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This page was generated on 2025-12-15 12:06 -0500 (Mon, 15 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4882
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4607
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4671
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 166/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.6.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-12-11 13:45 -0500 (Thu, 11 Dec 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_22
git_last_commit: 49dbe48
git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on merida1

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

raw results


Summary

Package: BERT
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2025-12-12 01:09:07 -0500 (Fri, 12 Dec 2025)
EndedAt: 2025-12-12 01:11:45 -0500 (Fri, 12 Dec 2025)
EllapsedTime: 158.1 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 43.556  2.661  39.814
* 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 ‘1.6.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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")
2025-12-12 01:11:06.231193 INFO::Formatting Data.
2025-12-12 01:11:06.239941 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:06.276978 INFO::Removing potential empty rows and columns
2025-12-12 01:11:07.081209 INFO::Found  0  missing values.
2025-12-12 01:11:07.092822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:07.094303 INFO::Done
2025-12-12 01:11:07.095593 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:07.132174 INFO::Starting hierarchical adjustment
2025-12-12 01:11:07.134149 INFO::Found  3  batches.
2025-12-12 01:11:07.135627 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:07.137999 INFO::Using default BPPARAM
2025-12-12 01:11:07.139381 INFO::Processing subtree level 1
2025-12-12 01:11:07.419215 INFO::Adjusting the last 1 batches sequentially
2025-12-12 01:11:07.426721 INFO::Done
2025-12-12 01:11:07.428687 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:07.43762 INFO::ASW Batch was -0.0630401109536236 prior to batch effect correction and is now -0.0630401109536236 .
2025-12-12 01:11:07.440231 INFO::Total function execution time is  1.21077609062195  s and adjustment time is  0.292980909347534 s ( 24.2 )
2025-12-12 01:11:07.47941 INFO::Formatting Data.
2025-12-12 01:11:07.481329 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:07.483855 INFO::Removing potential empty rows and columns
2025-12-12 01:11:07.486976 INFO::Found  0  missing values.
2025-12-12 01:11:07.49007 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.
2025-12-12 01:11:07.538591 INFO::Formatting Data.
2025-12-12 01:11:07.54019 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:07.542419 INFO::Removing potential empty rows and columns
2025-12-12 01:11:07.545651 INFO::Found  0  missing values.
2025-12-12 01:11:07.548246 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.
2025-12-12 01:11:07.620398 INFO::Formatting Data.
2025-12-12 01:11:07.625541 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:07.629533 INFO::Removing potential empty rows and columns
2025-12-12 01:11:07.632408 INFO::Found  0  missing values.
2025-12-12 01:11:07.634895 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.
2025-12-12 01:11:07.663432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:07.665046 INFO::Done
2025-12-12 01:11:07.666502 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:07.67169 INFO::Starting hierarchical adjustment
2025-12-12 01:11:07.674088 INFO::Found  2  batches.
2025-12-12 01:11:07.675698 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:07.677385 INFO::Using default BPPARAM
2025-12-12 01:11:07.678782 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:07.681219 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 01:11:07.793007 INFO::Done
2025-12-12 01:11:07.794465 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:07.799663 INFO::ASW Batch was 0.0147701181307456 prior to batch effect correction and is now -0.113484175191015 .
2025-12-12 01:11:07.801856 INFO::Total function execution time is  0.181491136550903  s and adjustment time is  0.119351148605347 s ( 65.76 )
2025-12-12 01:11:07.811516 INFO::Formatting Data.
2025-12-12 01:11:07.813207 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:07.853584 INFO::Formatting Data.
2025-12-12 01:11:07.855016 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:07.856904 INFO::Removing potential empty rows and columns
2025-12-12 01:11:07.859203 INFO::Found  0  missing values.
2025-12-12 01:11:07.874759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:07.882413 INFO::Done
2025-12-12 01:11:07.883777 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:07.967534 INFO::Starting hierarchical adjustment
2025-12-12 01:11:07.978146 INFO::Found  2  batches.
2025-12-12 01:11:07.984143 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:07.987131 INFO::Using default BPPARAM
2025-12-12 01:11:07.988497 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:07.992949 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 01:11:08.057321 INFO::Done
2025-12-12 01:11:08.058843 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:08.085143 INFO::ASW Batch was 0.00400146301737294 prior to batch effect correction and is now -0.117476538895705 .
2025-12-12 01:11:08.087177 INFO::Total function execution time is  0.23358416557312  s and adjustment time is  0.0882508754730225 s ( 37.78 )
2025-12-12 01:11:08.091942 INFO::Formatting Data.
2025-12-12 01:11:08.093926 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:08.109627 INFO::Removing potential empty rows and columns
2025-12-12 01:11:08.11268 INFO::Found  0  missing values.
2025-12-12 01:11:08.124518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:08.125919 INFO::Done
2025-12-12 01:11:08.127919 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:08.150348 INFO::Starting hierarchical adjustment
2025-12-12 01:11:08.154418 INFO::Found  2  batches.
2025-12-12 01:11:08.155712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:08.157217 INFO::Using default BPPARAM
2025-12-12 01:11:08.159372 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:08.162046 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 01:11:08.223984 INFO::Done
2025-12-12 01:11:08.228165 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:08.233823 INFO::ASW Batch was 0.00400146301737294 prior to batch effect correction and is now -0.117476538895705 .
2025-12-12 01:11:08.237904 INFO::Total function execution time is  0.146621942520142  s and adjustment time is  0.0700027942657471 s ( 47.74 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-12 01:11:16.446531 INFO::Formatting Data.
2025-12-12 01:11:16.447825 INFO::Recognized SummarizedExperiment
2025-12-12 01:11:16.449223 INFO::Typecasting input to dataframe.
2025-12-12 01:11:16.521282 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:16.524042 INFO::Removing potential empty rows and columns
2025-12-12 01:11:16.538011 INFO::Found  0  missing values.
2025-12-12 01:11:16.565061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:16.566792 INFO::Done
2025-12-12 01:11:16.568131 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:16.583767 INFO::Starting hierarchical adjustment
2025-12-12 01:11:16.585748 INFO::Found  2  batches.
2025-12-12 01:11:16.587155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:16.592129 INFO::Using default BPPARAM
2025-12-12 01:11:16.59359 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:16.596069 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 01:11:16.811631 INFO::Done
2025-12-12 01:11:16.812996 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:16.826068 INFO::ASW Batch was 0.00545593154253093 prior to batch effect correction and is now -0.0902984377970312 .
2025-12-12 01:11:16.828141 INFO::Total function execution time is  0.382301092147827  s and adjustment time is  0.226295948028564 s ( 59.19 )
Warning: stack imbalance in '{', 73 then 75
2025-12-12 01:11:16.879593 INFO::Formatting Data.
2025-12-12 01:11:16.881138 INFO::Recognized SummarizedExperiment
2025-12-12 01:11:16.882404 INFO::Typecasting input to dataframe.
2025-12-12 01:11:16.908018 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:16.910817 INFO::Removing potential empty rows and columns
2025-12-12 01:11:16.922719 INFO::Found  0  missing values.
2025-12-12 01:11:16.944659 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:16.946086 INFO::Done
2025-12-12 01:11:16.947411 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:16.957183 INFO::Starting hierarchical adjustment
2025-12-12 01:11:16.95931 INFO::Found  2  batches.
2025-12-12 01:11:16.960761 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:16.964794 INFO::Using default BPPARAM
2025-12-12 01:11:16.966238 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:16.96873 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 01:11:17.04688 INFO::Done
2025-12-12 01:11:17.048401 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:17.058683 INFO::ASW Batch was 0.0132331965872156 prior to batch effect correction and is now 0.0132331965872156 .
2025-12-12 01:11:17.060726 INFO::Total function execution time is  0.181056976318359  s and adjustment time is  0.0879600048065186 s ( 48.58 )
2025-12-12 01:11:17.111658 INFO::Formatting Data.
2025-12-12 01:11:17.113296 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:17.115366 INFO::Removing potential empty rows and columns
2025-12-12 01:11:17.118049 INFO::Found  0  missing values.
2025-12-12 01:11:17.128458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:17.129992 INFO::Done
2025-12-12 01:11:17.13289 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:17.138727 INFO::Starting hierarchical adjustment
2025-12-12 01:11:17.140525 INFO::Found  3  batches.
2025-12-12 01:11:17.141887 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:17.143516 INFO::Using default BPPARAM
2025-12-12 01:11:17.144937 INFO::Processing subtree level 1
2025-12-12 01:11:17.509892 INFO::Adjusting the last 1 batches sequentially
2025-12-12 01:11:17.522811 INFO::Done
2025-12-12 01:11:17.525201 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:17.538083 INFO::ASW Batch was -0.0644260313765657 prior to batch effect correction and is now -0.155799139270102 .
2025-12-12 01:11:17.541154 INFO::Total function execution time is  0.429461002349854  s and adjustment time is  0.382609128952026 s ( 89.09 )
2025-12-12 01:11:17.586001 INFO::Skipping initial DF formatting
2025-12-12 01:11:17.587653 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:17.59913 INFO::Starting hierarchical adjustment
2025-12-12 01:11:17.601318 INFO::Found  5  batches.
2025-12-12 01:11:17.602876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:17.60543 INFO::Using default BPPARAM
2025-12-12 01:11:17.607506 INFO::Processing subtree level 1
2025-12-12 01:11:18.296047 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:18.309658 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 01:11:18.405239 INFO::Done
2025-12-12 01:11:18.407171 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:18.423282 INFO::ASW Batch was 0.538650166540818 prior to batch effect correction and is now 0.538650166540818 .
2025-12-12 01:11:18.424856 INFO::ASW Label was 0.383357588112594 prior to batch effect correction and is now 0.383357588112594 .
2025-12-12 01:11:18.427424 INFO::Total function execution time is  0.841470956802368  s and adjustment time is  0.804349184036255 s ( 95.59 )
2025-12-12 01:11:18.572557 INFO::Formatting Data.
2025-12-12 01:11:18.574334 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:18.576709 INFO::Removing potential empty rows and columns
2025-12-12 01:11:18.579413 INFO::Found  0  missing values.
2025-12-12 01:11:18.590249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:18.591597 INFO::Done
2025-12-12 01:11:18.59286 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:18.600824 INFO::Starting hierarchical adjustment
2025-12-12 01:11:18.603412 INFO::Found  5  batches.
2025-12-12 01:11:18.605537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:18.607655 INFO::Using default BPPARAM
2025-12-12 01:11:18.609052 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.

2025-12-12 01:11:19.097432 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:19.117772 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 01:11:19.18185 INFO::Done
2025-12-12 01:11:19.183675 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:19.192199 INFO::ASW Batch was 0.319289915398573 prior to batch effect correction and is now -0.0272765949981949 .
2025-12-12 01:11:19.193901 INFO::ASW Label was 0.386275302166159 prior to batch effect correction and is now 0.818706123705665 .
2025-12-12 01:11:19.195997 INFO::Total function execution time is  0.62344217300415  s and adjustment time is  0.579032897949219 s ( 92.88 )
2025-12-12 01:11:19.198348 INFO::Formatting Data.
2025-12-12 01:11:19.200599 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:19.203103 INFO::Removing potential empty rows and columns
2025-12-12 01:11:19.205899 INFO::Found  0  missing values.
2025-12-12 01:11:19.218464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:19.220341 INFO::Done
2025-12-12 01:11:19.222152 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:19.236153 INFO::Starting hierarchical adjustment
2025-12-12 01:11:19.238602 INFO::Found  5  batches.
2025-12-12 01:11:19.240728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:19.242616 INFO::Using default BPPARAM
2025-12-12 01:11:19.30405 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.

2025-12-12 01:11:19.732589 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:19.745901 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 01:11:19.808782 INFO::Done
2025-12-12 01:11:19.810404 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:19.8197 INFO::ASW Batch was 0.319289915398573 prior to batch effect correction and is now -0.0272765949981949 .
2025-12-12 01:11:19.821374 INFO::ASW Label was 0.386275302166159 prior to batch effect correction and is now 0.818706123705665 .
2025-12-12 01:11:19.823873 INFO::Total function execution time is  0.62552809715271  s and adjustment time is  0.570852041244507 s ( 91.26 )
2025-12-12 01:11:19.869726 INFO::Formatting Data.
2025-12-12 01:11:19.872132 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:19.874994 INFO::Removing potential empty rows and columns
2025-12-12 01:11:19.877857 INFO::Found  0  missing values.
2025-12-12 01:11:19.899363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:19.901086 INFO::Done
2025-12-12 01:11:19.902464 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:19.911129 INFO::Starting hierarchical adjustment
2025-12-12 01:11:19.918047 INFO::Found  5  batches.
2025-12-12 01:11:19.919836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:19.921636 INFO::Using default BPPARAM
2025-12-12 01:11:19.930093 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.

2025-12-12 01:11:20.269237 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:20.282695 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 01:11:20.341431 INFO::Done
2025-12-12 01:11:20.343248 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:20.351616 INFO::ASW Batch was 0.421072048477624 prior to batch effect correction and is now -0.0682351758519724 .
2025-12-12 01:11:20.353145 INFO::ASW Label was 0.317680044283728 prior to batch effect correction and is now 0.79880972363163 .
2025-12-12 01:11:20.355247 INFO::Total function execution time is  0.4858078956604  s and adjustment time is  0.42411208152771 s ( 87.3 )
2025-12-12 01:11:20.357586 INFO::Formatting Data.
2025-12-12 01:11:20.35944 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:20.361898 INFO::Removing potential empty rows and columns
2025-12-12 01:11:20.364763 INFO::Found  0  missing values.
2025-12-12 01:11:20.376985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:20.3786 INFO::Done
2025-12-12 01:11:20.380715 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:20.388023 INFO::Starting hierarchical adjustment
2025-12-12 01:11:20.390068 INFO::Found  5  batches.
2025-12-12 01:11:20.39152 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:20.393301 INFO::Using default BPPARAM
2025-12-12 01:11:20.395035 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.

2025-12-12 01:11:20.703542 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:20.709874 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 01:11:20.773323 INFO::Done
2025-12-12 01:11:20.775342 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:20.78805 INFO::ASW Batch was 0.421072048477624 prior to batch effect correction and is now -0.0682351758519724 .
2025-12-12 01:11:20.790845 INFO::ASW Label was 0.317680044283728 prior to batch effect correction and is now 0.79880972363163 .
2025-12-12 01:11:20.795497 INFO::Total function execution time is  0.437083005905151  s and adjustment time is  0.383613109588623 s ( 87.77 )
2025-12-12 01:11:20.844703 INFO::Formatting Data.
2025-12-12 01:11:20.84688 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:20.849845 INFO::Removing potential empty rows and columns
2025-12-12 01:11:20.85328 INFO::Found  0  missing values.
2025-12-12 01:11:20.862862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:20.865013 INFO::Done
2025-12-12 01:11:20.866828 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:20.88575 INFO::Starting hierarchical adjustment
2025-12-12 01:11:20.888863 INFO::Found  2  batches.
2025-12-12 01:11:20.891528 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:20.897958 INFO::Using default BPPARAM
2025-12-12 01:11:20.900114 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:20.903562 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 01:11:20.96569 INFO::Done
2025-12-12 01:11:20.968978 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:20.979577 INFO::ASW Batch was 0.510809466027174 prior to batch effect correction and is now -0.0244025679492124 .
2025-12-12 01:11:20.983069 INFO::ASW Label was 0.561291854483268 prior to batch effect correction and is now 0.916538812151202 .
2025-12-12 01:11:20.985539 INFO::Total function execution time is  0.140915155410767  s and adjustment time is  0.0777490139007568 s ( 55.17 )
2025-12-12 01:11:20.987796 INFO::Formatting Data.
2025-12-12 01:11:20.989736 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:20.99418 INFO::Removing potential empty rows and columns
2025-12-12 01:11:20.999675 INFO::Found  0  missing values.
2025-12-12 01:11:21.019226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:21.021387 INFO::Done
2025-12-12 01:11:21.023353 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:21.037254 INFO::Starting hierarchical adjustment
2025-12-12 01:11:21.040808 INFO::Found  2  batches.
2025-12-12 01:11:21.042636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:21.046722 INFO::Using default BPPARAM
2025-12-12 01:11:21.04861 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:21.052853 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-12 01:11:21.135554 INFO::Done
2025-12-12 01:11:21.13764 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:21.15012 INFO::ASW Batch was 0.510809466027174 prior to batch effect correction and is now -0.0244025679492124 .
2025-12-12 01:11:21.152004 INFO::ASW Label was 0.561291854483268 prior to batch effect correction and is now 0.916538812151202 .
2025-12-12 01:11:21.154677 INFO::Total function execution time is  0.166806936264038  s and adjustment time is  0.0952901840209961 s ( 57.13 )
2025-12-12 01:11:21.1978 INFO::Formatting Data.
2025-12-12 01:11:21.200028 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:21.202708 INFO::Removing potential empty rows and columns
2025-12-12 01:11:21.205457 INFO::Found  0  missing values.
2025-12-12 01:11:21.211865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:21.213616 INFO::Done
2025-12-12 01:11:21.215555 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:21.221239 INFO::Starting hierarchical adjustment
2025-12-12 01:11:21.223449 INFO::Found  2  batches.
2025-12-12 01:11:21.22573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:21.227786 INFO::Using default BPPARAM
2025-12-12 01:11:21.229505 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:21.232416 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 01:11:21.348927 INFO::Done
2025-12-12 01:11:21.350583 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:21.355599 INFO::ASW Batch was 0.00179942925983822 prior to batch effect correction and is now -0.14283146057121 .
2025-12-12 01:11:21.358228 INFO::Total function execution time is  0.160531044006348  s and adjustment time is  0.125877857208252 s ( 78.41 )
2025-12-12 01:11:21.407176 INFO::Formatting Data.
2025-12-12 01:11:21.409349 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:21.411966 INFO::Removing potential empty rows and columns
2025-12-12 01:11:21.415814 INFO::Found  0  missing values.
2025-12-12 01:11:21.41951 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.
2025-12-12 01:11:21.437272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:21.439867 INFO::Done
2025-12-12 01:11:21.441703 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:21.453159 INFO::Starting hierarchical adjustment
2025-12-12 01:11:21.455503 INFO::Found  2  batches.
2025-12-12 01:11:21.45728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:21.45912 INFO::Using default BPPARAM
2025-12-12 01:11:21.460728 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:21.463699 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 01:11:21.522263 INFO::Done
2025-12-12 01:11:21.524119 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:21.532998 INFO::ASW Batch was 0.626751533002348 prior to batch effect correction and is now -0.0370447920450326 .
2025-12-12 01:11:21.534856 INFO::ASW Label was 0.449262707193508 prior to batch effect correction and is now 0.939971674677477 .
2025-12-12 01:11:21.537201 INFO::Total function execution time is  0.131657123565674  s and adjustment time is  0.067216157913208 s ( 51.05 )
2025-12-12 01:11:21.539633 INFO::Formatting Data.
2025-12-12 01:11:21.542037 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:21.544975 INFO::Removing potential empty rows and columns
2025-12-12 01:11:21.54816 INFO::Found  0  missing values.
2025-12-12 01:11:21.551863 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.
2025-12-12 01:11:21.570156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:21.573031 INFO::Done
2025-12-12 01:11:21.574644 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:21.582977 INFO::Starting hierarchical adjustment
2025-12-12 01:11:21.585263 INFO::Found  2  batches.
2025-12-12 01:11:21.586966 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:21.588807 INFO::Using default BPPARAM
2025-12-12 01:11:21.590444 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:21.593377 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 01:11:21.650633 INFO::Done
2025-12-12 01:11:21.652933 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:21.663495 INFO::ASW Batch was 0.626751533002348 prior to batch effect correction and is now -0.0370447920450326 .
2025-12-12 01:11:21.665654 INFO::ASW Label was 0.449262707193508 prior to batch effect correction and is now 0.939971674677477 .
2025-12-12 01:11:21.668902 INFO::Total function execution time is  0.129251003265381  s and adjustment time is  0.0657899379730225 s ( 50.9 )
2025-12-12 01:11:22.377974 INFO::Formatting Data.
2025-12-12 01:11:22.379634 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:22.381672 INFO::Removing potential empty rows and columns
2025-12-12 01:11:22.384878 INFO::Found  0  missing values.
2025-12-12 01:11:22.395223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:22.402687 INFO::Done
2025-12-12 01:11:22.404375 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:22.409168 INFO::Starting hierarchical adjustment
2025-12-12 01:11:22.411069 INFO::Found  3  batches.
2025-12-12 01:11:22.4154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:22.417006 INFO::Using default BPPARAM
2025-12-12 01:11:22.418492 INFO::Processing subtree level 1
2025-12-12 01:11:22.676722 INFO::Adjusting the last 1 batches sequentially
2025-12-12 01:11:22.687339 INFO::Done
2025-12-12 01:11:22.689461 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:22.700706 INFO::ASW Batch was -0.0352085755125313 prior to batch effect correction and is now -0.0352085755125313 .
2025-12-12 01:11:22.70597 INFO::Total function execution time is  0.327876091003418  s and adjustment time is  0.276641845703125 s ( 84.37 )
2025-12-12 01:11:22.709072 INFO::Formatting Data.
2025-12-12 01:11:22.7108 INFO::Typecasting input to dataframe.
2025-12-12 01:11:22.713157 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:22.715976 INFO::Removing potential empty rows and columns
2025-12-12 01:11:22.719012 INFO::Found  0  missing values.
2025-12-12 01:11:22.72779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:22.72924 INFO::Done
2025-12-12 01:11:22.73056 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:22.735287 INFO::Starting hierarchical adjustment
2025-12-12 01:11:22.737655 INFO::Found  3  batches.
2025-12-12 01:11:22.739005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:22.740514 INFO::Using default BPPARAM
2025-12-12 01:11:22.742287 INFO::Processing subtree level 1
2025-12-12 01:11:22.977278 INFO::Adjusting the last 1 batches sequentially
2025-12-12 01:11:22.986831 INFO::Done
2025-12-12 01:11:22.988404 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:23.000067 INFO::ASW Batch was -0.0352085755125313 prior to batch effect correction and is now -0.0352085755125313 .
2025-12-12 01:11:23.003513 INFO::Total function execution time is  0.294431924819946  s and adjustment time is  0.249633073806763 s ( 84.78 )
2025-12-12 01:11:23.047249 INFO::Formatting Data.
2025-12-12 01:11:23.049922 INFO::Typecasting input to dataframe.
2025-12-12 01:11:23.052082 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:23.054307 INFO::Removing potential empty rows and columns
2025-12-12 01:11:23.058973 INFO::Found  0  missing values.
2025-12-12 01:11:23.06792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:23.069546 INFO::Done
2025-12-12 01:11:23.070924 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:23.076063 INFO::Starting hierarchical adjustment
2025-12-12 01:11:23.078488 INFO::Found  3  batches.
2025-12-12 01:11:23.079918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:23.081529 INFO::Using default BPPARAM
2025-12-12 01:11:23.082957 INFO::Processing subtree level 1
2025-12-12 01:11:23.302072 INFO::Adjusting the last 1 batches sequentially
2025-12-12 01:11:23.313367 INFO::Done
2025-12-12 01:11:23.314839 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:23.326218 INFO::ASW Batch was -0.0371785130568593 prior to batch effect correction and is now -0.0371785130568593 .
2025-12-12 01:11:23.33037 INFO::Total function execution time is  0.282869815826416  s and adjustment time is  0.235217094421387 s ( 83.15 )
2025-12-12 01:11:23.731093 INFO::Formatting Data.
2025-12-12 01:11:23.733643 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:23.736483 INFO::Removing potential empty rows and columns
2025-12-12 01:11:23.745405 INFO::Found  1000  missing values.
2025-12-12 01:11:23.817173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:23.818705 INFO::Done
2025-12-12 01:11:23.820024 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:23.832165 INFO::Starting hierarchical adjustment
2025-12-12 01:11:23.834121 INFO::Found  10  batches.
2025-12-12 01:11:23.835597 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:23.837365 INFO::Using default BPPARAM
2025-12-12 01:11:23.839714 INFO::Processing subtree level 1
2025-12-12 01:11:24.15727 INFO::Processing subtree level 2
2025-12-12 01:11:24.594729 INFO::Adjusting the last 1 batches sequentially
2025-12-12 01:11:24.606819 INFO::Done
2025-12-12 01:11:24.608803 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:24.628971 INFO::ASW Batch was 0.460274008242714 prior to batch effect correction and is now 0.460274008242714 .
2025-12-12 01:11:24.635164 INFO::ASW Label was 0.342479380392365 prior to batch effect correction and is now 0.342479380392366 .
2025-12-12 01:11:24.641373 INFO::Total function execution time is  0.910308122634888  s and adjustment time is  0.773044109344482 s ( 84.92 )
2025-12-12 01:11:24.645541 INFO::Formatting Data.
2025-12-12 01:11:24.648963 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:24.651879 INFO::Removing potential empty rows and columns
2025-12-12 01:11:24.661007 INFO::Found  1000  missing values.
2025-12-12 01:11:24.721242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:24.722815 INFO::Done
2025-12-12 01:11:24.724196 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:24.736243 INFO::Starting hierarchical adjustment
2025-12-12 01:11:24.738248 INFO::Found  10  batches.
2025-12-12 01:11:26.153969 INFO::Set up parallel execution backend with 2 workers
2025-12-12 01:11:26.155301 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-12 01:11:28.060746 INFO::Adjusting the last 2 batches sequentially
2025-12-12 01:11:28.066825 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-12 01:11:28.114602 INFO::Done
2025-12-12 01:11:28.11593 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:28.128523 INFO::ASW Batch was 0.460274008242714 prior to batch effect correction and is now 0.460274008242714 .
2025-12-12 01:11:28.129827 INFO::ASW Label was 0.342479380392365 prior to batch effect correction and is now 0.342479380392366 .
2025-12-12 01:11:28.131518 INFO::Total function execution time is  3.48614406585693  s and adjustment time is  3.37677502632141 s ( 96.86 )
2025-12-12 01:11:28.539077 INFO::Formatting Data.
2025-12-12 01:11:28.540733 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:28.54426 INFO::Removing potential empty rows and columns
2025-12-12 01:11:28.547679 INFO::Found  0  missing values.
2025-12-12 01:11:28.559514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:28.561116 INFO::Done
2025-12-12 01:11:28.562742 INFO::Acquiring quality metrics before batch effect correction.
2025-12-12 01:11:28.571187 INFO::Starting hierarchical adjustment
2025-12-12 01:11:28.573255 INFO::Found  3  batches.
2025-12-12 01:11:28.574751 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-12 01:11:28.576363 INFO::Using default BPPARAM
2025-12-12 01:11:28.577719 INFO::Processing subtree level 1
2025-12-12 01:11:28.880408 INFO::Adjusting the last 1 batches sequentially
2025-12-12 01:11:28.889714 INFO::Done
2025-12-12 01:11:28.891076 INFO::Acquiring quality metrics after batch effect correction.
2025-12-12 01:11:28.905372 INFO::ASW Batch was 0.161969308165514 prior to batch effect correction and is now -0.152955581722585 .
2025-12-12 01:11:28.906991 INFO::ASW Label was -0.191578597951015 prior to batch effect correction and is now 0.083932803408051 .
2025-12-12 01:11:28.910645 INFO::Total function execution time is  0.371104001998901  s and adjustment time is  0.316885948181152 s ( 85.39 )
2025-12-12 01:11:29.286763 INFO::Formatting Data.
2025-12-12 01:11:29.288871 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:29.291226 INFO::Removing potential empty rows and columns
2025-12-12 01:11:29.294277 INFO::Found  2  missing values.
2025-12-12 01:11:29.302575 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:29.30427 INFO::Done
2025-12-12 01:11:29.397082 INFO::Found NA in Reference column
2025-12-12 01:11:29.429394 INFO::Require at least two references per batch.
2025-12-12 01:11:29.498984 INFO::Formatting Data.
2025-12-12 01:11:29.500742 INFO::Recognized SummarizedExperiment
2025-12-12 01:11:29.502418 INFO::Typecasting input to dataframe.
2025-12-12 01:11:29.530642 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:29.533566 INFO::Removing potential empty rows and columns
2025-12-12 01:11:29.546329 INFO::Found  0  missing values.
2025-12-12 01:11:29.56996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:29.571427 INFO::Done
2025-12-12 01:11:29.619164 INFO::Formatting Data.
2025-12-12 01:11:29.620752 INFO::Recognized SummarizedExperiment
2025-12-12 01:11:29.622095 INFO::Typecasting input to dataframe.
2025-12-12 01:11:29.673642 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:29.67643 INFO::Removing potential empty rows and columns
2025-12-12 01:11:29.68848 INFO::Found  0  missing values.
2025-12-12 01:11:29.730853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:29.732394 INFO::Done
2025-12-12 01:11:29.782259 INFO::Formatting Data.
2025-12-12 01:11:29.783944 INFO::Recognized SummarizedExperiment
2025-12-12 01:11:29.785342 INFO::Typecasting input to dataframe.
2025-12-12 01:11:29.840858 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:29.843122 INFO::Removing potential empty rows and columns
2025-12-12 01:11:29.8459 INFO::Found  0  missing values.
2025-12-12 01:11:29.853615 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.
2025-12-12 01:11:29.869081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:29.870523 INFO::Done
2025-12-12 01:11:29.900358 INFO::Formatting Data.
2025-12-12 01:11:29.902136 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:29.904241 INFO::Removing potential empty rows and columns
2025-12-12 01:11:29.90674 INFO::Found  0  missing values.
2025-12-12 01:11:29.914362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:29.915847 INFO::Done
2025-12-12 01:11:29.955793 INFO::Formatting Data.
2025-12-12 01:11:29.957779 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:29.959986 INFO::Removing potential empty rows and columns
2025-12-12 01:11:29.962806 INFO::Found  0  missing values.
2025-12-12 01:11:29.97059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:29.972132 INFO::Done
2025-12-12 01:11:30.068885 INFO::Formatting Data.
2025-12-12 01:11:30.070846 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:30.07356 INFO::Removing potential empty rows and columns
2025-12-12 01:11:30.078422 INFO::Found  1  missing values.
2025-12-12 01:11:30.08644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:30.088085 INFO::Done
2025-12-12 01:11:30.149466 INFO::Formatting Data.
2025-12-12 01:11:30.151146 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:30.153556 INFO::Removing potential empty rows and columns
2025-12-12 01:11:30.158059 INFO::Found  2  missing values.
2025-12-12 01:11:30.160358 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.
2025-12-12 01:11:30.166498 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:30.168054 INFO::Done
2025-12-12 01:11:30.200498 INFO::Formatting Data.
2025-12-12 01:11:30.202909 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:30.205197 INFO::Removing potential empty rows and columns
2025-12-12 01:11:30.207742 INFO::Found  2  missing values.
2025-12-12 01:11:30.213434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:30.215045 INFO::Done
2025-12-12 01:11:30.254167 INFO::Formatting Data.
2025-12-12 01:11:30.255874 INFO::Typecasting input to dataframe.
2025-12-12 01:11:30.25789 INFO::Replacing NaNs with NAs.
2025-12-12 01:11:30.260187 INFO::Removing potential empty rows and columns
2025-12-12 01:11:30.263332 INFO::Found  0  missing values.
2025-12-12 01:11:30.27211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-12 01:11:30.273615 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 35.166   6.727  49.029

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT43.556 2.66139.814
compute_asw0.0580.0030.069
count_existing0.0280.0010.038
generate_data_covariables0.0250.0020.029
generate_dataset0.0240.0020.031