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This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 163/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.4.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_21
git_last_commit: dedce04
git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for BERT on kjohnson1

To the developers/maintainers of the BERT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BERT
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2025-08-01 12:59:38 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 13:01:06 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 87.9 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* 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 28.614  1.415  21.549
* 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 ‘1.4.0’
** 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 (2025-06-14 r88325) -- "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")
2025-08-01 13:00:42.213188 INFO::Formatting Data.
2025-08-01 13:00:42.218271 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:42.233965 INFO::Removing potential empty rows and columns
2025-08-01 13:00:42.588396 INFO::Found  0  missing values.
2025-08-01 13:00:42.592458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:42.593261 INFO::Done
2025-08-01 13:00:42.593895 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:42.617653 INFO::Starting hierarchical adjustment
2025-08-01 13:00:42.618966 INFO::Found  3  batches.
2025-08-01 13:00:42.619783 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:42.621508 INFO::Using default BPPARAM
2025-08-01 13:00:42.622285 INFO::Processing subtree level 1
2025-08-01 13:00:42.808594 INFO::Adjusting the last 1 batches sequentially
2025-08-01 13:00:42.814241 INFO::Done
2025-08-01 13:00:42.815124 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:42.820896 INFO::ASW Batch was 0.0525741312206555 prior to batch effect correction and is now 0.0525741312206555 .
2025-08-01 13:00:42.823346 INFO::Total function execution time is  0.61090898513794  s and adjustment time is  0.195528984069824 s ( 32.01 )
2025-08-01 13:00:42.855047 INFO::Formatting Data.
2025-08-01 13:00:42.856976 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:42.858799 INFO::Removing potential empty rows and columns
2025-08-01 13:00:42.86083 INFO::Found  0  missing values.
2025-08-01 13:00:42.862873 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.
2025-08-01 13:00:42.87893 INFO::Formatting Data.
2025-08-01 13:00:42.879985 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:42.881279 INFO::Removing potential empty rows and columns
2025-08-01 13:00:42.882411 INFO::Found  0  missing values.
2025-08-01 13:00:42.883382 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.
2025-08-01 13:00:42.908004 INFO::Formatting Data.
2025-08-01 13:00:42.910974 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:42.912103 INFO::Removing potential empty rows and columns
2025-08-01 13:00:42.914858 INFO::Found  0  missing values.
2025-08-01 13:00:42.916683 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.
2025-08-01 13:00:42.924533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:42.925566 INFO::Done
2025-08-01 13:00:42.926186 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:42.928795 INFO::Starting hierarchical adjustment
2025-08-01 13:00:42.929573 INFO::Found  2  batches.
2025-08-01 13:00:42.930097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:42.930949 INFO::Using default BPPARAM
2025-08-01 13:00:42.931485 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:42.932454 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 13:00:42.981707 INFO::Done
2025-08-01 13:00:42.98269 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:42.989367 INFO::ASW Batch was 0.0788736072822083 prior to batch effect correction and is now -0.122814509024535 .
2025-08-01 13:00:42.990708 INFO::Total function execution time is  0.0831930637359619  s and adjustment time is  0.0521831512451172 s ( 62.73 )
2025-08-01 13:00:42.994547 INFO::Formatting Data.
2025-08-01 13:00:42.995221 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:43.005236 INFO::Formatting Data.
2025-08-01 13:00:43.005979 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:43.069974 INFO::Removing potential empty rows and columns
2025-08-01 13:00:43.071403 INFO::Found  0  missing values.
2025-08-01 13:00:43.07451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:43.075328 INFO::Done
2025-08-01 13:00:43.075885 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:43.078112 INFO::Starting hierarchical adjustment
2025-08-01 13:00:43.078869 INFO::Found  2  batches.
2025-08-01 13:00:43.079395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:43.079958 INFO::Using default BPPARAM
2025-08-01 13:00:43.080403 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:43.081181 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 13:00:43.096417 INFO::Done
2025-08-01 13:00:43.097963 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:43.100957 INFO::ASW Batch was -0.0180244391307817 prior to batch effect correction and is now -0.112250062760211 .
2025-08-01 13:00:43.10195 INFO::Total function execution time is  0.0967020988464355  s and adjustment time is  0.0176680088043213 s ( 18.27 )
2025-08-01 13:00:43.103015 INFO::Formatting Data.
2025-08-01 13:00:43.103571 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:43.104386 INFO::Removing potential empty rows and columns
2025-08-01 13:00:43.105377 INFO::Found  0  missing values.
2025-08-01 13:00:43.108175 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:43.108725 INFO::Done
2025-08-01 13:00:43.109206 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:43.111022 INFO::Starting hierarchical adjustment
2025-08-01 13:00:43.111719 INFO::Found  2  batches.
2025-08-01 13:00:43.11225 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:43.112842 INFO::Using default BPPARAM
2025-08-01 13:00:43.113309 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:43.114128 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 13:00:43.129848 INFO::Done
2025-08-01 13:00:43.130553 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:43.132732 INFO::ASW Batch was -0.0180244391307817 prior to batch effect correction and is now -0.112250062760211 .
2025-08-01 13:00:43.133609 INFO::Total function execution time is  0.0305840969085693  s and adjustment time is  0.0182309150695801 s ( 59.61 )
2025-08-01 13:00:46.773382 INFO::Formatting Data.
2025-08-01 13:00:46.774225 INFO::Recognized SummarizedExperiment
2025-08-01 13:00:46.775276 INFO::Typecasting input to dataframe.
2025-08-01 13:00:46.81437 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:46.815872 INFO::Removing potential empty rows and columns
2025-08-01 13:00:46.819719 INFO::Found  0  missing values.
2025-08-01 13:00:46.826723 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:46.827476 INFO::Done
2025-08-01 13:00:46.82799 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:46.832003 INFO::Starting hierarchical adjustment
2025-08-01 13:00:46.832751 INFO::Found  2  batches.
2025-08-01 13:00:46.833239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:46.834428 INFO::Using default BPPARAM
2025-08-01 13:00:46.834905 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:46.835899 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 13:00:46.909973 INFO::Done
2025-08-01 13:00:46.910813 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:46.915909 INFO::ASW Batch was 0.0106442095518023 prior to batch effect correction and is now -0.0921612659435057 .
2025-08-01 13:00:46.917418 INFO::Total function execution time is  0.144280910491943  s and adjustment time is  0.0772881507873535 s ( 53.57 )
2025-08-01 13:00:46.94041 INFO::Formatting Data.
2025-08-01 13:00:46.941345 INFO::Recognized SummarizedExperiment
2025-08-01 13:00:46.941862 INFO::Typecasting input to dataframe.
2025-08-01 13:00:46.951524 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:46.952705 INFO::Removing potential empty rows and columns
2025-08-01 13:00:46.956218 INFO::Found  0  missing values.
2025-08-01 13:00:46.962791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:46.963422 INFO::Done
2025-08-01 13:00:46.963956 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:46.967862 INFO::Starting hierarchical adjustment
2025-08-01 13:00:46.968651 INFO::Found  2  batches.
2025-08-01 13:00:46.96914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:46.969705 INFO::Using default BPPARAM
2025-08-01 13:00:46.970197 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:46.971161 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 13:00:46.999725 INFO::Done
2025-08-01 13:00:47.001528 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:47.005731 INFO::ASW Batch was -0.00108481348071974 prior to batch effect correction and is now -0.00108481348071974 .
2025-08-01 13:00:47.006891 INFO::Total function execution time is  0.0663280487060547  s and adjustment time is  0.0309591293334961 s ( 46.68 )
2025-08-01 13:00:47.028762 INFO::Formatting Data.
2025-08-01 13:00:47.029655 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:47.030589 INFO::Removing potential empty rows and columns
2025-08-01 13:00:47.031606 INFO::Found  0  missing values.
2025-08-01 13:00:47.034341 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:47.034967 INFO::Done
2025-08-01 13:00:47.035474 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:47.037594 INFO::Starting hierarchical adjustment
2025-08-01 13:00:47.038326 INFO::Found  3  batches.
2025-08-01 13:00:47.038812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:47.03938 INFO::Using default BPPARAM
2025-08-01 13:00:47.039836 INFO::Processing subtree level 1
2025-08-01 13:00:47.502003 INFO::Adjusting the last 1 batches sequentially
2025-08-01 13:00:47.508621 INFO::Done
2025-08-01 13:00:47.510374 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:47.515851 INFO::ASW Batch was -0.113150088015841 prior to batch effect correction and is now -0.186014452966773 .
2025-08-01 13:00:47.517809 INFO::Total function execution time is  0.489025115966797  s and adjustment time is  0.47036600112915 s ( 96.18 )
2025-08-01 13:00:47.671281 INFO::Skipping initial DF formatting
2025-08-01 13:00:47.67231 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:47.676929 INFO::Starting hierarchical adjustment
2025-08-01 13:00:47.67788 INFO::Found  5  batches.
2025-08-01 13:00:47.678583 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:47.679381 INFO::Using default BPPARAM
2025-08-01 13:00:47.679855 INFO::Processing subtree level 1
2025-08-01 13:00:47.956721 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:47.965735 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 13:00:48.012809 INFO::Done
2025-08-01 13:00:48.013924 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:48.027303 INFO::ASW Batch was 0.511444672399942 prior to batch effect correction and is now 0.511444672399942 .
2025-08-01 13:00:48.030116 INFO::ASW Label was 0.405831846247961 prior to batch effect correction and is now 0.405831846247961 .
2025-08-01 13:00:48.031685 INFO::Total function execution time is  0.360388994216919  s and adjustment time is  0.3350830078125 s ( 92.98 )
2025-08-01 13:00:48.085323 INFO::Formatting Data.
2025-08-01 13:00:48.086648 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:48.089003 INFO::Removing potential empty rows and columns
2025-08-01 13:00:48.092958 INFO::Found  0  missing values.
2025-08-01 13:00:48.10138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:48.102625 INFO::Done
2025-08-01 13:00:48.103462 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:48.10834 INFO::Starting hierarchical adjustment
2025-08-01 13:00:48.109499 INFO::Found  5  batches.
2025-08-01 13:00:48.110246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:48.111034 INFO::Using default BPPARAM
2025-08-01 13:00:48.111676 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.

2025-08-01 13:00:48.380433 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:48.387849 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 13:00:48.427209 INFO::Done
2025-08-01 13:00:48.428169 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:48.435651 INFO::ASW Batch was 0.524534060904593 prior to batch effect correction and is now -0.0291005573773538 .
2025-08-01 13:00:48.437056 INFO::ASW Label was 0.217401156111185 prior to batch effect correction and is now 0.667044489130173 .
2025-08-01 13:00:48.439799 INFO::Total function execution time is  0.354451894760132  s and adjustment time is  0.317870140075684 s ( 89.68 )
2025-08-01 13:00:48.440952 INFO::Formatting Data.
2025-08-01 13:00:48.441841 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:48.444831 INFO::Removing potential empty rows and columns
2025-08-01 13:00:48.446463 INFO::Found  0  missing values.
2025-08-01 13:00:48.45336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:48.454449 INFO::Done
2025-08-01 13:00:48.485336 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:48.491559 INFO::Starting hierarchical adjustment
2025-08-01 13:00:48.492531 INFO::Found  5  batches.
2025-08-01 13:00:48.493134 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:48.494624 INFO::Using default BPPARAM
2025-08-01 13:00:48.495341 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.

2025-08-01 13:00:48.73385 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:48.739104 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 13:00:48.772476 INFO::Done
2025-08-01 13:00:48.773531 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:48.778844 INFO::ASW Batch was 0.524534060904593 prior to batch effect correction and is now -0.0291005573773538 .
2025-08-01 13:00:48.779625 INFO::ASW Label was 0.217401156111185 prior to batch effect correction and is now 0.667044489130173 .
2025-08-01 13:00:48.780698 INFO::Total function execution time is  0.339721918106079  s and adjustment time is  0.280073165893555 s ( 82.44 )
2025-08-01 13:00:48.805003 INFO::Formatting Data.
2025-08-01 13:00:48.80618 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:48.807523 INFO::Removing potential empty rows and columns
2025-08-01 13:00:48.808831 INFO::Found  0  missing values.
2025-08-01 13:00:48.814076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:48.814915 INFO::Done
2025-08-01 13:00:48.815589 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:48.820847 INFO::Starting hierarchical adjustment
2025-08-01 13:00:48.821978 INFO::Found  5  batches.
2025-08-01 13:00:48.822581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:48.823374 INFO::Using default BPPARAM
2025-08-01 13:00:48.825218 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.

2025-08-01 13:00:49.022426 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:49.028256 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 13:00:49.065229 INFO::Done
2025-08-01 13:00:49.069037 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:49.077007 INFO::ASW Batch was 0.470714734901068 prior to batch effect correction and is now -0.0455391700452347 .
2025-08-01 13:00:49.078241 INFO::ASW Label was 0.27363809314325 prior to batch effect correction and is now 0.811447715574333 .
2025-08-01 13:00:49.079407 INFO::Total function execution time is  0.274467945098877  s and adjustment time is  0.243373155593872 s ( 88.67 )
2025-08-01 13:00:49.080522 INFO::Formatting Data.
2025-08-01 13:00:49.081351 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:49.082591 INFO::Removing potential empty rows and columns
2025-08-01 13:00:49.083936 INFO::Found  0  missing values.
2025-08-01 13:00:49.088579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:49.08937 INFO::Done
2025-08-01 13:00:49.090018 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:49.09367 INFO::Starting hierarchical adjustment
2025-08-01 13:00:49.094665 INFO::Found  5  batches.
2025-08-01 13:00:49.095287 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:49.0961 INFO::Using default BPPARAM
2025-08-01 13:00:49.097165 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.

2025-08-01 13:00:49.304185 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:49.310777 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 13:00:49.352309 INFO::Done
2025-08-01 13:00:49.353375 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:49.358835 INFO::ASW Batch was 0.470714734901068 prior to batch effect correction and is now -0.0455391700452347 .
2025-08-01 13:00:49.359695 INFO::ASW Label was 0.27363809314325 prior to batch effect correction and is now 0.811447715574333 .
2025-08-01 13:00:49.360844 INFO::Total function execution time is  0.280176877975464  s and adjustment time is  0.257788896560669 s ( 92.01 )
2025-08-01 13:00:49.387406 INFO::Formatting Data.
2025-08-01 13:00:49.388454 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:49.389653 INFO::Removing potential empty rows and columns
2025-08-01 13:00:49.39095 INFO::Found  0  missing values.
2025-08-01 13:00:49.395076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:49.395752 INFO::Done
2025-08-01 13:00:49.396339 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:49.40003 INFO::Starting hierarchical adjustment
2025-08-01 13:00:49.401961 INFO::Found  2  batches.
2025-08-01 13:00:49.404043 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:49.404985 INFO::Using default BPPARAM
2025-08-01 13:00:49.405583 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:49.406644 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 13:00:49.428109 INFO::Done
2025-08-01 13:00:49.429066 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:49.433133 INFO::ASW Batch was 0.63255476365755 prior to batch effect correction and is now 0.0811567144733356 .
2025-08-01 13:00:49.434089 INFO::ASW Label was 0.369060535063936 prior to batch effect correction and is now 0.846691055169851 .
2025-08-01 13:00:49.435155 INFO::Total function execution time is  0.0479528903961182  s and adjustment time is  0.0272760391235352 s ( 56.88 )
2025-08-01 13:00:49.436081 INFO::Formatting Data.
2025-08-01 13:00:49.436772 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:49.437977 INFO::Removing potential empty rows and columns
2025-08-01 13:00:49.439087 INFO::Found  0  missing values.
2025-08-01 13:00:49.442069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:49.4427 INFO::Done
2025-08-01 13:00:49.443248 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:49.446555 INFO::Starting hierarchical adjustment
2025-08-01 13:00:49.44749 INFO::Found  2  batches.
2025-08-01 13:00:49.44805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:49.448698 INFO::Using default BPPARAM
2025-08-01 13:00:49.449251 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:49.450288 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 13:00:49.46873 INFO::Done
2025-08-01 13:00:49.469658 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:49.473415 INFO::ASW Batch was 0.63255476365755 prior to batch effect correction and is now 0.0811567144733356 .
2025-08-01 13:00:49.475411 INFO::ASW Label was 0.369060535063936 prior to batch effect correction and is now 0.846691055169851 .
2025-08-01 13:00:49.47703 INFO::Total function execution time is  0.040895938873291  s and adjustment time is  0.0213570594787598 s ( 52.22 )
2025-08-01 13:00:49.521162 INFO::Formatting Data.
2025-08-01 13:00:49.522431 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:49.523809 INFO::Removing potential empty rows and columns
2025-08-01 13:00:49.525371 INFO::Found  0  missing values.
2025-08-01 13:00:49.528795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:49.529848 INFO::Done
2025-08-01 13:00:49.530483 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:49.533145 INFO::Starting hierarchical adjustment
2025-08-01 13:00:49.534161 INFO::Found  2  batches.
2025-08-01 13:00:49.534818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:49.535576 INFO::Using default BPPARAM
2025-08-01 13:00:49.536128 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:49.537212 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 13:00:49.576246 INFO::Done
2025-08-01 13:00:49.577184 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:49.579705 INFO::ASW Batch was -0.0615969925728752 prior to batch effect correction and is now -0.125396141538137 .
2025-08-01 13:00:49.580739 INFO::Total function execution time is  0.0602560043334961  s and adjustment time is  0.042248010635376 s ( 70.11 )
2025-08-01 13:00:49.59618 INFO::Formatting Data.
2025-08-01 13:00:49.59713 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:49.598045 INFO::Removing potential empty rows and columns
2025-08-01 13:00:49.599095 INFO::Found  0  missing values.
2025-08-01 13:00:49.600537 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.
2025-08-01 13:00:49.605166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:49.605859 INFO::Done
2025-08-01 13:00:49.606405 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:49.609623 INFO::Starting hierarchical adjustment
2025-08-01 13:00:49.610443 INFO::Found  2  batches.
2025-08-01 13:00:49.610981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:49.611566 INFO::Using default BPPARAM
2025-08-01 13:00:49.612067 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:49.612966 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 13:00:49.630695 INFO::Done
2025-08-01 13:00:49.631624 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:49.635543 INFO::ASW Batch was 0.662156445855856 prior to batch effect correction and is now -0.0218735744478527 .
2025-08-01 13:00:49.636439 INFO::ASW Label was 0.401187716478134 prior to batch effect correction and is now 0.895946987183127 .
2025-08-01 13:00:49.63748 INFO::Total function execution time is  0.0413970947265625  s and adjustment time is  0.0203211307525635 s ( 49.09 )
2025-08-01 13:00:49.638474 INFO::Formatting Data.
2025-08-01 13:00:49.639266 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:49.640474 INFO::Removing potential empty rows and columns
2025-08-01 13:00:49.641816 INFO::Found  0  missing values.
2025-08-01 13:00:49.643067 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.
2025-08-01 13:00:49.649334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:49.652841 INFO::Done
2025-08-01 13:00:49.654141 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:49.65921 INFO::Starting hierarchical adjustment
2025-08-01 13:00:49.660441 INFO::Found  2  batches.
2025-08-01 13:00:49.661108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:49.661787 INFO::Using default BPPARAM
2025-08-01 13:00:49.662302 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:49.663808 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 13:00:49.686238 INFO::Done
2025-08-01 13:00:49.687147 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:49.690469 INFO::ASW Batch was 0.662156445855856 prior to batch effect correction and is now -0.0218735744478527 .
2025-08-01 13:00:49.691158 INFO::ASW Label was 0.401187716478134 prior to batch effect correction and is now 0.895946987183127 .
2025-08-01 13:00:49.691991 INFO::Total function execution time is  0.0535488128662109  s and adjustment time is  0.0259959697723389 s ( 48.55 )
2025-08-01 13:00:49.916092 INFO::Formatting Data.
2025-08-01 13:00:49.916944 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:49.91783 INFO::Removing potential empty rows and columns
2025-08-01 13:00:49.918865 INFO::Found  0  missing values.
2025-08-01 13:00:49.921624 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:49.922332 INFO::Done
2025-08-01 13:00:49.922839 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:49.925031 INFO::Starting hierarchical adjustment
2025-08-01 13:00:49.925954 INFO::Found  3  batches.
2025-08-01 13:00:49.92647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:49.927981 INFO::Using default BPPARAM
2025-08-01 13:00:49.928784 INFO::Processing subtree level 1
2025-08-01 13:00:50.055603 INFO::Adjusting the last 1 batches sequentially
2025-08-01 13:00:50.059555 INFO::Done
2025-08-01 13:00:50.060975 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:50.06654 INFO::ASW Batch was -0.0608313498274232 prior to batch effect correction and is now -0.0608313498274232 .
2025-08-01 13:00:50.06836 INFO::Total function execution time is  0.152233839035034  s and adjustment time is  0.133713006973267 s ( 87.83 )
2025-08-01 13:00:50.06966 INFO::Formatting Data.
2025-08-01 13:00:50.070281 INFO::Typecasting input to dataframe.
2025-08-01 13:00:50.071026 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:50.072006 INFO::Removing potential empty rows and columns
2025-08-01 13:00:50.073286 INFO::Found  0  missing values.
2025-08-01 13:00:50.076966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:50.077598 INFO::Done
2025-08-01 13:00:50.078106 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:50.080241 INFO::Starting hierarchical adjustment
2025-08-01 13:00:50.080968 INFO::Found  3  batches.
2025-08-01 13:00:50.081821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:50.082911 INFO::Using default BPPARAM
2025-08-01 13:00:50.083429 INFO::Processing subtree level 1
2025-08-01 13:00:50.223344 INFO::Adjusting the last 1 batches sequentially
2025-08-01 13:00:50.228373 INFO::Done
2025-08-01 13:00:50.228837 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:50.234264 INFO::ASW Batch was -0.0608313498274232 prior to batch effect correction and is now -0.0608313498274232 .
2025-08-01 13:00:50.236967 INFO::Total function execution time is  0.167236089706421  s and adjustment time is  0.147561073303223 s ( 88.24 )
2025-08-01 13:00:50.259905 INFO::Formatting Data.
2025-08-01 13:00:50.261105 INFO::Typecasting input to dataframe.
2025-08-01 13:00:50.262192 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:50.26325 INFO::Removing potential empty rows and columns
2025-08-01 13:00:50.265474 INFO::Found  0  missing values.
2025-08-01 13:00:50.273578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:50.274897 INFO::Done
2025-08-01 13:00:50.276444 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:50.279638 INFO::Starting hierarchical adjustment
2025-08-01 13:00:50.280578 INFO::Found  3  batches.
2025-08-01 13:00:50.28126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:50.282119 INFO::Using default BPPARAM
2025-08-01 13:00:50.282705 INFO::Processing subtree level 1
2025-08-01 13:00:50.416873 INFO::Adjusting the last 1 batches sequentially
2025-08-01 13:00:50.443008 INFO::Done
2025-08-01 13:00:50.444983 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:50.454224 INFO::ASW Batch was 0.0283355913934227 prior to batch effect correction and is now 0.0283355913934227 .
2025-08-01 13:00:50.45626 INFO::Total function execution time is  0.196591854095459  s and adjustment time is  0.161116123199463 s ( 81.95 )
2025-08-01 13:00:50.709705 INFO::Formatting Data.
2025-08-01 13:00:50.710954 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:50.712854 INFO::Removing potential empty rows and columns
2025-08-01 13:00:50.716603 INFO::Found  1000  missing values.
2025-08-01 13:00:50.734948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:50.735977 INFO::Done
2025-08-01 13:00:50.736605 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:50.743221 INFO::Starting hierarchical adjustment
2025-08-01 13:00:50.744829 INFO::Found  10  batches.
2025-08-01 13:00:50.745393 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:50.746143 INFO::Using default BPPARAM
2025-08-01 13:00:50.746681 INFO::Processing subtree level 1
2025-08-01 13:00:50.93567 INFO::Processing subtree level 2
2025-08-01 13:00:51.169851 INFO::Adjusting the last 1 batches sequentially
2025-08-01 13:00:51.177919 INFO::Done
2025-08-01 13:00:51.17887 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:51.187422 INFO::ASW Batch was 0.504687897633452 prior to batch effect correction and is now 0.504687897633452 .
2025-08-01 13:00:51.188335 INFO::ASW Label was 0.299709738161134 prior to batch effect correction and is now 0.299709738161134 .
2025-08-01 13:00:51.190824 INFO::Total function execution time is  0.480398893356323  s and adjustment time is  0.433260202407837 s ( 90.19 )
2025-08-01 13:00:51.191964 INFO::Formatting Data.
2025-08-01 13:00:51.192682 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:51.194906 INFO::Removing potential empty rows and columns
2025-08-01 13:00:51.201117 INFO::Found  1000  missing values.
2025-08-01 13:00:51.230443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:51.231732 INFO::Done
2025-08-01 13:00:51.232332 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:51.240595 INFO::Starting hierarchical adjustment
2025-08-01 13:00:51.241564 INFO::Found  10  batches.
2025-08-01 13:00:52.917357 INFO::Set up parallel execution backend with 2 workers
2025-08-01 13:00:52.918327 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-01 13:00:54.653548 INFO::Adjusting the last 2 batches sequentially
2025-08-01 13:00:54.655282 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 13:00:54.672495 INFO::Done
2025-08-01 13:00:54.673265 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:54.678914 INFO::ASW Batch was 0.504687897633452 prior to batch effect correction and is now 0.504687897633452 .
2025-08-01 13:00:54.679558 INFO::ASW Label was 0.299709738161134 prior to batch effect correction and is now 0.299709738161134 .
2025-08-01 13:00:54.682114 INFO::Total function execution time is  3.49008202552795  s and adjustment time is  3.43105292320251 s ( 98.31 )
2025-08-01 13:00:54.885847 INFO::Formatting Data.
2025-08-01 13:00:54.887302 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:54.888801 INFO::Removing potential empty rows and columns
2025-08-01 13:00:54.890325 INFO::Found  0  missing values.
2025-08-01 13:00:54.894493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:54.895248 INFO::Done
2025-08-01 13:00:54.895905 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 13:00:54.899433 INFO::Starting hierarchical adjustment
2025-08-01 13:00:54.900367 INFO::Found  3  batches.
2025-08-01 13:00:54.901452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 13:00:54.90222 INFO::Using default BPPARAM
2025-08-01 13:00:54.902775 INFO::Processing subtree level 1
2025-08-01 13:00:55.062616 INFO::Adjusting the last 1 batches sequentially
2025-08-01 13:00:55.067281 INFO::Done
2025-08-01 13:00:55.067815 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 13:00:55.074023 INFO::ASW Batch was 0.0795576494318088 prior to batch effect correction and is now -0.144456595593604 .
2025-08-01 13:00:55.07481 INFO::ASW Label was -0.163351995562323 prior to batch effect correction and is now 0.0636768472540417 .
2025-08-01 13:00:55.078579 INFO::Total function execution time is  0.192512989044189  s and adjustment time is  0.167114019393921 s ( 86.81 )
2025-08-01 13:00:55.283438 INFO::Formatting Data.
2025-08-01 13:00:55.284135 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.284727 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.285451 INFO::Found  2  missing values.
2025-08-01 13:00:55.28727 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.28761 INFO::Done
2025-08-01 13:00:55.324516 INFO::Found NA in Reference column
2025-08-01 13:00:55.337037 INFO::Require at least two references per batch.
2025-08-01 13:00:55.366022 INFO::Formatting Data.
2025-08-01 13:00:55.367844 INFO::Recognized SummarizedExperiment
2025-08-01 13:00:55.368622 INFO::Typecasting input to dataframe.
2025-08-01 13:00:55.37736 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.380181 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.385006 INFO::Found  0  missing values.
2025-08-01 13:00:55.393929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.394533 INFO::Done
2025-08-01 13:00:55.413503 INFO::Formatting Data.
2025-08-01 13:00:55.414596 INFO::Recognized SummarizedExperiment
2025-08-01 13:00:55.415209 INFO::Typecasting input to dataframe.
2025-08-01 13:00:55.434638 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.436455 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.441138 INFO::Found  0  missing values.
2025-08-01 13:00:55.454994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.455962 INFO::Done
2025-08-01 13:00:55.474505 INFO::Formatting Data.
2025-08-01 13:00:55.475373 INFO::Recognized SummarizedExperiment
2025-08-01 13:00:55.475643 INFO::Typecasting input to dataframe.
2025-08-01 13:00:55.487038 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.487553 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.488007 INFO::Found  0  missing values.
2025-08-01 13:00:55.488428 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.
2025-08-01 13:00:55.494612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.494916 INFO::Done
2025-08-01 13:00:55.503425 INFO::Formatting Data.
2025-08-01 13:00:55.503855 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.504255 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.504695 INFO::Found  0  missing values.
2025-08-01 13:00:55.505984 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.506292 INFO::Done
2025-08-01 13:00:55.518843 INFO::Formatting Data.
2025-08-01 13:00:55.519647 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.520512 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.521487 INFO::Found  0  missing values.
2025-08-01 13:00:55.524398 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.524958 INFO::Done
2025-08-01 13:00:55.559144 INFO::Formatting Data.
2025-08-01 13:00:55.559718 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.560459 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.56186 INFO::Found  1  missing values.
2025-08-01 13:00:55.565965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.566628 INFO::Done
2025-08-01 13:00:55.590657 INFO::Formatting Data.
2025-08-01 13:00:55.592453 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.593273 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.594154 INFO::Found  2  missing values.
2025-08-01 13:00:55.595023 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.
2025-08-01 13:00:55.598307 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.599227 INFO::Done
2025-08-01 13:00:55.609433 INFO::Formatting Data.
2025-08-01 13:00:55.610218 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.610991 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.611917 INFO::Found  2  missing values.
2025-08-01 13:00:55.613447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.614037 INFO::Done
2025-08-01 13:00:55.627034 INFO::Formatting Data.
2025-08-01 13:00:55.62929 INFO::Typecasting input to dataframe.
2025-08-01 13:00:55.630358 INFO::Replacing NaNs with NAs.
2025-08-01 13:00:55.631392 INFO::Removing potential empty rows and columns
2025-08-01 13:00:55.632532 INFO::Found  0  missing values.
2025-08-01 13:00:55.63752 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 13:00:55.638269 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 20.402   5.759  28.016 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT28.614 1.41521.549
compute_asw0.0310.0020.032
count_existing0.0160.0010.017
generate_data_covariables0.0150.0020.018
generate_dataset0.0140.0020.017