusting the last 2 batches sequentially
2025-03-18 00:39:26.400164 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-18 00:39:26.449752 INFO::Done
2025-03-18 00:39:26.451058 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:26.462167 INFO::ASW Batch was 0.522227128950135 prior to batch effect correction and is now 0.522227128950135 .
2025-03-18 00:39:26.463445 INFO::ASW Label was 0.319017760346387 prior to batch effect correction and is now 0.319017760346387 .
2025-03-18 00:39:26.465573 INFO::Total function execution time is  3.34899806976318  s and adjustment time is  3.23434114456177 s ( 96.58 )
2025-03-18 00:39:26.870989 INFO::Formatting Data.
2025-03-18 00:39:26.872768 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:26.875009 INFO::Removing potential empty rows and columns
2025-03-18 00:39:26.879119 INFO::Found  0  missing values.
2025-03-18 00:39:26.889422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:26.890754 INFO::Done
2025-03-18 00:39:26.891939 INFO::Acquiring quality metrics before batch effect correction.
2025-03-18 00:39:26.898898 INFO::Starting hierarchical adjustment
2025-03-18 00:39:26.901449 INFO::Found  3  batches.
2025-03-18 00:39:26.902845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-18 00:39:26.904255 INFO::Using default BPPARAM
2025-03-18 00:39:26.905466 INFO::Processing subtree level 1
2025-03-18 00:39:27.206584 INFO::Adjusting the last 1 batches sequentially
2025-03-18 00:39:27.216044 INFO::Done
2025-03-18 00:39:27.217704 INFO::Acquiring quality metrics after batch effect correction.
2025-03-18 00:39:27.234824 INFO::ASW Batch was 0.247934469211128 prior to batch effect correction and is now -0.145657928336364 .
2025-03-18 00:39:27.236343 INFO::ASW Label was -0.218305602679492 prior to batch effect correction and is now -0.0155542320160975 .
2025-03-18 00:39:27.240727 INFO::Total function execution time is  0.36943507194519  s and adjustment time is  0.314984083175659 s ( 85.26 )
2025-03-18 00:39:27.604499 INFO::Formatting Data.
2025-03-18 00:39:27.60687 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:27.609957 INFO::Removing potential empty rows and columns
2025-03-18 00:39:27.613931 INFO::Found  2  missing values.
2025-03-18 00:39:27.624686 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:27.626399 INFO::Done
2025-03-18 00:39:27.747995 INFO::Found NA in Reference column
2025-03-18 00:39:27.776448 INFO::Require at least two references per batch.
2025-03-18 00:39:27.83959 INFO::Formatting Data.
2025-03-18 00:39:27.84112 INFO::Recognized SummarizedExperiment
2025-03-18 00:39:27.842513 INFO::Typecasting input to dataframe.
2025-03-18 00:39:27.872546 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:27.875433 INFO::Removing potential empty rows and columns
2025-03-18 00:39:27.887804 INFO::Found  0  missing values.
2025-03-18 00:39:27.912996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:27.91443 INFO::Done
2025-03-18 00:39:27.958335 INFO::Formatting Data.
2025-03-18 00:39:27.959834 INFO::Recognized SummarizedExperiment
2025-03-18 00:39:27.961328 INFO::Typecasting input to dataframe.
2025-03-18 00:39:28.008966 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:28.012839 INFO::Removing potential empty rows and columns
2025-03-18 00:39:28.025704 INFO::Found  0  missing values.
2025-03-18 00:39:28.066571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:28.068119 INFO::Done
2025-03-18 00:39:28.112113 INFO::Formatting Data.
2025-03-18 00:39:28.113785 INFO::Recognized SummarizedExperiment
2025-03-18 00:39:28.115503 INFO::Typecasting input to dataframe.
2025-03-18 00:39:28.167929 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:28.170238 INFO::Removing potential empty rows and columns
2025-03-18 00:39:28.17334 INFO::Found  0  missing values.
2025-03-18 00:39:28.175711 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 00:39:28.189255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:28.1908 INFO::Done
2025-03-18 00:39:28.221747 INFO::Formatting Data.
2025-03-18 00:39:28.223466 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:28.226491 INFO::Removing potential empty rows and columns
2025-03-18 00:39:28.229118 INFO::Found  0  missing values.
2025-03-18 00:39:28.237412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:28.238832 INFO::Done
2025-03-18 00:39:28.268209 INFO::Formatting Data.
2025-03-18 00:39:28.269922 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:28.272036 INFO::Removing potential empty rows and columns
2025-03-18 00:39:28.27465 INFO::Found  0  missing values.
2025-03-18 00:39:28.282782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:28.284253 INFO::Done
2025-03-18 00:39:28.36719 INFO::Formatting Data.
2025-03-18 00:39:28.368856 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:28.371517 INFO::Removing potential empty rows and columns
2025-03-18 00:39:28.374757 INFO::Found  1  missing values.
2025-03-18 00:39:28.381787 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:28.384353 INFO::Done
2025-03-18 00:39:28.435791 INFO::Formatting Data.
2025-03-18 00:39:28.437469 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:28.439545 INFO::Removing potential empty rows and columns
2025-03-18 00:39:28.443582 INFO::Found  2  missing values.
2025-03-18 00:39:28.445953 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 00:39:28.452207 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:28.453841 INFO::Done
2025-03-18 00:39:28.481102 INFO::Formatting Data.
2025-03-18 00:39:28.48279 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:28.485233 INFO::Removing potential empty rows and columns
2025-03-18 00:39:28.489907 INFO::Found  2  missing values.
2025-03-18 00:39:28.494456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:28.497756 INFO::Done
2025-03-18 00:39:28.52789 INFO::Formatting Data.
2025-03-18 00:39:28.529683 INFO::Typecasting input to dataframe.
2025-03-18 00:39:28.531714 INFO::Replacing NaNs with NAs.
2025-03-18 00:39:28.533881 INFO::Removing potential empty rows and columns
2025-03-18 00:39:28.536798 INFO::Found  0  missing values.
2025-03-18 00:39:28.546192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-18 00:39:28.547666 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 34.970   6.520  43.733

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT43.953 2.54634.069
compute_asw0.0580.0030.063
count_existing0.0290.0010.031
generate_data_covariables0.0260.0010.030
generate_dataset0.0250.0020.030