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This page was generated on 2025-11-28 11:38 -0500 (Fri, 28 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4866
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4614
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4571
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 167/2328HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.7.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-11-27 13:40 -0500 (Thu, 27 Nov 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: devel
git_last_commit: 2e49878
git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for BERT on lconway

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: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2025-11-27 20:16:44 -0500 (Thu, 27 Nov 2025)
EndedAt: 2025-11-27 20:18:19 -0500 (Thu, 27 Nov 2025)
EllapsedTime: 94.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 26.206  1.677  22.819
* 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/4.6-x86_64/Resources/library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.7.0’
** 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 Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-11-27 20:17:56.824883 INFO::Formatting Data.
2025-11-27 20:17:56.828761 INFO::Replacing NaNs with NAs.
2025-11-27 20:17:56.841294 INFO::Removing potential empty rows and columns
2025-11-27 20:17:57.144322 INFO::Found  0  missing values.
2025-11-27 20:17:57.149335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:17:57.150363 INFO::Done
2025-11-27 20:17:57.151124 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:17:57.16891 INFO::Starting hierarchical adjustment
2025-11-27 20:17:57.170174 INFO::Found  3  batches.
2025-11-27 20:17:57.171174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:17:57.172608 INFO::Using default BPPARAM
2025-11-27 20:17:57.173187 INFO::Processing subtree level 1
2025-11-27 20:17:57.360686 INFO::Adjusting the last 1 batches sequentially
2025-11-27 20:17:57.368195 INFO::Done
2025-11-27 20:17:57.36933 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:17:57.372853 INFO::ASW Batch was -0.0542432120603488 prior to batch effect correction and is now -0.0542432120603488 .
2025-11-27 20:17:57.37412 INFO::Total function execution time is  0.54999303817749  s and adjustment time is  0.198148012161255 s ( 36.03 )
2025-11-27 20:17:57.394118 INFO::Formatting Data.
2025-11-27 20:17:57.395478 INFO::Replacing NaNs with NAs.
2025-11-27 20:17:57.396843 INFO::Removing potential empty rows and columns
2025-11-27 20:17:57.398191 INFO::Found  0  missing values.
2025-11-27 20:17:57.399222 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.
2025-11-27 20:17:57.414118 INFO::Formatting Data.
2025-11-27 20:17:57.415134 INFO::Replacing NaNs with NAs.
2025-11-27 20:17:57.416579 INFO::Removing potential empty rows and columns
2025-11-27 20:17:57.41801 INFO::Found  0  missing values.
2025-11-27 20:17:57.419447 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.
2025-11-27 20:17:57.443718 INFO::Formatting Data.
2025-11-27 20:17:57.44489 INFO::Replacing NaNs with NAs.
2025-11-27 20:17:57.44619 INFO::Removing potential empty rows and columns
2025-11-27 20:17:57.447611 INFO::Found  0  missing values.
2025-11-27 20:17:57.449022 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.
2025-11-27 20:17:57.455206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:17:57.456261 INFO::Done
2025-11-27 20:17:57.457175 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:17:57.459965 INFO::Starting hierarchical adjustment
2025-11-27 20:17:57.461193 INFO::Found  2  batches.
2025-11-27 20:17:57.461816 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:17:57.462704 INFO::Using default BPPARAM
2025-11-27 20:17:57.463252 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:17:57.464267 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 20:17:57.492926 INFO::Done
2025-11-27 20:17:57.49409 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:17:57.497521 INFO::ASW Batch was -0.0646308428585884 prior to batch effect correction and is now -0.117372133479928 .
2025-11-27 20:17:57.498612 INFO::Total function execution time is  0.0549249649047852  s and adjustment time is  0.0319280624389648 s ( 58.13 )
2025-11-27 20:17:57.502906 INFO::Formatting Data.
2025-11-27 20:17:57.504105 INFO::Replacing NaNs with NAs.
2025-11-27 20:17:57.515201 INFO::Formatting Data.
2025-11-27 20:17:57.516368 INFO::Replacing NaNs with NAs.
2025-11-27 20:17:57.517803 INFO::Removing potential empty rows and columns
2025-11-27 20:17:57.519319 INFO::Found  0  missing values.
2025-11-27 20:17:57.523617 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:17:57.524527 INFO::Done
2025-11-27 20:17:57.525484 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:17:57.528082 INFO::Starting hierarchical adjustment
2025-11-27 20:17:57.529078 INFO::Found  2  batches.
2025-11-27 20:17:57.529609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:17:57.530315 INFO::Using default BPPARAM
2025-11-27 20:17:57.531146 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:17:57.532496 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 20:17:57.593358 INFO::Done
2025-11-27 20:17:57.594404 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:17:57.596707 INFO::ASW Batch was -0.0438662159573288 prior to batch effect correction and is now -0.0992641473822415 .
2025-11-27 20:17:57.597491 INFO::Total function execution time is  0.0824639797210693  s and adjustment time is  0.0643417835235596 s ( 78.02 )
2025-11-27 20:17:57.598505 INFO::Formatting Data.
2025-11-27 20:17:57.599069 INFO::Replacing NaNs with NAs.
2025-11-27 20:17:57.60019 INFO::Removing potential empty rows and columns
2025-11-27 20:17:57.601574 INFO::Found  0  missing values.
2025-11-27 20:17:57.605518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:17:57.606037 INFO::Done
2025-11-27 20:17:57.606514 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:17:57.608629 INFO::Starting hierarchical adjustment
2025-11-27 20:17:57.609329 INFO::Found  2  batches.
2025-11-27 20:17:57.610049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:17:57.610776 INFO::Using default BPPARAM
2025-11-27 20:17:57.611443 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:17:57.612458 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 20:17:57.63248 INFO::Done
2025-11-27 20:17:57.633462 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:17:57.636142 INFO::ASW Batch was -0.0438662159573288 prior to batch effect correction and is now -0.0992641473822415 .
2025-11-27 20:17:57.63722 INFO::Total function execution time is  0.0386369228363037  s and adjustment time is  0.0232028961181641 s ( 60.05 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-11-27 20:18:01.076334 INFO::Formatting Data.
2025-11-27 20:18:01.076948 INFO::Recognized SummarizedExperiment
2025-11-27 20:18:01.077393 INFO::Typecasting input to dataframe.
2025-11-27 20:18:01.104485 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:01.105542 INFO::Removing potential empty rows and columns
2025-11-27 20:18:01.120285 INFO::Found  0  missing values.
2025-11-27 20:18:01.125798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:01.126434 INFO::Done
2025-11-27 20:18:01.126914 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:01.129695 INFO::Starting hierarchical adjustment
2025-11-27 20:18:01.130543 INFO::Found  2  batches.
2025-11-27 20:18:01.131217 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:01.132556 INFO::Using default BPPARAM
2025-11-27 20:18:01.133215 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:01.134473 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 20:18:01.200693 INFO::Done
2025-11-27 20:18:01.201628 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:01.20672 INFO::ASW Batch was -0.0290883732351809 prior to batch effect correction and is now -0.0943477044371479 .
2025-11-27 20:18:01.207656 INFO::Total function execution time is  0.131535053253174  s and adjustment time is  0.0702998638153076 s ( 53.45 )
Warning: stack imbalance in '{', 73 then 75
2025-11-27 20:18:01.233953 INFO::Formatting Data.
2025-11-27 20:18:01.23506 INFO::Recognized SummarizedExperiment
2025-11-27 20:18:01.235975 INFO::Typecasting input to dataframe.
2025-11-27 20:18:01.254733 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:01.256361 INFO::Removing potential empty rows and columns
2025-11-27 20:18:01.261881 INFO::Found  0  missing values.
2025-11-27 20:18:01.272144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:01.272929 INFO::Done
2025-11-27 20:18:01.273601 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:01.277587 INFO::Starting hierarchical adjustment
2025-11-27 20:18:01.278561 INFO::Found  2  batches.
2025-11-27 20:18:01.279249 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:01.28012 INFO::Using default BPPARAM
2025-11-27 20:18:01.280913 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:01.282424 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 20:18:01.315439 INFO::Done
2025-11-27 20:18:01.316405 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:01.321694 INFO::ASW Batch was -0.00546803872998154 prior to batch effect correction and is now -0.00546803872998154 .
2025-11-27 20:18:01.323027 INFO::Total function execution time is  0.0890319347381592  s and adjustment time is  0.0370101928710938 s ( 41.57 )
2025-11-27 20:18:01.354855 INFO::Formatting Data.
2025-11-27 20:18:01.356081 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:01.357559 INFO::Removing potential empty rows and columns
2025-11-27 20:18:01.35918 INFO::Found  0  missing values.
2025-11-27 20:18:01.36337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:01.364224 INFO::Done
2025-11-27 20:18:01.365177 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:01.367867 INFO::Starting hierarchical adjustment
2025-11-27 20:18:01.368751 INFO::Found  3  batches.
2025-11-27 20:18:01.369508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:01.370407 INFO::Using default BPPARAM
2025-11-27 20:18:01.371169 INFO::Processing subtree level 1
2025-11-27 20:18:01.568525 INFO::Adjusting the last 1 batches sequentially
2025-11-27 20:18:01.578344 INFO::Done
2025-11-27 20:18:01.58013 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:01.587214 INFO::ASW Batch was -0.0955835207332473 prior to batch effect correction and is now -0.143878123845605 .
2025-11-27 20:18:01.588584 INFO::Total function execution time is  0.233839988708496  s and adjustment time is  0.209722995758057 s ( 89.69 )
2025-11-27 20:18:01.610387 INFO::Skipping initial DF formatting
2025-11-27 20:18:01.611151 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:01.614919 INFO::Starting hierarchical adjustment
2025-11-27 20:18:01.61573 INFO::Found  5  batches.
2025-11-27 20:18:01.616672 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:01.617351 INFO::Using default BPPARAM
2025-11-27 20:18:01.617904 INFO::Processing subtree level 1
2025-11-27 20:18:01.776059 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:01.778561 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 20:18:01.804786 INFO::Done
2025-11-27 20:18:01.805596 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:01.811517 INFO::ASW Batch was 0.494239379850785 prior to batch effect correction and is now 0.494239379850785 .
2025-11-27 20:18:01.812299 INFO::ASW Label was 0.393753274372894 prior to batch effect correction and is now 0.393753274372894 .
2025-11-27 20:18:01.813785 INFO::Total function execution time is  0.203356027603149  s and adjustment time is  0.189198017120361 s ( 93.04 )
2025-11-27 20:18:01.843579 INFO::Formatting Data.
2025-11-27 20:18:01.844463 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:01.845489 INFO::Removing potential empty rows and columns
2025-11-27 20:18:01.846679 INFO::Found  0  missing values.
2025-11-27 20:18:01.85303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:01.854058 INFO::Done
2025-11-27 20:18:01.855064 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:01.85806 INFO::Starting hierarchical adjustment
2025-11-27 20:18:01.858835 INFO::Found  5  batches.
2025-11-27 20:18:01.859383 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:01.860097 INFO::Using default BPPARAM
2025-11-27 20:18:01.860671 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.

2025-11-27 20:18:01.981438 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:01.983857 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 20:18:02.005902 INFO::Done
2025-11-27 20:18:02.00679 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.011066 INFO::ASW Batch was 0.417862806183053 prior to batch effect correction and is now -0.0634416117471615 .
2025-11-27 20:18:02.011779 INFO::ASW Label was 0.353100734209385 prior to batch effect correction and is now 0.785240123635802 .
2025-11-27 20:18:02.012659 INFO::Total function execution time is  0.169152021408081  s and adjustment time is  0.147174119949341 s ( 87.01 )
2025-11-27 20:18:02.013527 INFO::Formatting Data.
2025-11-27 20:18:02.014149 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:02.015042 INFO::Removing potential empty rows and columns
2025-11-27 20:18:02.016591 INFO::Found  0  missing values.
2025-11-27 20:18:02.020495 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:02.02108 INFO::Done
2025-11-27 20:18:02.021614 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:02.024574 INFO::Starting hierarchical adjustment
2025-11-27 20:18:02.025418 INFO::Found  5  batches.
2025-11-27 20:18:02.025947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:02.026569 INFO::Using default BPPARAM
2025-11-27 20:18:02.027084 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.

2025-11-27 20:18:02.155504 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:02.158035 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 20:18:02.176201 INFO::Done
2025-11-27 20:18:02.177314 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.180846 INFO::ASW Batch was 0.417862806183053 prior to batch effect correction and is now -0.0634416117471615 .
2025-11-27 20:18:02.181528 INFO::ASW Label was 0.353100734209385 prior to batch effect correction and is now 0.785240123635802 .
2025-11-27 20:18:02.182366 INFO::Total function execution time is  0.168807029724121  s and adjustment time is  0.150841951370239 s ( 89.36 )
2025-11-27 20:18:02.202633 INFO::Formatting Data.
2025-11-27 20:18:02.203905 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:02.205189 INFO::Removing potential empty rows and columns
2025-11-27 20:18:02.206314 INFO::Found  0  missing values.
2025-11-27 20:18:02.210498 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:02.211118 INFO::Done
2025-11-27 20:18:02.211681 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:02.214947 INFO::Starting hierarchical adjustment
2025-11-27 20:18:02.215748 INFO::Found  5  batches.
2025-11-27 20:18:02.216319 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:02.217182 INFO::Using default BPPARAM
2025-11-27 20:18:02.217861 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.

2025-11-27 20:18:02.338591 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:02.343135 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 20:18:02.366876 INFO::Done
2025-11-27 20:18:02.368031 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.372013 INFO::ASW Batch was 0.463333835440312 prior to batch effect correction and is now -0.0207324713207474 .
2025-11-27 20:18:02.372777 INFO::ASW Label was 0.372640515998096 prior to batch effect correction and is now 0.677223893697126 .
2025-11-27 20:18:02.37377 INFO::Total function execution time is  0.171249866485596  s and adjustment time is  0.151180028915405 s ( 88.28 )
2025-11-27 20:18:02.374631 INFO::Formatting Data.
2025-11-27 20:18:02.375289 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:02.376183 INFO::Removing potential empty rows and columns
2025-11-27 20:18:02.377145 INFO::Found  0  missing values.
2025-11-27 20:18:02.382649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:02.38388 INFO::Done
2025-11-27 20:18:02.384777 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:02.388231 INFO::Starting hierarchical adjustment
2025-11-27 20:18:02.38995 INFO::Found  5  batches.
2025-11-27 20:18:02.391076 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:02.39211 INFO::Using default BPPARAM
2025-11-27 20:18:02.392921 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.

2025-11-27 20:18:02.522154 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:02.529776 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 20:18:02.552048 INFO::Done
2025-11-27 20:18:02.553685 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.559426 INFO::ASW Batch was 0.463333835440312 prior to batch effect correction and is now -0.0207324713207474 .
2025-11-27 20:18:02.560317 INFO::ASW Label was 0.372640515998096 prior to batch effect correction and is now 0.677223893697126 .
2025-11-27 20:18:02.561982 INFO::Total function execution time is  0.187201023101807  s and adjustment time is  0.162626981735229 s ( 86.87 )
2025-11-27 20:18:02.585088 INFO::Formatting Data.
2025-11-27 20:18:02.586704 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:02.588249 INFO::Removing potential empty rows and columns
2025-11-27 20:18:02.589699 INFO::Found  0  missing values.
2025-11-27 20:18:02.593393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:02.594362 INFO::Done
2025-11-27 20:18:02.595292 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:02.600316 INFO::Starting hierarchical adjustment
2025-11-27 20:18:02.601587 INFO::Found  2  batches.
2025-11-27 20:18:02.602518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:02.603308 INFO::Using default BPPARAM
2025-11-27 20:18:02.603883 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:02.604889 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 20:18:02.623522 INFO::Done
2025-11-27 20:18:02.624594 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.627867 INFO::ASW Batch was 0.650260848142961 prior to batch effect correction and is now -0.0250088432884935 .
2025-11-27 20:18:02.628788 INFO::ASW Label was 0.299055220596434 prior to batch effect correction and is now 0.746005760454641 .
2025-11-27 20:18:02.62981 INFO::Total function execution time is  0.0449850559234619  s and adjustment time is  0.0221688747406006 s ( 49.28 )
2025-11-27 20:18:02.630833 INFO::Formatting Data.
2025-11-27 20:18:02.631443 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:02.632329 INFO::Removing potential empty rows and columns
2025-11-27 20:18:02.633279 INFO::Found  0  missing values.
2025-11-27 20:18:02.6358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:02.636365 INFO::Done
2025-11-27 20:18:02.636851 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:02.639668 INFO::Starting hierarchical adjustment
2025-11-27 20:18:02.640387 INFO::Found  2  batches.
2025-11-27 20:18:02.640906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:02.641489 INFO::Using default BPPARAM
2025-11-27 20:18:02.642146 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:02.643427 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-11-27 20:18:02.659498 INFO::Done
2025-11-27 20:18:02.660842 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.665471 INFO::ASW Batch was 0.650260848142961 prior to batch effect correction and is now -0.0250088432884935 .
2025-11-27 20:18:02.666472 INFO::ASW Label was 0.299055220596434 prior to batch effect correction and is now 0.746005760454641 .
2025-11-27 20:18:02.667629 INFO::Total function execution time is  0.0367319583892822  s and adjustment time is  0.019179105758667 s ( 52.21 )
2025-11-27 20:18:02.686885 INFO::Formatting Data.
2025-11-27 20:18:02.688158 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:02.689096 INFO::Removing potential empty rows and columns
2025-11-27 20:18:02.68999 INFO::Found  0  missing values.
2025-11-27 20:18:02.691904 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:02.692438 INFO::Done
2025-11-27 20:18:02.69292 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:02.695404 INFO::Starting hierarchical adjustment
2025-11-27 20:18:02.696047 INFO::Found  2  batches.
2025-11-27 20:18:02.696615 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:02.697201 INFO::Using default BPPARAM
2025-11-27 20:18:02.697702 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:02.698551 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 20:18:02.737577 INFO::Done
2025-11-27 20:18:02.738507 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.741421 INFO::ASW Batch was -0.067542804870169 prior to batch effect correction and is now -0.147844259700081 .
2025-11-27 20:18:02.742804 INFO::Total function execution time is  0.0560569763183594  s and adjustment time is  0.0414860248565674 s ( 74.01 )
2025-11-27 20:18:02.761912 INFO::Formatting Data.
2025-11-27 20:18:02.763124 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:02.764453 INFO::Removing potential empty rows and columns
2025-11-27 20:18:02.765694 INFO::Found  0  missing values.
2025-11-27 20:18:02.76744 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.
2025-11-27 20:18:02.774179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:02.77525 INFO::Done
2025-11-27 20:18:02.77603 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:02.780659 INFO::Starting hierarchical adjustment
2025-11-27 20:18:02.781932 INFO::Found  2  batches.
2025-11-27 20:18:02.78276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:02.783946 INFO::Using default BPPARAM
2025-11-27 20:18:02.78481 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:02.786317 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 20:18:02.810747 INFO::Done
2025-11-27 20:18:02.811925 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.815143 INFO::ASW Batch was 0.513644727753926 prior to batch effect correction and is now -0.0114960499045326 .
2025-11-27 20:18:02.815916 INFO::ASW Label was 0.503561373062074 prior to batch effect correction and is now 0.891478212105605 .
2025-11-27 20:18:02.817147 INFO::Total function execution time is  0.0552630424499512  s and adjustment time is  0.0290138721466064 s ( 52.5 )
2025-11-27 20:18:02.818454 INFO::Formatting Data.
2025-11-27 20:18:02.819445 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:02.820876 INFO::Removing potential empty rows and columns
2025-11-27 20:18:02.822456 INFO::Found  0  missing values.
2025-11-27 20:18:02.823794 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.
2025-11-27 20:18:02.830015 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:02.830917 INFO::Done
2025-11-27 20:18:02.831806 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:02.836423 INFO::Starting hierarchical adjustment
2025-11-27 20:18:02.83743 INFO::Found  2  batches.
2025-11-27 20:18:02.838224 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:02.839121 INFO::Using default BPPARAM
2025-11-27 20:18:02.839924 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:02.841329 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 20:18:02.862223 INFO::Done
2025-11-27 20:18:02.863416 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:02.867005 INFO::ASW Batch was 0.513644727753926 prior to batch effect correction and is now -0.0114960499045326 .
2025-11-27 20:18:02.868236 INFO::ASW Label was 0.503561373062074 prior to batch effect correction and is now 0.891478212105605 .
2025-11-27 20:18:02.869681 INFO::Total function execution time is  0.0512518882751465  s and adjustment time is  0.0248990058898926 s ( 48.58 )
2025-11-27 20:18:03.17234 INFO::Formatting Data.
2025-11-27 20:18:03.174176 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:03.176547 INFO::Removing potential empty rows and columns
2025-11-27 20:18:03.178006 INFO::Found  0  missing values.
2025-11-27 20:18:03.182101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:03.184211 INFO::Done
2025-11-27 20:18:03.185767 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:03.188609 INFO::Starting hierarchical adjustment
2025-11-27 20:18:03.19021 INFO::Found  3  batches.
2025-11-27 20:18:03.192151 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:03.19292 INFO::Using default BPPARAM
2025-11-27 20:18:03.193483 INFO::Processing subtree level 1
2025-11-27 20:18:03.364006 INFO::Adjusting the last 1 batches sequentially
2025-11-27 20:18:03.377266 INFO::Done
2025-11-27 20:18:03.378502 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:03.384864 INFO::ASW Batch was -0.0546225334755912 prior to batch effect correction and is now -0.0546225334755912 .
2025-11-27 20:18:03.387419 INFO::Total function execution time is  0.215188026428223  s and adjustment time is  0.187877893447876 s ( 87.31 )
2025-11-27 20:18:03.388688 INFO::Formatting Data.
2025-11-27 20:18:03.389562 INFO::Typecasting input to dataframe.
2025-11-27 20:18:03.390688 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:03.392039 INFO::Removing potential empty rows and columns
2025-11-27 20:18:03.393303 INFO::Found  0  missing values.
2025-11-27 20:18:03.396831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:03.397815 INFO::Done
2025-11-27 20:18:03.398412 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:03.400818 INFO::Starting hierarchical adjustment
2025-11-27 20:18:03.401566 INFO::Found  3  batches.
2025-11-27 20:18:03.402328 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:03.403374 INFO::Using default BPPARAM
2025-11-27 20:18:03.403968 INFO::Processing subtree level 1
2025-11-27 20:18:03.547005 INFO::Adjusting the last 1 batches sequentially
2025-11-27 20:18:03.563203 INFO::Done
2025-11-27 20:18:03.564279 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:03.573509 INFO::ASW Batch was -0.0546225334755912 prior to batch effect correction and is now -0.0546225334755912 .
2025-11-27 20:18:03.577185 INFO::Total function execution time is  0.188438892364502  s and adjustment time is  0.161751985549927 s ( 85.84 )
2025-11-27 20:18:03.598865 INFO::Formatting Data.
2025-11-27 20:18:03.600071 INFO::Typecasting input to dataframe.
2025-11-27 20:18:03.601488 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:03.602779 INFO::Removing potential empty rows and columns
2025-11-27 20:18:03.604419 INFO::Found  0  missing values.
2025-11-27 20:18:03.612295 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:03.613812 INFO::Done
2025-11-27 20:18:03.614623 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:03.617129 INFO::Starting hierarchical adjustment
2025-11-27 20:18:03.617894 INFO::Found  3  batches.
2025-11-27 20:18:03.618619 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:03.61925 INFO::Using default BPPARAM
2025-11-27 20:18:03.619749 INFO::Processing subtree level 1
2025-11-27 20:18:03.765518 INFO::Adjusting the last 1 batches sequentially
2025-11-27 20:18:03.785967 INFO::Done
2025-11-27 20:18:03.788843 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:03.804878 INFO::ASW Batch was -0.115729139218139 prior to batch effect correction and is now -0.115729139218139 .
2025-11-27 20:18:03.80742 INFO::Total function execution time is  0.208243846893311  s and adjustment time is  0.168149948120117 s ( 80.75 )
2025-11-27 20:18:04.044745 INFO::Formatting Data.
2025-11-27 20:18:04.046239 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:04.048182 INFO::Removing potential empty rows and columns
2025-11-27 20:18:04.051877 INFO::Found  1000  missing values.
2025-11-27 20:18:04.076807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:04.077923 INFO::Done
2025-11-27 20:18:04.078945 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:04.085176 INFO::Starting hierarchical adjustment
2025-11-27 20:18:04.086337 INFO::Found  10  batches.
2025-11-27 20:18:04.087192 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:04.088107 INFO::Using default BPPARAM
2025-11-27 20:18:04.089528 INFO::Processing subtree level 1
2025-11-27 20:18:04.269833 INFO::Processing subtree level 2
2025-11-27 20:18:04.693854 INFO::Adjusting the last 1 batches sequentially
2025-11-27 20:18:04.698115 INFO::Done
2025-11-27 20:18:04.699121 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:04.706951 INFO::ASW Batch was 0.466190200115288 prior to batch effect correction and is now 0.466190200115288 .
2025-11-27 20:18:04.718012 INFO::ASW Label was 0.382137070604401 prior to batch effect correction and is now 0.382137070604401 .
2025-11-27 20:18:04.730484 INFO::Total function execution time is  0.682668924331665  s and adjustment time is  0.611919164657593 s ( 89.64 )
2025-11-27 20:18:04.734264 INFO::Formatting Data.
2025-11-27 20:18:04.736951 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:04.742524 INFO::Removing potential empty rows and columns
2025-11-27 20:18:04.819265 INFO::Found  1000  missing values.
2025-11-27 20:18:04.844802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:04.845632 INFO::Done
2025-11-27 20:18:04.846197 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:04.852501 INFO::Starting hierarchical adjustment
2025-11-27 20:18:04.853697 INFO::Found  10  batches.
2025-11-27 20:18:06.012374 INFO::Set up parallel execution backend with 2 workers
2025-11-27 20:18:06.013385 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-11-27 20:18:07.411909 INFO::Adjusting the last 2 batches sequentially
2025-11-27 20:18:07.413504 INFO::Adjusting sequential tree level 1 with 2 batches
2025-11-27 20:18:07.435596 INFO::Done
2025-11-27 20:18:07.436541 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:07.443119 INFO::ASW Batch was 0.466190200115288 prior to batch effect correction and is now 0.466190200115288 .
2025-11-27 20:18:07.444002 INFO::ASW Label was 0.382137070604401 prior to batch effect correction and is now 0.382137070604401 .
2025-11-27 20:18:07.445042 INFO::Total function execution time is  2.71082305908203  s and adjustment time is  2.58211088180542 s ( 95.25 )
2025-11-27 20:18:07.689701 INFO::Formatting Data.
2025-11-27 20:18:07.691278 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:07.692813 INFO::Removing potential empty rows and columns
2025-11-27 20:18:07.694939 INFO::Found  0  missing values.
2025-11-27 20:18:07.700893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:07.701591 INFO::Done
2025-11-27 20:18:07.702139 INFO::Acquiring quality metrics before batch effect correction.
2025-11-27 20:18:07.704794 INFO::Starting hierarchical adjustment
2025-11-27 20:18:07.705508 INFO::Found  3  batches.
2025-11-27 20:18:07.705986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-11-27 20:18:07.706567 INFO::Using default BPPARAM
2025-11-27 20:18:07.707065 INFO::Processing subtree level 1
2025-11-27 20:18:07.871796 INFO::Adjusting the last 1 batches sequentially
2025-11-27 20:18:07.876162 INFO::Done
2025-11-27 20:18:07.877547 INFO::Acquiring quality metrics after batch effect correction.
2025-11-27 20:18:07.883464 INFO::ASW Batch was 0.126551978705045 prior to batch effect correction and is now -0.149686855525413 .
2025-11-27 20:18:07.884481 INFO::ASW Label was -0.168304091737818 prior to batch effect correction and is now -0.0489082164045355 .
2025-11-27 20:18:07.885849 INFO::Total function execution time is  0.196094036102295  s and adjustment time is  0.170665979385376 s ( 87.03 )
2025-11-27 20:18:08.134316 INFO::Formatting Data.
2025-11-27 20:18:08.135789 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.137901 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.141302 INFO::Found  2  missing values.
2025-11-27 20:18:08.148813 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.149879 INFO::Done
2025-11-27 20:18:08.204375 INFO::Found NA in Reference column
2025-11-27 20:18:08.22341 INFO::Require at least two references per batch.
2025-11-27 20:18:08.263025 INFO::Formatting Data.
2025-11-27 20:18:08.264241 INFO::Recognized SummarizedExperiment
2025-11-27 20:18:08.265185 INFO::Typecasting input to dataframe.
2025-11-27 20:18:08.283454 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.285275 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.291933 INFO::Found  0  missing values.
2025-11-27 20:18:08.304286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.305549 INFO::Done
2025-11-27 20:18:08.330469 INFO::Formatting Data.
2025-11-27 20:18:08.331787 INFO::Recognized SummarizedExperiment
2025-11-27 20:18:08.332925 INFO::Typecasting input to dataframe.
2025-11-27 20:18:08.363343 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.36553 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.373139 INFO::Found  0  missing values.
2025-11-27 20:18:08.393642 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.394696 INFO::Done
2025-11-27 20:18:08.422465 INFO::Formatting Data.
2025-11-27 20:18:08.423373 INFO::Recognized SummarizedExperiment
2025-11-27 20:18:08.424094 INFO::Typecasting input to dataframe.
2025-11-27 20:18:08.452598 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.45431 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.456216 INFO::Found  0  missing values.
2025-11-27 20:18:08.457652 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.
2025-11-27 20:18:08.4646 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.466213 INFO::Done
2025-11-27 20:18:08.488363 INFO::Formatting Data.
2025-11-27 20:18:08.48982 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.49155 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.492975 INFO::Found  0  missing values.
2025-11-27 20:18:08.497164 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.497998 INFO::Done
2025-11-27 20:18:08.521138 INFO::Formatting Data.
2025-11-27 20:18:08.523407 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.524984 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.526467 INFO::Found  0  missing values.
2025-11-27 20:18:08.530911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.53182 INFO::Done
2025-11-27 20:18:08.59139 INFO::Formatting Data.
2025-11-27 20:18:08.592865 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.594804 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.596998 INFO::Found  1  missing values.
2025-11-27 20:18:08.601672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.60275 INFO::Done
2025-11-27 20:18:08.640401 INFO::Formatting Data.
2025-11-27 20:18:08.641679 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.643077 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.644466 INFO::Found  2  missing values.
2025-11-27 20:18:08.64637 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.
2025-11-27 20:18:08.649786 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.650561 INFO::Done
2025-11-27 20:18:08.67406 INFO::Formatting Data.
2025-11-27 20:18:08.675628 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.677407 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.679023 INFO::Found  2  missing values.
2025-11-27 20:18:08.68149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.682349 INFO::Done
2025-11-27 20:18:08.702047 INFO::Formatting Data.
2025-11-27 20:18:08.703077 INFO::Typecasting input to dataframe.
2025-11-27 20:18:08.704457 INFO::Replacing NaNs with NAs.
2025-11-27 20:18:08.705615 INFO::Removing potential empty rows and columns
2025-11-27 20:18:08.706902 INFO::Found  0  missing values.
2025-11-27 20:18:08.711943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-11-27 20:18:08.712746 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 20.667   4.419  26.987

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT26.206 1.67722.819
compute_asw0.0250.0010.026
count_existing0.0140.0020.015
generate_data_covariables0.0150.0020.016
generate_dataset0.0140.0020.016