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This page was generated on 2025-10-08 12:52 -0400 (Wed, 08 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 164/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.5.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-10-07 13:45 -0400 (Tue, 07 Oct 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: devel
git_last_commit: 3fb455b
git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BERT on kjohnson3

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: 1.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz
StartedAt: 2025-10-07 18:24:09 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 18:24:40 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 31.4 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
      user system elapsed
BERT 9.905  0.391   7.256
* 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/4.5-arm64/Resources/library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.5.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: 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")
2025-10-07 18:24:33.290151 INFO::Formatting Data.
2025-10-07 18:24:33.291805 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:33.296382 INFO::Removing potential empty rows and columns
2025-10-07 18:24:33.395053 INFO::Found  0  missing values.
2025-10-07 18:24:33.396317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:33.396913 INFO::Done
2025-10-07 18:24:33.397092 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:33.402698 INFO::Starting hierarchical adjustment
2025-10-07 18:24:33.40303 INFO::Found  3  batches.
2025-10-07 18:24:33.403239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:33.403693 INFO::Using default BPPARAM
2025-10-07 18:24:33.403899 INFO::Processing subtree level 1
2025-10-07 18:24:33.451362 INFO::Adjusting the last 1 batches sequentially
2025-10-07 18:24:33.452986 INFO::Done
2025-10-07 18:24:33.453228 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:33.454825 INFO::ASW Batch was -0.0419507458483108 prior to batch effect correction and is now -0.0419507458483108 .
2025-10-07 18:24:33.455273 INFO::Total function execution time is  0.165558099746704  s and adjustment time is  0.0500268936157227 s ( 30.22 )
2025-10-07 18:24:33.462145 INFO::Formatting Data.
2025-10-07 18:24:33.462418 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:33.462861 INFO::Removing potential empty rows and columns
2025-10-07 18:24:33.463293 INFO::Found  0  missing values.
2025-10-07 18:24:33.463614 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.
2025-10-07 18:24:33.467725 INFO::Formatting Data.
2025-10-07 18:24:33.467956 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:33.468241 INFO::Removing potential empty rows and columns
2025-10-07 18:24:33.468574 INFO::Found  0  missing values.
2025-10-07 18:24:33.468878 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.
2025-10-07 18:24:33.474897 INFO::Formatting Data.
2025-10-07 18:24:33.475151 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:33.475435 INFO::Removing potential empty rows and columns
2025-10-07 18:24:33.475763 INFO::Found  0  missing values.
2025-10-07 18:24:33.476052 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.
2025-10-07 18:24:33.477487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:33.477672 INFO::Done
2025-10-07 18:24:33.477852 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:33.478606 INFO::Starting hierarchical adjustment
2025-10-07 18:24:33.47883 INFO::Found  2  batches.
2025-10-07 18:24:33.479009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:33.479258 INFO::Using default BPPARAM
2025-10-07 18:24:33.479433 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:33.479733 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-07 18:24:33.488496 INFO::Done
2025-10-07 18:24:33.488741 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:33.489424 INFO::ASW Batch was 0.0322701625094353 prior to batch effect correction and is now -0.118373460322215 .
2025-10-07 18:24:33.489689 INFO::Total function execution time is  0.014815092086792  s and adjustment time is  0.00969195365905762 s ( 65.42 )
2025-10-07 18:24:33.490726 INFO::Formatting Data.
2025-10-07 18:24:33.490925 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:33.493894 INFO::Formatting Data.
2025-10-07 18:24:33.494109 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:33.494379 INFO::Removing potential empty rows and columns
2025-10-07 18:24:33.494715 INFO::Found  0  missing values.
2025-10-07 18:24:33.495583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:33.495746 INFO::Done
2025-10-07 18:24:33.495916 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:33.496652 INFO::Starting hierarchical adjustment
2025-10-07 18:24:33.496866 INFO::Found  2  batches.
2025-10-07 18:24:33.497034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:33.497229 INFO::Using default BPPARAM
2025-10-07 18:24:33.497404 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:33.497694 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-07 18:24:33.523859 INFO::Done
2025-10-07 18:24:33.524194 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:33.524964 INFO::ASW Batch was 0.0798572429982884 prior to batch effect correction and is now -0.119039042052907 .
2025-10-07 18:24:33.525236 INFO::Total function execution time is  0.0313420295715332  s and adjustment time is  0.0270161628723145 s ( 86.2 )
2025-10-07 18:24:33.525573 INFO::Formatting Data.
2025-10-07 18:24:33.525769 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:33.526048 INFO::Removing potential empty rows and columns
2025-10-07 18:24:33.526404 INFO::Found  0  missing values.
2025-10-07 18:24:33.527298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:33.527481 INFO::Done
2025-10-07 18:24:33.527645 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:33.528282 INFO::Starting hierarchical adjustment
2025-10-07 18:24:33.528495 INFO::Found  2  batches.
2025-10-07 18:24:33.528649 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:33.528838 INFO::Using default BPPARAM
2025-10-07 18:24:33.528992 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:33.529252 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-07 18:24:33.535165 INFO::Done
2025-10-07 18:24:33.535421 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:33.536203 INFO::ASW Batch was 0.0798572429982884 prior to batch effect correction and is now -0.119039042052907 .
2025-10-07 18:24:33.536495 INFO::Total function execution time is  0.0108997821807861  s and adjustment time is  0.00669598579406738 s ( 61.43 )
2025-10-07 18:24:34.750872 INFO::Formatting Data.
2025-10-07 18:24:34.751171 INFO::Recognized SummarizedExperiment
2025-10-07 18:24:34.751344 INFO::Typecasting input to dataframe.
2025-10-07 18:24:34.762023 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:34.762496 INFO::Removing potential empty rows and columns
2025-10-07 18:24:34.763693 INFO::Found  0  missing values.
2025-10-07 18:24:34.76583 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:34.766026 INFO::Done
2025-10-07 18:24:34.766183 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:34.772215 INFO::Starting hierarchical adjustment
2025-10-07 18:24:34.772588 INFO::Found  2  batches.
2025-10-07 18:24:34.772784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:34.773238 INFO::Using default BPPARAM
2025-10-07 18:24:34.773411 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:34.773764 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-07 18:24:34.792141 INFO::Done
2025-10-07 18:24:34.792399 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:34.793625 INFO::ASW Batch was 0.00164040857446402 prior to batch effect correction and is now -0.0988512506787319 .
2025-10-07 18:24:34.793891 INFO::Total function execution time is  0.0431249141693115  s and adjustment time is  0.0196099281311035 s ( 45.47 )
2025-10-07 18:24:34.800115 INFO::Formatting Data.
2025-10-07 18:24:34.800324 INFO::Recognized SummarizedExperiment
2025-10-07 18:24:34.800484 INFO::Typecasting input to dataframe.
2025-10-07 18:24:34.803431 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:34.803778 INFO::Removing potential empty rows and columns
2025-10-07 18:24:34.804937 INFO::Found  0  missing values.
2025-10-07 18:24:34.807011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:34.807179 INFO::Done
2025-10-07 18:24:34.807344 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:34.80851 INFO::Starting hierarchical adjustment
2025-10-07 18:24:34.808721 INFO::Found  2  batches.
2025-10-07 18:24:34.808868 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:34.809046 INFO::Using default BPPARAM
2025-10-07 18:24:34.80919 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:34.809463 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-07 18:24:34.817243 INFO::Done
2025-10-07 18:24:34.817444 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:34.818608 INFO::ASW Batch was 0.0125325857771221 prior to batch effect correction and is now 0.0125325857771221 .
2025-10-07 18:24:34.81887 INFO::Total function execution time is  0.0187499523162842  s and adjustment time is  0.00856280326843262 s ( 45.67 )
2025-10-07 18:24:34.825725 INFO::Formatting Data.
2025-10-07 18:24:34.826001 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:34.826306 INFO::Removing potential empty rows and columns
2025-10-07 18:24:34.826645 INFO::Found  0  missing values.
2025-10-07 18:24:34.827523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:34.827687 INFO::Done
2025-10-07 18:24:34.827835 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:34.828474 INFO::Starting hierarchical adjustment
2025-10-07 18:24:34.828672 INFO::Found  3  batches.
2025-10-07 18:24:34.828817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:34.828994 INFO::Using default BPPARAM
2025-10-07 18:24:34.829132 INFO::Processing subtree level 1
2025-10-07 18:24:34.884401 INFO::Adjusting the last 1 batches sequentially
2025-10-07 18:24:34.903974 INFO::Done
2025-10-07 18:24:34.90513 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:34.921754 INFO::ASW Batch was 0.0659537862837951 prior to batch effect correction and is now -0.151925773270213 .
2025-10-07 18:24:34.927225 INFO::Total function execution time is  0.100177049636841  s and adjustment time is  0.0752830505371094 s ( 75.15 )
2025-10-07 18:24:34.942582 INFO::Skipping initial DF formatting
2025-10-07 18:24:34.942895 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:34.944349 INFO::Starting hierarchical adjustment
2025-10-07 18:24:34.94461 INFO::Found  5  batches.
2025-10-07 18:24:34.944803 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:34.946457 INFO::Using default BPPARAM
2025-10-07 18:24:34.946641 INFO::Processing subtree level 1
2025-10-07 18:24:35.073236 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.074559 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-07 18:24:35.089881 INFO::Done
2025-10-07 18:24:35.090619 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.093295 INFO::ASW Batch was 0.471136178245373 prior to batch effect correction and is now 0.471136178245373 .
2025-10-07 18:24:35.09362 INFO::ASW Label was 0.46685213177118 prior to batch effect correction and is now 0.46685213177118 .
2025-10-07 18:24:35.142231 INFO::Total function execution time is  0.199460983276367  s and adjustment time is  0.14531397819519 s ( 72.85 )
2025-10-07 18:24:35.157361 INFO::Formatting Data.
2025-10-07 18:24:35.157681 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.158009 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.15838 INFO::Found  0  missing values.
2025-10-07 18:24:35.159845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.160069 INFO::Done
2025-10-07 18:24:35.160312 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.1615 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.161878 INFO::Found  5  batches.
2025-10-07 18:24:35.162214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.16261 INFO::Using default BPPARAM
2025-10-07 18:24:35.162803 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-10-07 18:24:35.236123 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.238786 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-07 18:24:35.249313 INFO::Done
2025-10-07 18:24:35.249662 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.25206 INFO::ASW Batch was 0.25132418907821 prior to batch effect correction and is now -0.0582521018056134 .
2025-10-07 18:24:35.252348 INFO::ASW Label was 0.494605199161336 prior to batch effect correction and is now 0.861750754642464 .
2025-10-07 18:24:35.252908 INFO::Total function execution time is  0.0955140590667725  s and adjustment time is  0.0874960422515869 s ( 91.61 )
2025-10-07 18:24:35.253325 INFO::Formatting Data.
2025-10-07 18:24:35.253573 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.253999 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.254624 INFO::Found  0  missing values.
2025-10-07 18:24:35.256642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.257046 INFO::Done
2025-10-07 18:24:35.25729 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.258651 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.258972 INFO::Found  5  batches.
2025-10-07 18:24:35.259185 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.259498 INFO::Using default BPPARAM
2025-10-07 18:24:35.259732 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-10-07 18:24:35.318099 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.320212 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-07 18:24:35.331046 INFO::Done
2025-10-07 18:24:35.331474 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.333267 INFO::ASW Batch was 0.25132418907821 prior to batch effect correction and is now -0.0582521018056134 .
2025-10-07 18:24:35.333505 INFO::ASW Label was 0.494605199161336 prior to batch effect correction and is now 0.861750754642464 .
2025-10-07 18:24:35.334246 INFO::Total function execution time is  0.0808389186859131  s and adjustment time is  0.0721487998962402 s ( 89.25 )
2025-10-07 18:24:35.341333 INFO::Formatting Data.
2025-10-07 18:24:35.341663 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.342044 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.342471 INFO::Found  0  missing values.
2025-10-07 18:24:35.344129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.344517 INFO::Done
2025-10-07 18:24:35.344765 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.34619 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.346498 INFO::Found  5  batches.
2025-10-07 18:24:35.346698 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.346972 INFO::Using default BPPARAM
2025-10-07 18:24:35.347184 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-10-07 18:24:35.415724 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.418635 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-07 18:24:35.435198 INFO::Done
2025-10-07 18:24:35.435648 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.437539 INFO::ASW Batch was 0.4285326950965 prior to batch effect correction and is now -0.0789434042604863 .
2025-10-07 18:24:35.437839 INFO::ASW Label was 0.311081188551639 prior to batch effect correction and is now 0.840280581915496 .
2025-10-07 18:24:35.438556 INFO::Total function execution time is  0.0972239971160889  s and adjustment time is  0.0887570381164551 s ( 91.29 )
2025-10-07 18:24:35.442687 INFO::Formatting Data.
2025-10-07 18:24:35.443 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.443353 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.443734 INFO::Found  0  missing values.
2025-10-07 18:24:35.445086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.445285 INFO::Done
2025-10-07 18:24:35.445467 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.446479 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.446723 INFO::Found  5  batches.
2025-10-07 18:24:35.446902 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.447261 INFO::Using default BPPARAM
2025-10-07 18:24:35.447433 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-10-07 18:24:35.502861 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.505201 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-07 18:24:35.515227 INFO::Done
2025-10-07 18:24:35.515765 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.517468 INFO::ASW Batch was 0.4285326950965 prior to batch effect correction and is now -0.0789434042604863 .
2025-10-07 18:24:35.517674 INFO::ASW Label was 0.311081188551639 prior to batch effect correction and is now 0.840280581915496 .
2025-10-07 18:24:35.518171 INFO::Total function execution time is  0.075502872467041  s and adjustment time is  0.0685350894927979 s ( 90.77 )
2025-10-07 18:24:35.524023 INFO::Formatting Data.
2025-10-07 18:24:35.524264 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.524573 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.524946 INFO::Found  0  missing values.
2025-10-07 18:24:35.52584 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.526011 INFO::Done
2025-10-07 18:24:35.52618 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.527156 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.527519 INFO::Found  2  batches.
2025-10-07 18:24:35.527692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.527926 INFO::Using default BPPARAM
2025-10-07 18:24:35.528098 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.528379 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-07 18:24:35.53336 INFO::Done
2025-10-07 18:24:35.533563 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.534443 INFO::ASW Batch was 0.453340660936856 prior to batch effect correction and is now 0.169876089775295 .
2025-10-07 18:24:35.534618 INFO::ASW Label was 0.702136547094127 prior to batch effect correction and is now 0.836266152268206 .
2025-10-07 18:24:35.534844 INFO::Total function execution time is  0.0108439922332764  s and adjustment time is  0.00589299201965332 s ( 54.34 )
2025-10-07 18:24:35.535073 INFO::Formatting Data.
2025-10-07 18:24:35.535249 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.535507 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.535792 INFO::Found  0  missing values.
2025-10-07 18:24:35.536573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.536731 INFO::Done
2025-10-07 18:24:35.536883 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.537746 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.537963 INFO::Found  2  batches.
2025-10-07 18:24:35.538127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.538312 INFO::Using default BPPARAM
2025-10-07 18:24:35.538455 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.538702 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-07 18:24:35.543233 INFO::Done
2025-10-07 18:24:35.543431 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.544311 INFO::ASW Batch was 0.453340660936856 prior to batch effect correction and is now 0.169876089775295 .
2025-10-07 18:24:35.544506 INFO::ASW Label was 0.702136547094127 prior to batch effect correction and is now 0.836266152268206 .
2025-10-07 18:24:35.544742 INFO::Total function execution time is  0.00966691970825195  s and adjustment time is  0.00531005859375 s ( 54.93 )
2025-10-07 18:24:35.549093 INFO::Formatting Data.
2025-10-07 18:24:35.549317 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.5496 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.549865 INFO::Found  0  missing values.
2025-10-07 18:24:35.550529 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.5507 INFO::Done
2025-10-07 18:24:35.550864 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.551456 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.551666 INFO::Found  2  batches.
2025-10-07 18:24:35.551837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.552024 INFO::Using default BPPARAM
2025-10-07 18:24:35.552177 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.552432 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-07 18:24:35.562926 INFO::Done
2025-10-07 18:24:35.563147 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.563757 INFO::ASW Batch was 0.112066750703266 prior to batch effect correction and is now -0.0671206803915446 .
2025-10-07 18:24:35.564016 INFO::Total function execution time is  0.0149469375610352  s and adjustment time is  0.0112988948822021 s ( 75.59 )
2025-10-07 18:24:35.568226 INFO::Formatting Data.
2025-10-07 18:24:35.568449 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.56871 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.56903 INFO::Found  0  missing values.
2025-10-07 18:24:35.56945 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.
2025-10-07 18:24:35.570853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.571037 INFO::Done
2025-10-07 18:24:35.571202 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.572115 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.572344 INFO::Found  2  batches.
2025-10-07 18:24:35.572508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.572704 INFO::Using default BPPARAM
2025-10-07 18:24:35.572858 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.573137 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-07 18:24:35.57854 INFO::Done
2025-10-07 18:24:35.578751 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.579621 INFO::ASW Batch was 0.313787374142159 prior to batch effect correction and is now -0.0194840701743281 .
2025-10-07 18:24:35.579807 INFO::ASW Label was 0.706239750164887 prior to batch effect correction and is now 0.95864244661609 .
2025-10-07 18:24:35.580042 INFO::Total function execution time is  0.0118250846862793  s and adjustment time is  0.00623798370361328 s ( 52.75 )
2025-10-07 18:24:35.580256 INFO::Formatting Data.
2025-10-07 18:24:35.580415 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.580684 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.580964 INFO::Found  0  missing values.
2025-10-07 18:24:35.581215 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.
2025-10-07 18:24:35.582497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.582668 INFO::Done
2025-10-07 18:24:35.582817 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.58377 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.58399 INFO::Found  2  batches.
2025-10-07 18:24:35.584141 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.58432 INFO::Using default BPPARAM
2025-10-07 18:24:35.584472 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:35.584741 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-07 18:24:35.591314 INFO::Done
2025-10-07 18:24:35.591573 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.592569 INFO::ASW Batch was 0.313787374142159 prior to batch effect correction and is now -0.0194840701743281 .
2025-10-07 18:24:35.592759 INFO::ASW Label was 0.706239750164887 prior to batch effect correction and is now 0.95864244661609 .
2025-10-07 18:24:35.592997 INFO::Total function execution time is  0.0127339363098145  s and adjustment time is  0.00735998153686523 s ( 57.8 )
2025-10-07 18:24:35.659489 INFO::Formatting Data.
2025-10-07 18:24:35.659748 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.660027 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.660328 INFO::Found  0  missing values.
2025-10-07 18:24:35.661175 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.661344 INFO::Done
2025-10-07 18:24:35.661493 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.662111 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.662308 INFO::Found  3  batches.
2025-10-07 18:24:35.662451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.662622 INFO::Using default BPPARAM
2025-10-07 18:24:35.662759 INFO::Processing subtree level 1
2025-10-07 18:24:35.699715 INFO::Adjusting the last 1 batches sequentially
2025-10-07 18:24:35.702322 INFO::Done
2025-10-07 18:24:35.702683 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.704733 INFO::ASW Batch was 0.0642274206617588 prior to batch effect correction and is now 0.0642274206617588 .
2025-10-07 18:24:35.70556 INFO::Total function execution time is  0.0460829734802246  s and adjustment time is  0.040046215057373 s ( 86.9 )
2025-10-07 18:24:35.706032 INFO::Formatting Data.
2025-10-07 18:24:35.706292 INFO::Typecasting input to dataframe.
2025-10-07 18:24:35.706522 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.706825 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.707228 INFO::Found  0  missing values.
2025-10-07 18:24:35.708184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.708489 INFO::Done
2025-10-07 18:24:35.708651 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.70929 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.709518 INFO::Found  3  batches.
2025-10-07 18:24:35.709682 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.709894 INFO::Using default BPPARAM
2025-10-07 18:24:35.710057 INFO::Processing subtree level 1
2025-10-07 18:24:35.752357 INFO::Adjusting the last 1 batches sequentially
2025-10-07 18:24:35.754199 INFO::Done
2025-10-07 18:24:35.754467 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.75607 INFO::ASW Batch was 0.0642274206617588 prior to batch effect correction and is now 0.0642274206617588 .
2025-10-07 18:24:35.756942 INFO::Total function execution time is  0.0508768558502197  s and adjustment time is  0.0447189807891846 s ( 87.9 )
2025-10-07 18:24:35.763752 INFO::Formatting Data.
2025-10-07 18:24:35.764013 INFO::Typecasting input to dataframe.
2025-10-07 18:24:35.764274 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.764609 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.765017 INFO::Found  0  missing values.
2025-10-07 18:24:35.76596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.766127 INFO::Done
2025-10-07 18:24:35.766286 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.766981 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.767203 INFO::Found  3  batches.
2025-10-07 18:24:35.767359 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.767618 INFO::Using default BPPARAM
2025-10-07 18:24:35.767778 INFO::Processing subtree level 1
2025-10-07 18:24:35.808869 INFO::Adjusting the last 1 batches sequentially
2025-10-07 18:24:35.810841 INFO::Done
2025-10-07 18:24:35.811125 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:35.812956 INFO::ASW Batch was -0.0694788776598902 prior to batch effect correction and is now -0.0694788776598902 .
2025-10-07 18:24:35.813975 INFO::Total function execution time is  0.0502159595489502  s and adjustment time is  0.0436830520629883 s ( 86.99 )
2025-10-07 18:24:35.879658 INFO::Formatting Data.
2025-10-07 18:24:35.879929 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:35.880432 INFO::Removing potential empty rows and columns
2025-10-07 18:24:35.881357 INFO::Found  1000  missing values.
2025-10-07 18:24:35.886955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:35.887184 INFO::Done
2025-10-07 18:24:35.887365 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:35.889346 INFO::Starting hierarchical adjustment
2025-10-07 18:24:35.889625 INFO::Found  10  batches.
2025-10-07 18:24:35.889796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:35.890222 INFO::Using default BPPARAM
2025-10-07 18:24:35.890392 INFO::Processing subtree level 1
2025-10-07 18:24:35.947451 INFO::Processing subtree level 2
2025-10-07 18:24:36.008279 INFO::Adjusting the last 1 batches sequentially
2025-10-07 18:24:36.010522 INFO::Done
2025-10-07 18:24:36.010903 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:36.014403 INFO::ASW Batch was 0.520914881283367 prior to batch effect correction and is now 0.520914881283367 .
2025-10-07 18:24:36.014659 INFO::ASW Label was 0.339730581238368 prior to batch effect correction and is now 0.339730581238368 .
2025-10-07 18:24:36.015727 INFO::Total function execution time is  0.136041164398193  s and adjustment time is  0.120946884155273 s ( 88.9 )
2025-10-07 18:24:36.016116 INFO::Formatting Data.
2025-10-07 18:24:36.01635 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:36.016846 INFO::Removing potential empty rows and columns
2025-10-07 18:24:36.017991 INFO::Found  1000  missing values.
2025-10-07 18:24:36.024076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:36.024344 INFO::Done
2025-10-07 18:24:36.024525 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:36.026572 INFO::Starting hierarchical adjustment
2025-10-07 18:24:36.02684 INFO::Found  10  batches.
2025-10-07 18:24:36.501057 INFO::Set up parallel execution backend with 2 workers
2025-10-07 18:24:36.50135 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-07 18:24:37.035939 INFO::Adjusting the last 2 batches sequentially
2025-10-07 18:24:37.036536 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-07 18:24:37.042394 INFO::Done
2025-10-07 18:24:37.042593 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:37.044436 INFO::ASW Batch was 0.520914881283367 prior to batch effect correction and is now 0.520914881283367 .
2025-10-07 18:24:37.044604 INFO::ASW Label was 0.339730581238368 prior to batch effect correction and is now 0.339730581238368 .
2025-10-07 18:24:37.044838 INFO::Total function execution time is  1.02872896194458  s and adjustment time is  1.01560688018799 s ( 98.72 )
2025-10-07 18:24:37.122256 INFO::Formatting Data.
2025-10-07 18:24:37.122525 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.123234 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.123677 INFO::Found  0  missing values.
2025-10-07 18:24:37.124964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.125138 INFO::Done
2025-10-07 18:24:37.125313 INFO::Acquiring quality metrics before batch effect correction.
2025-10-07 18:24:37.126276 INFO::Starting hierarchical adjustment
2025-10-07 18:24:37.126507 INFO::Found  3  batches.
2025-10-07 18:24:37.126674 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-07 18:24:37.12689 INFO::Using default BPPARAM
2025-10-07 18:24:37.127045 INFO::Processing subtree level 1
2025-10-07 18:24:37.176326 INFO::Adjusting the last 1 batches sequentially
2025-10-07 18:24:37.178504 INFO::Done
2025-10-07 18:24:37.178839 INFO::Acquiring quality metrics after batch effect correction.
2025-10-07 18:24:37.181 INFO::ASW Batch was 0.119747990172284 prior to batch effect correction and is now -0.152407986529489 .
2025-10-07 18:24:37.181278 INFO::ASW Label was -0.207504606439169 prior to batch effect correction and is now -0.165536860000608 .
2025-10-07 18:24:37.182017 INFO::Total function execution time is  0.0597810745239258  s and adjustment time is  0.0520360469818115 s ( 87.04 )
2025-10-07 18:24:37.22806 INFO::Formatting Data.
2025-10-07 18:24:37.228372 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.228689 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.229098 INFO::Found  2  missing values.
2025-10-07 18:24:37.230092 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.230283 INFO::Done
2025-10-07 18:24:37.240668 INFO::Found NA in Reference column
2025-10-07 18:24:37.244214 INFO::Require at least two references per batch.
2025-10-07 18:24:37.25286 INFO::Formatting Data.
2025-10-07 18:24:37.253218 INFO::Recognized SummarizedExperiment
2025-10-07 18:24:37.253404 INFO::Typecasting input to dataframe.
2025-10-07 18:24:37.257507 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.257916 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.259157 INFO::Found  0  missing values.
2025-10-07 18:24:37.261636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.261896 INFO::Done
2025-10-07 18:24:37.267493 INFO::Formatting Data.
2025-10-07 18:24:37.267705 INFO::Recognized SummarizedExperiment
2025-10-07 18:24:37.267885 INFO::Typecasting input to dataframe.
2025-10-07 18:24:37.273256 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.273658 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.274873 INFO::Found  0  missing values.
2025-10-07 18:24:37.280282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.280642 INFO::Done
2025-10-07 18:24:37.28626 INFO::Formatting Data.
2025-10-07 18:24:37.286503 INFO::Recognized SummarizedExperiment
2025-10-07 18:24:37.286674 INFO::Typecasting input to dataframe.
2025-10-07 18:24:37.291844 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.292166 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.292518 INFO::Found  0  missing values.
2025-10-07 18:24:37.292818 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.
2025-10-07 18:24:37.294218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.294392 INFO::Done
2025-10-07 18:24:37.298202 INFO::Formatting Data.
2025-10-07 18:24:37.298424 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.298707 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.298999 INFO::Found  0  missing values.
2025-10-07 18:24:37.299859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.300069 INFO::Done
2025-10-07 18:24:37.304378 INFO::Formatting Data.
2025-10-07 18:24:37.304604 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.304875 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.305215 INFO::Found  0  missing values.
2025-10-07 18:24:37.306097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.306261 INFO::Done
2025-10-07 18:24:37.317639 INFO::Formatting Data.
2025-10-07 18:24:37.317929 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.318278 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.318708 INFO::Found  1  missing values.
2025-10-07 18:24:37.319618 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.319825 INFO::Done
2025-10-07 18:24:37.327679 INFO::Formatting Data.
2025-10-07 18:24:37.327927 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.328194 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.328478 INFO::Found  2  missing values.
2025-10-07 18:24:37.328765 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.
2025-10-07 18:24:37.329513 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.329697 INFO::Done
2025-10-07 18:24:37.333362 INFO::Formatting Data.
2025-10-07 18:24:37.333586 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.333837 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.334166 INFO::Found  2  missing values.
2025-10-07 18:24:37.334655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.334815 INFO::Done
2025-10-07 18:24:37.338759 INFO::Formatting Data.
2025-10-07 18:24:37.338986 INFO::Typecasting input to dataframe.
2025-10-07 18:24:37.339235 INFO::Replacing NaNs with NAs.
2025-10-07 18:24:37.339478 INFO::Removing potential empty rows and columns
2025-10-07 18:24:37.33981 INFO::Found  0  missing values.
2025-10-07 18:24:37.340649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-07 18:24:37.340811 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
  6.767   1.612   9.078 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT9.9050.3917.256
compute_asw0.0100.0010.011
count_existing0.0050.0010.005
generate_data_covariables0.0050.0000.005
generate_dataset0.0040.0010.005