Back to Multiple platform build/check report for BioC 3.21:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-04 11:43 -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 merida1

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

raw results


Summary

Package: BERT
Version: 1.4.0
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 00:17:48 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 00:20:11 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 143.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* 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 44.749  2.621  34.621
* 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-x86_64/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 RC (2025-06-05 r88288) -- "Great Square Root"
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")
2025-08-01 00:19:34.822327 INFO::Formatting Data.
2025-08-01 00:19:34.830665 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:34.861981 INFO::Removing potential empty rows and columns
2025-08-01 00:19:35.556519 INFO::Found  0  missing values.
2025-08-01 00:19:35.565706 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:35.567396 INFO::Done
2025-08-01 00:19:35.568844 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:35.595842 INFO::Starting hierarchical adjustment
2025-08-01 00:19:35.597921 INFO::Found  3  batches.
2025-08-01 00:19:35.599714 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:35.602783 INFO::Using default BPPARAM
2025-08-01 00:19:35.604457 INFO::Processing subtree level 1
2025-08-01 00:19:35.887631 INFO::Adjusting the last 1 batches sequentially
2025-08-01 00:19:35.896914 INFO::Done
2025-08-01 00:19:35.899418 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:35.907107 INFO::ASW Batch was -0.0171010664774609 prior to batch effect correction and is now -0.0171010664774609 .
2025-08-01 00:19:35.910075 INFO::Total function execution time is  1.08913803100586  s and adjustment time is  0.299391984939575 s ( 27.49 )
2025-08-01 00:19:35.949096 INFO::Formatting Data.
2025-08-01 00:19:35.95103 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:35.953719 INFO::Removing potential empty rows and columns
2025-08-01 00:19:35.957142 INFO::Found  0  missing values.
2025-08-01 00:19:35.960012 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 00:19:35.989507 INFO::Formatting Data.
2025-08-01 00:19:35.991328 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:35.993803 INFO::Removing potential empty rows and columns
2025-08-01 00:19:35.996796 INFO::Found  0  missing values.
2025-08-01 00:19:35.999363 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 00:19:36.045284 INFO::Formatting Data.
2025-08-01 00:19:36.047195 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:36.049593 INFO::Removing potential empty rows and columns
2025-08-01 00:19:36.052705 INFO::Found  0  missing values.
2025-08-01 00:19:36.056252 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 00:19:36.068852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:36.070522 INFO::Done
2025-08-01 00:19:36.071989 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:36.077587 INFO::Starting hierarchical adjustment
2025-08-01 00:19:36.079794 INFO::Found  2  batches.
2025-08-01 00:19:36.081432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:36.083358 INFO::Using default BPPARAM
2025-08-01 00:19:36.086016 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:36.088662 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 00:19:36.152867 INFO::Done
2025-08-01 00:19:36.154537 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:36.160264 INFO::ASW Batch was 0.0843375280909136 prior to batch effect correction and is now -0.120318244490119 .
2025-08-01 00:19:36.162526 INFO::Total function execution time is  0.11726713180542  s and adjustment time is  0.073477029800415 s ( 62.66 )
2025-08-01 00:19:36.169611 INFO::Formatting Data.
2025-08-01 00:19:36.171475 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:36.196225 INFO::Formatting Data.
2025-08-01 00:19:36.198397 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:36.265848 INFO::Removing potential empty rows and columns
2025-08-01 00:19:36.269315 INFO::Found  0  missing values.
2025-08-01 00:19:36.279848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:36.28181 INFO::Done
2025-08-01 00:19:36.283665 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:36.289843 INFO::Starting hierarchical adjustment
2025-08-01 00:19:36.291907 INFO::Found  2  batches.
2025-08-01 00:19:36.293508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:36.295351 INFO::Using default BPPARAM
2025-08-01 00:19:36.297292 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:36.300896 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 00:19:36.34152 INFO::Done
2025-08-01 00:19:36.34329 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:36.348641 INFO::ASW Batch was 0.0620307693141076 prior to batch effect correction and is now -0.123038326231274 .
2025-08-01 00:19:36.350908 INFO::Total function execution time is  0.154719114303589  s and adjustment time is  0.0500180721282959 s ( 32.33 )
2025-08-01 00:19:36.353923 INFO::Formatting Data.
2025-08-01 00:19:36.355886 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:36.358432 INFO::Removing potential empty rows and columns
2025-08-01 00:19:36.361621 INFO::Found  0  missing values.
2025-08-01 00:19:36.370413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:36.371952 INFO::Done
2025-08-01 00:19:36.373541 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:36.378601 INFO::Starting hierarchical adjustment
2025-08-01 00:19:36.381159 INFO::Found  2  batches.
2025-08-01 00:19:36.382914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:36.384887 INFO::Using default BPPARAM
2025-08-01 00:19:36.386637 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:36.389874 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 00:19:36.437236 INFO::Done
2025-08-01 00:19:36.439097 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:36.445079 INFO::ASW Batch was 0.0620307693141076 prior to batch effect correction and is now -0.123038326231274 .
2025-08-01 00:19:36.44729 INFO::Total function execution time is  0.0934162139892578  s and adjustment time is  0.0565400123596191 s ( 60.52 )
2025-08-01 00:19:42.879166 INFO::Formatting Data.
2025-08-01 00:19:42.880481 INFO::Recognized SummarizedExperiment
2025-08-01 00:19:42.881586 INFO::Typecasting input to dataframe.
2025-08-01 00:19:42.951015 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:42.953493 INFO::Removing potential empty rows and columns
2025-08-01 00:19:42.964118 INFO::Found  0  missing values.
2025-08-01 00:19:42.987001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:42.98857 INFO::Done
2025-08-01 00:19:42.989967 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:43.000003 INFO::Starting hierarchical adjustment
2025-08-01 00:19:43.003334 INFO::Found  2  batches.
2025-08-01 00:19:43.004806 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:43.007075 INFO::Using default BPPARAM
2025-08-01 00:19:43.008408 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:43.011114 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 00:19:43.179065 INFO::Done
2025-08-01 00:19:43.18061 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:43.19045 INFO::ASW Batch was -0.00249541406161744 prior to batch effect correction and is now -0.101497326475412 .
2025-08-01 00:19:43.193243 INFO::Total function execution time is  0.313971042633057  s and adjustment time is  0.177538871765137 s ( 56.55 )
2025-08-01 00:19:43.243796 INFO::Formatting Data.
2025-08-01 00:19:43.245376 INFO::Recognized SummarizedExperiment
2025-08-01 00:19:43.246661 INFO::Typecasting input to dataframe.
2025-08-01 00:19:43.272474 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:43.275313 INFO::Removing potential empty rows and columns
2025-08-01 00:19:43.286376 INFO::Found  0  missing values.
2025-08-01 00:19:43.308588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:43.310104 INFO::Done
2025-08-01 00:19:43.311432 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:43.320516 INFO::Starting hierarchical adjustment
2025-08-01 00:19:43.322305 INFO::Found  2  batches.
2025-08-01 00:19:43.323663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:43.325251 INFO::Using default BPPARAM
2025-08-01 00:19:43.326583 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:43.329058 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 00:19:43.408094 INFO::Done
2025-08-01 00:19:43.410033 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:43.419167 INFO::ASW Batch was -0.0212526881718092 prior to batch effect correction and is now -0.0212526881718092 .
2025-08-01 00:19:43.421266 INFO::Total function execution time is  0.177433967590332  s and adjustment time is  0.0861020088195801 s ( 48.53 )
2025-08-01 00:19:43.47136 INFO::Formatting Data.
2025-08-01 00:19:43.473658 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:43.475795 INFO::Removing potential empty rows and columns
2025-08-01 00:19:43.478411 INFO::Found  0  missing values.
2025-08-01 00:19:43.486956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:43.488465 INFO::Done
2025-08-01 00:19:43.489833 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:43.495047 INFO::Starting hierarchical adjustment
2025-08-01 00:19:43.49691 INFO::Found  3  batches.
2025-08-01 00:19:43.49817 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:43.499676 INFO::Using default BPPARAM
2025-08-01 00:19:43.500975 INFO::Processing subtree level 1
2025-08-01 00:19:44.172474 INFO::Adjusting the last 1 batches sequentially
2025-08-01 00:19:44.178112 INFO::Done
2025-08-01 00:19:44.1798 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:44.218815 INFO::ASW Batch was -0.0269582233256816 prior to batch effect correction and is now -0.146834423613 .
2025-08-01 00:19:44.225678 INFO::Total function execution time is  0.752819061279297  s and adjustment time is  0.681495904922485 s ( 90.53 )
2025-08-01 00:19:44.381064 INFO::Skipping initial DF formatting
2025-08-01 00:19:44.3826 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:44.392091 INFO::Starting hierarchical adjustment
2025-08-01 00:19:44.393973 INFO::Found  5  batches.
2025-08-01 00:19:44.395326 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:44.39685 INFO::Using default BPPARAM
2025-08-01 00:19:44.398182 INFO::Processing subtree level 1
2025-08-01 00:19:44.853137 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:44.862383 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 00:19:44.935764 INFO::Done
2025-08-01 00:19:44.937483 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:44.950144 INFO::ASW Batch was 0.578477045903699 prior to batch effect correction and is now 0.578477045903699 .
2025-08-01 00:19:44.951871 INFO::ASW Label was 0.414622197133578 prior to batch effect correction and is now 0.414622197133578 .
2025-08-01 00:19:44.954392 INFO::Total function execution time is  0.573310852050781  s and adjustment time is  0.542105197906494 s ( 94.56 )
2025-08-01 00:19:45.011383 INFO::Formatting Data.
2025-08-01 00:19:45.013249 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:45.015556 INFO::Removing potential empty rows and columns
2025-08-01 00:19:45.01838 INFO::Found  0  missing values.
2025-08-01 00:19:45.030656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:45.03232 INFO::Done
2025-08-01 00:19:45.033747 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:45.041429 INFO::Starting hierarchical adjustment
2025-08-01 00:19:45.043614 INFO::Found  5  batches.
2025-08-01 00:19:45.045159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:45.046904 INFO::Using default BPPARAM
2025-08-01 00:19:45.048927 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 00:19:45.384415 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:45.396263 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 00:19:45.452818 INFO::Done
2025-08-01 00:19:45.454382 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:45.462314 INFO::ASW Batch was 0.309870424701714 prior to batch effect correction and is now -0.0301342540254979 .
2025-08-01 00:19:45.464119 INFO::ASW Label was 0.429726037745961 prior to batch effect correction and is now 0.817706429970574 .
2025-08-01 00:19:45.466982 INFO::Total function execution time is  0.455615997314453  s and adjustment time is  0.409702062606812 s ( 89.92 )
2025-08-01 00:19:45.469324 INFO::Formatting Data.
2025-08-01 00:19:45.471222 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:45.473864 INFO::Removing potential empty rows and columns
2025-08-01 00:19:45.476855 INFO::Found  0  missing values.
2025-08-01 00:19:45.48943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:45.49143 INFO::Done
2025-08-01 00:19:45.49318 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:45.500773 INFO::Starting hierarchical adjustment
2025-08-01 00:19:45.502864 INFO::Found  5  batches.
2025-08-01 00:19:45.504377 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:45.505935 INFO::Using default BPPARAM
2025-08-01 00:19:45.507388 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 00:19:45.837002 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:45.852748 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 00:19:45.91229 INFO::Done
2025-08-01 00:19:45.914343 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:45.922342 INFO::ASW Batch was 0.309870424701714 prior to batch effect correction and is now -0.0301342540254979 .
2025-08-01 00:19:45.923847 INFO::ASW Label was 0.429726037745961 prior to batch effect correction and is now 0.817706429970574 .
2025-08-01 00:19:45.9258 INFO::Total function execution time is  0.456547021865845  s and adjustment time is  0.409872055053711 s ( 89.78 )
2025-08-01 00:19:45.962767 INFO::Formatting Data.
2025-08-01 00:19:45.964774 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:45.967067 INFO::Removing potential empty rows and columns
2025-08-01 00:19:45.969482 INFO::Found  0  missing values.
2025-08-01 00:19:45.981149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:45.98321 INFO::Done
2025-08-01 00:19:45.985033 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:45.992274 INFO::Starting hierarchical adjustment
2025-08-01 00:19:45.994349 INFO::Found  5  batches.
2025-08-01 00:19:45.996716 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:45.998585 INFO::Using default BPPARAM
2025-08-01 00:19:46.000179 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 00:19:46.327707 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:46.339917 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 00:19:46.391654 INFO::Done
2025-08-01 00:19:46.39318 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:46.400909 INFO::ASW Batch was 0.29695104773976 prior to batch effect correction and is now -0.0686673356688345 .
2025-08-01 00:19:46.402607 INFO::ASW Label was 0.403636124240137 prior to batch effect correction and is now 0.857039770679403 .
2025-08-01 00:19:46.404706 INFO::Total function execution time is  0.442166090011597  s and adjustment time is  0.397835969924927 s ( 89.97 )
2025-08-01 00:19:46.407948 INFO::Formatting Data.
2025-08-01 00:19:46.410535 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:46.412916 INFO::Removing potential empty rows and columns
2025-08-01 00:19:46.415518 INFO::Found  0  missing values.
2025-08-01 00:19:46.426975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:46.428542 INFO::Done
2025-08-01 00:19:46.429901 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:46.437148 INFO::Starting hierarchical adjustment
2025-08-01 00:19:46.439148 INFO::Found  5  batches.
2025-08-01 00:19:46.440543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:46.442189 INFO::Using default BPPARAM
2025-08-01 00:19:46.445954 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 00:19:46.75599 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:46.76893 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 00:19:46.82235 INFO::Done
2025-08-01 00:19:46.823981 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:46.831728 INFO::ASW Batch was 0.29695104773976 prior to batch effect correction and is now -0.0686673356688345 .
2025-08-01 00:19:46.833323 INFO::ASW Label was 0.403636124240137 prior to batch effect correction and is now 0.857039770679403 .
2025-08-01 00:19:46.835552 INFO::Total function execution time is  0.427491903305054  s and adjustment time is  0.383570194244385 s ( 89.73 )
2025-08-01 00:19:46.877861 INFO::Formatting Data.
2025-08-01 00:19:46.879816 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:46.882156 INFO::Removing potential empty rows and columns
2025-08-01 00:19:46.885706 INFO::Found  0  missing values.
2025-08-01 00:19:46.894488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:46.89607 INFO::Done
2025-08-01 00:19:46.89743 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:46.904657 INFO::Starting hierarchical adjustment
2025-08-01 00:19:46.906909 INFO::Found  2  batches.
2025-08-01 00:19:46.908503 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:46.910262 INFO::Using default BPPARAM
2025-08-01 00:19:46.911658 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:46.914107 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 00:19:46.956427 INFO::Done
2025-08-01 00:19:46.958022 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:46.966659 INFO::ASW Batch was 0.680832904084125 prior to batch effect correction and is now -0.02517859733081 .
2025-08-01 00:19:46.968519 INFO::ASW Label was 0.391518585388852 prior to batch effect correction and is now 0.924859217653391 .
2025-08-01 00:19:46.971962 INFO::Total function execution time is  0.0941910743713379  s and adjustment time is  0.0500919818878174 s ( 53.18 )
2025-08-01 00:19:46.974028 INFO::Formatting Data.
2025-08-01 00:19:46.975658 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:46.978206 INFO::Removing potential empty rows and columns
2025-08-01 00:19:46.981035 INFO::Found  0  missing values.
2025-08-01 00:19:46.98873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:46.993322 INFO::Done
2025-08-01 00:19:46.99504 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:47.002507 INFO::Starting hierarchical adjustment
2025-08-01 00:19:47.004621 INFO::Found  2  batches.
2025-08-01 00:19:47.006095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:47.007739 INFO::Using default BPPARAM
2025-08-01 00:19:47.00917 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:47.011591 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-01 00:19:47.054532 INFO::Done
2025-08-01 00:19:47.056525 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:47.063943 INFO::ASW Batch was 0.680832904084125 prior to batch effect correction and is now -0.02517859733081 .
2025-08-01 00:19:47.065482 INFO::ASW Label was 0.391518585388852 prior to batch effect correction and is now 0.924859217653391 .
2025-08-01 00:19:47.069528 INFO::Total function execution time is  0.0954790115356445  s and adjustment time is  0.0502979755401611 s ( 52.68 )
2025-08-01 00:19:47.103432 INFO::Formatting Data.
2025-08-01 00:19:47.105049 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:47.107149 INFO::Removing potential empty rows and columns
2025-08-01 00:19:47.109438 INFO::Found  0  missing values.
2025-08-01 00:19:47.115247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:47.11761 INFO::Done
2025-08-01 00:19:47.118973 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:47.124876 INFO::Starting hierarchical adjustment
2025-08-01 00:19:47.12686 INFO::Found  2  batches.
2025-08-01 00:19:47.128293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:47.129932 INFO::Using default BPPARAM
2025-08-01 00:19:47.131397 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:47.134508 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 00:19:47.218722 INFO::Done
2025-08-01 00:19:47.220234 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:47.224737 INFO::ASW Batch was 0.140261830604384 prior to batch effect correction and is now -0.170429093574004 .
2025-08-01 00:19:47.226822 INFO::Total function execution time is  0.123485088348389  s and adjustment time is  0.0922310352325439 s ( 74.69 )
2025-08-01 00:19:47.262565 INFO::Formatting Data.
2025-08-01 00:19:47.264275 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:47.266367 INFO::Removing potential empty rows and columns
2025-08-01 00:19:47.268935 INFO::Found  0  missing values.
2025-08-01 00:19:47.271663 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 00:19:47.284661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:47.286384 INFO::Done
2025-08-01 00:19:47.287736 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:47.294776 INFO::Starting hierarchical adjustment
2025-08-01 00:19:47.296645 INFO::Found  2  batches.
2025-08-01 00:19:47.297994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:47.299625 INFO::Using default BPPARAM
2025-08-01 00:19:47.300979 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:47.303382 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 00:19:47.348532 INFO::Done
2025-08-01 00:19:47.350703 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:47.357797 INFO::ASW Batch was 0.582909359226468 prior to batch effect correction and is now 0.0857280511131234 .
2025-08-01 00:19:47.359356 INFO::ASW Label was 0.546744102851104 prior to batch effect correction and is now 0.878222386194266 .
2025-08-01 00:19:47.361245 INFO::Total function execution time is  0.0988011360168457  s and adjustment time is  0.0522449016571045 s ( 52.88 )
2025-08-01 00:19:47.363261 INFO::Formatting Data.
2025-08-01 00:19:47.364911 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:47.367206 INFO::Removing potential empty rows and columns
2025-08-01 00:19:47.369774 INFO::Found  0  missing values.
2025-08-01 00:19:47.372055 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 00:19:47.384082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:47.385496 INFO::Done
2025-08-01 00:19:47.386752 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:47.393445 INFO::Starting hierarchical adjustment
2025-08-01 00:19:47.395351 INFO::Found  2  batches.
2025-08-01 00:19:47.396702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:47.39821 INFO::Using default BPPARAM
2025-08-01 00:19:47.399529 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:47.401858 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 00:19:47.44748 INFO::Done
2025-08-01 00:19:47.448996 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:47.455931 INFO::ASW Batch was 0.582909359226468 prior to batch effect correction and is now 0.0857280511131234 .
2025-08-01 00:19:47.457544 INFO::ASW Label was 0.546744102851104 prior to batch effect correction and is now 0.878222386194266 .
2025-08-01 00:19:47.459523 INFO::Total function execution time is  0.0963149070739746  s and adjustment time is  0.0524852275848389 s ( 54.49 )
2025-08-01 00:19:48.042969 INFO::Formatting Data.
2025-08-01 00:19:48.044767 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:48.047043 INFO::Removing potential empty rows and columns
2025-08-01 00:19:48.04989 INFO::Found  0  missing values.
2025-08-01 00:19:48.058006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:48.059614 INFO::Done
2025-08-01 00:19:48.061015 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:48.065852 INFO::Starting hierarchical adjustment
2025-08-01 00:19:48.067782 INFO::Found  3  batches.
2025-08-01 00:19:48.070564 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:48.072206 INFO::Using default BPPARAM
2025-08-01 00:19:48.073543 INFO::Processing subtree level 1
2025-08-01 00:19:48.310259 INFO::Adjusting the last 1 batches sequentially
2025-08-01 00:19:48.32095 INFO::Done
2025-08-01 00:19:48.324424 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:48.334757 INFO::ASW Batch was -0.0242515997669701 prior to batch effect correction and is now -0.0242515997669701 .
2025-08-01 00:19:48.338793 INFO::Total function execution time is  0.295831918716431  s and adjustment time is  0.253515005111694 s ( 85.7 )
2025-08-01 00:19:48.343659 INFO::Formatting Data.
2025-08-01 00:19:48.345283 INFO::Typecasting input to dataframe.
2025-08-01 00:19:48.347575 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:48.351048 INFO::Removing potential empty rows and columns
2025-08-01 00:19:48.353847 INFO::Found  0  missing values.
2025-08-01 00:19:48.361667 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:48.363845 INFO::Done
2025-08-01 00:19:48.365223 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:48.369866 INFO::Starting hierarchical adjustment
2025-08-01 00:19:48.37167 INFO::Found  3  batches.
2025-08-01 00:19:48.373075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:48.375182 INFO::Using default BPPARAM
2025-08-01 00:19:48.37647 INFO::Processing subtree level 1
2025-08-01 00:19:48.615893 INFO::Adjusting the last 1 batches sequentially
2025-08-01 00:19:48.62693 INFO::Done
2025-08-01 00:19:48.630033 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:48.641419 INFO::ASW Batch was -0.0242515997669701 prior to batch effect correction and is now -0.0242515997669701 .
2025-08-01 00:19:48.64467 INFO::Total function execution time is  0.300991058349609  s and adjustment time is  0.25554895401001 s ( 84.9 )
2025-08-01 00:19:48.686417 INFO::Formatting Data.
2025-08-01 00:19:48.688309 INFO::Typecasting input to dataframe.
2025-08-01 00:19:48.68991 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:48.691398 INFO::Removing potential empty rows and columns
2025-08-01 00:19:48.694904 INFO::Found  0  missing values.
2025-08-01 00:19:48.701409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:48.703144 INFO::Done
2025-08-01 00:19:48.705578 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:48.710227 INFO::Starting hierarchical adjustment
2025-08-01 00:19:48.712088 INFO::Found  3  batches.
2025-08-01 00:19:48.713473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:48.715012 INFO::Using default BPPARAM
2025-08-01 00:19:48.717983 INFO::Processing subtree level 1
2025-08-01 00:19:48.961492 INFO::Adjusting the last 1 batches sequentially
2025-08-01 00:19:48.971066 INFO::Done
2025-08-01 00:19:48.972637 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:48.983857 INFO::ASW Batch was -0.0409201037871868 prior to batch effect correction and is now -0.0409201037871868 .
2025-08-01 00:19:48.987184 INFO::Total function execution time is  0.30073618888855  s and adjustment time is  0.25927996635437 s ( 86.22 )
2025-08-01 00:19:49.386161 INFO::Formatting Data.
2025-08-01 00:19:49.387907 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:49.390653 INFO::Removing potential empty rows and columns
2025-08-01 00:19:49.398626 INFO::Found  1000  missing values.
2025-08-01 00:19:49.461254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:49.462986 INFO::Done
2025-08-01 00:19:49.465066 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:49.478704 INFO::Starting hierarchical adjustment
2025-08-01 00:19:49.481605 INFO::Found  10  batches.
2025-08-01 00:19:49.48326 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:49.485032 INFO::Using default BPPARAM
2025-08-01 00:19:49.487805 INFO::Processing subtree level 1
2025-08-01 00:19:49.837536 INFO::Processing subtree level 2
2025-08-01 00:19:50.265445 INFO::Adjusting the last 1 batches sequentially
2025-08-01 00:19:50.277664 INFO::Done
2025-08-01 00:19:50.281213 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:50.300268 INFO::ASW Batch was 0.4886553313173 prior to batch effect correction and is now 0.4886553313173 .
2025-08-01 00:19:50.302922 INFO::ASW Label was 0.32800939383381 prior to batch effect correction and is now 0.32800939383381 .
2025-08-01 00:19:50.306466 INFO::Total function execution time is  0.919924020767212  s and adjustment time is  0.796661853790283 s ( 86.6 )
2025-08-01 00:19:50.310376 INFO::Formatting Data.
2025-08-01 00:19:50.312034 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:50.315806 INFO::Removing potential empty rows and columns
2025-08-01 00:19:50.324293 INFO::Found  1000  missing values.
2025-08-01 00:19:50.389964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:50.391586 INFO::Done
2025-08-01 00:19:50.393988 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:50.407587 INFO::Starting hierarchical adjustment
2025-08-01 00:19:50.409643 INFO::Found  10  batches.
2025-08-01 00:19:51.851453 INFO::Set up parallel execution backend with 2 workers
2025-08-01 00:19:51.852804 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-01 00:19:53.765728 INFO::Adjusting the last 2 batches sequentially
2025-08-01 00:19:53.768635 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-01 00:19:53.819578 INFO::Done
2025-08-01 00:19:53.821682 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:53.833134 INFO::ASW Batch was 0.4886553313173 prior to batch effect correction and is now 0.4886553313173 .
2025-08-01 00:19:53.834556 INFO::ASW Label was 0.32800939383381 prior to batch effect correction and is now 0.32800939383381 .
2025-08-01 00:19:53.836299 INFO::Total function execution time is  3.5261378288269  s and adjustment time is  3.41035795211792 s ( 96.72 )
2025-08-01 00:19:54.25736 INFO::Formatting Data.
2025-08-01 00:19:54.259403 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:54.26192 INFO::Removing potential empty rows and columns
2025-08-01 00:19:54.265909 INFO::Found  0  missing values.
2025-08-01 00:19:54.276989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:54.278696 INFO::Done
2025-08-01 00:19:54.280137 INFO::Acquiring quality metrics before batch effect correction.
2025-08-01 00:19:54.287483 INFO::Starting hierarchical adjustment
2025-08-01 00:19:54.28991 INFO::Found  3  batches.
2025-08-01 00:19:54.291514 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-01 00:19:54.294532 INFO::Using default BPPARAM
2025-08-01 00:19:54.296211 INFO::Processing subtree level 1
2025-08-01 00:19:54.612552 INFO::Adjusting the last 1 batches sequentially
2025-08-01 00:19:54.622529 INFO::Done
2025-08-01 00:19:54.625908 INFO::Acquiring quality metrics after batch effect correction.
2025-08-01 00:19:54.642561 INFO::ASW Batch was 0.179179470441154 prior to batch effect correction and is now -0.141128623090846 .
2025-08-01 00:19:54.644877 INFO::ASW Label was -0.173415952791633 prior to batch effect correction and is now -0.0856941180087421 .
2025-08-01 00:19:54.64871 INFO::Total function execution time is  0.390669107437134  s and adjustment time is  0.333040952682495 s ( 85.25 )
2025-08-01 00:19:55.007163 INFO::Formatting Data.
2025-08-01 00:19:55.009047 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.011393 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.014276 INFO::Found  2  missing values.
2025-08-01 00:19:55.022659 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.024208 INFO::Done
2025-08-01 00:19:55.112814 INFO::Found NA in Reference column
2025-08-01 00:19:55.142807 INFO::Require at least two references per batch.
2025-08-01 00:19:55.205867 INFO::Formatting Data.
2025-08-01 00:19:55.207468 INFO::Recognized SummarizedExperiment
2025-08-01 00:19:55.208839 INFO::Typecasting input to dataframe.
2025-08-01 00:19:55.238529 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.241353 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.253814 INFO::Found  0  missing values.
2025-08-01 00:19:55.28015 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.281745 INFO::Done
2025-08-01 00:19:55.325756 INFO::Formatting Data.
2025-08-01 00:19:55.327529 INFO::Recognized SummarizedExperiment
2025-08-01 00:19:55.32908 INFO::Typecasting input to dataframe.
2025-08-01 00:19:55.377914 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.380609 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.392486 INFO::Found  0  missing values.
2025-08-01 00:19:55.432537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.43443 INFO::Done
2025-08-01 00:19:55.481646 INFO::Formatting Data.
2025-08-01 00:19:55.483214 INFO::Recognized SummarizedExperiment
2025-08-01 00:19:55.484518 INFO::Typecasting input to dataframe.
2025-08-01 00:19:55.533905 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.536509 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.539582 INFO::Found  0  missing values.
2025-08-01 00:19:55.541898 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 00:19:55.55511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.556552 INFO::Done
2025-08-01 00:19:55.585089 INFO::Formatting Data.
2025-08-01 00:19:55.586788 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.588933 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.592294 INFO::Found  0  missing values.
2025-08-01 00:19:55.6016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.603323 INFO::Done
2025-08-01 00:19:55.637631 INFO::Formatting Data.
2025-08-01 00:19:55.639384 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.641433 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.644189 INFO::Found  0  missing values.
2025-08-01 00:19:55.652883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.654307 INFO::Done
2025-08-01 00:19:55.739448 INFO::Formatting Data.
2025-08-01 00:19:55.741464 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.744652 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.748343 INFO::Found  1  missing values.
2025-08-01 00:19:55.75701 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.758641 INFO::Done
2025-08-01 00:19:55.814716 INFO::Formatting Data.
2025-08-01 00:19:55.816775 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.819452 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.822468 INFO::Found  2  missing values.
2025-08-01 00:19:55.825536 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 00:19:55.832883 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.834518 INFO::Done
2025-08-01 00:19:55.862826 INFO::Formatting Data.
2025-08-01 00:19:55.864629 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.866833 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.869221 INFO::Found  2  missing values.
2025-08-01 00:19:55.873556 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.875149 INFO::Done
2025-08-01 00:19:55.907622 INFO::Formatting Data.
2025-08-01 00:19:55.909479 INFO::Typecasting input to dataframe.
2025-08-01 00:19:55.911566 INFO::Replacing NaNs with NAs.
2025-08-01 00:19:55.913793 INFO::Removing potential empty rows and columns
2025-08-01 00:19:55.916901 INFO::Found  0  missing values.
2025-08-01 00:19:55.925244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-01 00:19:55.927679 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 35.512   6.897  44.368 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT44.749 2.62134.621
compute_asw0.0560.0020.059
count_existing0.0270.0030.031
generate_data_covariables0.0260.0020.028
generate_dataset0.0250.0020.028