Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-08 12:05 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 162/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.5.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: devel
git_last_commit: 3fb455b
git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BERT on nebbiolo2

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

raw results


Summary

Package: BERT
Version: 1.5.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz
StartedAt: 2025-08-07 20:23:50 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 20:25:20 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 90.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 22.699  1.367  16.497
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.5.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
2025-08-07 20:24:41.783251 INFO::Formatting Data.
2025-08-07 20:24:41.784665 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:41.796349 INFO::Removing potential empty rows and columns
2025-08-07 20:24:42.047991 INFO::Found  0  missing values.
2025-08-07 20:24:42.05144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:42.052109 INFO::Done
2025-08-07 20:24:42.052658 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:42.06449 INFO::Starting hierarchical adjustment
2025-08-07 20:24:42.065374 INFO::Found  3  batches.
2025-08-07 20:24:42.065956 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:42.067148 INFO::Using default BPPARAM
2025-08-07 20:24:42.067713 INFO::Processing subtree level 1
2025-08-07 20:24:42.169896 INFO::Adjusting the last 1 batches sequentially
2025-08-07 20:24:42.171793 INFO::Done
2025-08-07 20:24:42.17247 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:42.175184 INFO::ASW Batch was -0.0329488016784291 prior to batch effect correction and is now -0.0329488016784291 .
2025-08-07 20:24:42.176349 INFO::Total function execution time is  0.39377498626709  s and adjustment time is  0.106616973876953 s ( 27.08 )
2025-08-07 20:24:42.19002 INFO::Formatting Data.
2025-08-07 20:24:42.190834 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:42.19178 INFO::Removing potential empty rows and columns
2025-08-07 20:24:42.192888 INFO::Found  0  missing values.
2025-08-07 20:24:42.19383 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.
2025-08-07 20:24:42.204741 INFO::Formatting Data.
2025-08-07 20:24:42.20544 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:42.206326 INFO::Removing potential empty rows and columns
2025-08-07 20:24:42.207395 INFO::Found  0  missing values.
2025-08-07 20:24:42.208317 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.
2025-08-07 20:24:42.22412 INFO::Formatting Data.
2025-08-07 20:24:42.224875 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:42.22576 INFO::Removing potential empty rows and columns
2025-08-07 20:24:42.226811 INFO::Found  0  missing values.
2025-08-07 20:24:42.227737 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.
2025-08-07 20:24:42.232042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:42.232594 INFO::Done
2025-08-07 20:24:42.233118 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:42.23517 INFO::Starting hierarchical adjustment
2025-08-07 20:24:42.235875 INFO::Found  2  batches.
2025-08-07 20:24:42.236415 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:42.237035 INFO::Using default BPPARAM
2025-08-07 20:24:42.237571 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:42.238498 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-07 20:24:42.261668 INFO::Done
2025-08-07 20:24:42.262455 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:42.264636 INFO::ASW Batch was -0.0389584238541837 prior to batch effect correction and is now -0.127181439195448 .
2025-08-07 20:24:42.26548 INFO::Total function execution time is  0.0414557456970215  s and adjustment time is  0.0258960723876953 s ( 62.47 )
2025-08-07 20:24:42.268395 INFO::Formatting Data.
2025-08-07 20:24:42.269041 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:42.278115 INFO::Formatting Data.
2025-08-07 20:24:42.278791 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:42.279697 INFO::Removing potential empty rows and columns
2025-08-07 20:24:42.280753 INFO::Found  0  missing values.
2025-08-07 20:24:42.283664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:42.284211 INFO::Done
2025-08-07 20:24:42.284731 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:42.286929 INFO::Starting hierarchical adjustment
2025-08-07 20:24:42.287652 INFO::Found  2  batches.
2025-08-07 20:24:42.288205 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:42.288825 INFO::Using default BPPARAM
2025-08-07 20:24:42.2894 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:42.290352 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-07 20:24:42.333645 INFO::Done
2025-08-07 20:24:42.334379 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:42.336455 INFO::ASW Batch was -0.00996730902351056 prior to batch effect correction and is now -0.12963647012623 .
2025-08-07 20:24:42.337286 INFO::Total function execution time is  0.0592076778411865  s and adjustment time is  0.0460915565490723 s ( 77.85 )
2025-08-07 20:24:42.338355 INFO::Formatting Data.
2025-08-07 20:24:42.338955 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:42.339831 INFO::Removing potential empty rows and columns
2025-08-07 20:24:42.34087 INFO::Found  0  missing values.
2025-08-07 20:24:42.343649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:42.344174 INFO::Done
2025-08-07 20:24:42.344679 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:42.346772 INFO::Starting hierarchical adjustment
2025-08-07 20:24:42.347493 INFO::Found  2  batches.
2025-08-07 20:24:42.348005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:42.34861 INFO::Using default BPPARAM
2025-08-07 20:24:42.349113 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:42.34998 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-07 20:24:42.364957 INFO::Done
2025-08-07 20:24:42.365624 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:42.367692 INFO::ASW Batch was -0.00996730902351056 prior to batch effect correction and is now -0.12963647012623 .
2025-08-07 20:24:42.368492 INFO::Total function execution time is  0.0301332473754883  s and adjustment time is  0.0176012516021729 s ( 58.41 )
2025-08-07 20:24:45.592786 INFO::Formatting Data.
2025-08-07 20:24:45.593571 INFO::Recognized SummarizedExperiment
2025-08-07 20:24:45.594067 INFO::Typecasting input to dataframe.
2025-08-07 20:24:45.624613 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:45.62589 INFO::Removing potential empty rows and columns
2025-08-07 20:24:45.629755 INFO::Found  0  missing values.
2025-08-07 20:24:45.637001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:45.637637 INFO::Done
2025-08-07 20:24:45.638169 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:45.64186 INFO::Starting hierarchical adjustment
2025-08-07 20:24:45.642587 INFO::Found  2  batches.
2025-08-07 20:24:45.643116 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:45.644235 INFO::Using default BPPARAM
2025-08-07 20:24:45.644767 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:45.645756 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-07 20:24:45.703702 INFO::Done
2025-08-07 20:24:45.704483 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:45.708248 INFO::ASW Batch was -0.0079233364089109 prior to batch effect correction and is now -0.089241338922326 .
2025-08-07 20:24:45.709146 INFO::Total function execution time is  0.116619110107422  s and adjustment time is  0.0612213611602783 s ( 52.5 )
2025-08-07 20:24:45.728474 INFO::Formatting Data.
2025-08-07 20:24:45.729279 INFO::Recognized SummarizedExperiment
2025-08-07 20:24:45.729822 INFO::Typecasting input to dataframe.
2025-08-07 20:24:45.739364 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:45.74057 INFO::Removing potential empty rows and columns
2025-08-07 20:24:45.744355 INFO::Found  0  missing values.
2025-08-07 20:24:45.751689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:45.752334 INFO::Done
2025-08-07 20:24:45.752873 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:45.756565 INFO::Starting hierarchical adjustment
2025-08-07 20:24:45.757335 INFO::Found  2  batches.
2025-08-07 20:24:45.757852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:45.75847 INFO::Using default BPPARAM
2025-08-07 20:24:45.758981 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:45.759956 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-07 20:24:45.785295 INFO::Done
2025-08-07 20:24:45.786085 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:45.789853 INFO::ASW Batch was 0.00734595522249008 prior to batch effect correction and is now 0.00734595522249008 .
2025-08-07 20:24:45.790777 INFO::Total function execution time is  0.0623297691345215  s and adjustment time is  0.0280940532684326 s ( 45.07 )
2025-08-07 20:24:45.809664 INFO::Formatting Data.
2025-08-07 20:24:45.81048 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:45.811423 INFO::Removing potential empty rows and columns
2025-08-07 20:24:45.812471 INFO::Found  0  missing values.
2025-08-07 20:24:45.815463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:45.816011 INFO::Done
2025-08-07 20:24:45.816539 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:45.818645 INFO::Starting hierarchical adjustment
2025-08-07 20:24:45.819397 INFO::Found  3  batches.
2025-08-07 20:24:45.819914 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:45.820536 INFO::Using default BPPARAM
2025-08-07 20:24:45.821051 INFO::Processing subtree level 1
2025-08-07 20:24:45.970055 INFO::Adjusting the last 1 batches sequentially
2025-08-07 20:24:45.972522 INFO::Done
2025-08-07 20:24:45.973309 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:45.976207 INFO::ASW Batch was 0.0762675587322632 prior to batch effect correction and is now -0.169648384976034 .
2025-08-07 20:24:45.977281 INFO::Total function execution time is  0.167642593383789  s and adjustment time is  0.15324068069458 s ( 91.41 )
2025-08-07 20:24:45.99593 INFO::Skipping initial DF formatting
2025-08-07 20:24:45.996919 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:46.001706 INFO::Starting hierarchical adjustment
2025-08-07 20:24:46.002595 INFO::Found  5  batches.
2025-08-07 20:24:46.003191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:46.003852 INFO::Using default BPPARAM
2025-08-07 20:24:46.004421 INFO::Processing subtree level 1
2025-08-07 20:24:46.243581 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:46.245303 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-07 20:24:46.26519 INFO::Done
2025-08-07 20:24:46.265963 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:46.270384 INFO::ASW Batch was 0.555246196674861 prior to batch effect correction and is now 0.555246196674861 .
2025-08-07 20:24:46.270998 INFO::ASW Label was 0.356336249601859 prior to batch effect correction and is now 0.356336249601859 .
2025-08-07 20:24:46.271888 INFO::Total function execution time is  0.276193380355835  s and adjustment time is  0.262750387191772 s ( 95.13 )
2025-08-07 20:24:46.33952 INFO::Formatting Data.
2025-08-07 20:24:46.340387 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:46.341378 INFO::Removing potential empty rows and columns
2025-08-07 20:24:46.342416 INFO::Found  0  missing values.
2025-08-07 20:24:46.346663 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:46.347275 INFO::Done
2025-08-07 20:24:46.347846 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:46.351221 INFO::Starting hierarchical adjustment
2025-08-07 20:24:46.352 INFO::Found  5  batches.
2025-08-07 20:24:46.352564 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:46.353229 INFO::Using default BPPARAM
2025-08-07 20:24:46.353789 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.

2025-08-07 20:24:46.509618 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:46.511467 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-07 20:24:46.530048 INFO::Done
2025-08-07 20:24:46.530911 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:46.534806 INFO::ASW Batch was 0.432222812487966 prior to batch effect correction and is now 0.00574491043986252 .
2025-08-07 20:24:46.535544 INFO::ASW Label was 0.326615394517766 prior to batch effect correction and is now 0.788660179051607 .
2025-08-07 20:24:46.536474 INFO::Total function execution time is  0.197044134140015  s and adjustment time is  0.178173303604126 s ( 90.42 )
2025-08-07 20:24:46.537466 INFO::Formatting Data.
2025-08-07 20:24:46.538166 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:46.53915 INFO::Removing potential empty rows and columns
2025-08-07 20:24:46.54033 INFO::Found  0  missing values.
2025-08-07 20:24:46.545199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:46.545835 INFO::Done
2025-08-07 20:24:46.546412 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:46.549768 INFO::Starting hierarchical adjustment
2025-08-07 20:24:46.550596 INFO::Found  5  batches.
2025-08-07 20:24:46.55116 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:46.551827 INFO::Using default BPPARAM
2025-08-07 20:24:46.552403 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.

2025-08-07 20:24:46.695374 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:46.697159 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-07 20:24:46.714381 INFO::Done
2025-08-07 20:24:46.715206 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:46.718867 INFO::ASW Batch was 0.432222812487966 prior to batch effect correction and is now 0.00574491043986252 .
2025-08-07 20:24:46.719538 INFO::ASW Label was 0.326615394517766 prior to batch effect correction and is now 0.788660179051607 .
2025-08-07 20:24:46.720416 INFO::Total function execution time is  0.182950973510742  s and adjustment time is  0.163930892944336 s ( 89.6 )
2025-08-07 20:24:46.73526 INFO::Formatting Data.
2025-08-07 20:24:46.73623 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:46.737292 INFO::Removing potential empty rows and columns
2025-08-07 20:24:46.738418 INFO::Found  0  missing values.
2025-08-07 20:24:46.742773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:46.743395 INFO::Done
2025-08-07 20:24:46.743944 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:46.747523 INFO::Starting hierarchical adjustment
2025-08-07 20:24:46.748303 INFO::Found  5  batches.
2025-08-07 20:24:46.748863 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:46.749528 INFO::Using default BPPARAM
2025-08-07 20:24:46.750105 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.

2025-08-07 20:24:46.894622 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:46.901596 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-07 20:24:46.925481 INFO::Done
2025-08-07 20:24:46.926511 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:46.930823 INFO::ASW Batch was 0.565280571002149 prior to batch effect correction and is now -0.0946232764353979 .
2025-08-07 20:24:46.931666 INFO::ASW Label was 0.214428708377441 prior to batch effect correction and is now 0.803474326398136 .
2025-08-07 20:24:46.932909 INFO::Total function execution time is  0.197751998901367  s and adjustment time is  0.177268028259277 s ( 89.64 )
2025-08-07 20:24:46.93403 INFO::Formatting Data.
2025-08-07 20:24:46.934858 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:46.93604 INFO::Removing potential empty rows and columns
2025-08-07 20:24:46.937374 INFO::Found  0  missing values.
2025-08-07 20:24:46.942912 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:46.943637 INFO::Done
2025-08-07 20:24:46.944291 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:46.948672 INFO::Starting hierarchical adjustment
2025-08-07 20:24:46.949557 INFO::Found  5  batches.
2025-08-07 20:24:46.950233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:46.951049 INFO::Using default BPPARAM
2025-08-07 20:24:46.951868 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.

2025-08-07 20:24:47.096186 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:47.097941 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-07 20:24:47.115633 INFO::Done
2025-08-07 20:24:47.116496 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.120457 INFO::ASW Batch was 0.565280571002149 prior to batch effect correction and is now -0.0946232764353979 .
2025-08-07 20:24:47.121184 INFO::ASW Label was 0.214428708377441 prior to batch effect correction and is now 0.803474326398136 .
2025-08-07 20:24:47.122084 INFO::Total function execution time is  0.188093662261963  s and adjustment time is  0.166246175765991 s ( 88.38 )
2025-08-07 20:24:47.136979 INFO::Formatting Data.
2025-08-07 20:24:47.137873 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:47.138948 INFO::Removing potential empty rows and columns
2025-08-07 20:24:47.140078 INFO::Found  0  missing values.
2025-08-07 20:24:47.143052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:47.143632 INFO::Done
2025-08-07 20:24:47.144179 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:47.14747 INFO::Starting hierarchical adjustment
2025-08-07 20:24:47.148228 INFO::Found  2  batches.
2025-08-07 20:24:47.14878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:47.149424 INFO::Using default BPPARAM
2025-08-07 20:24:47.149987 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:47.150975 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-07 20:24:47.166991 INFO::Done
2025-08-07 20:24:47.167688 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.170994 INFO::ASW Batch was 0.494331662607473 prior to batch effect correction and is now -0.0193727954162693 .
2025-08-07 20:24:47.171629 INFO::ASW Label was 0.57472234908802 prior to batch effect correction and is now 0.950773191820959 .
2025-08-07 20:24:47.172453 INFO::Total function execution time is  0.0355820655822754  s and adjustment time is  0.0189225673675537 s ( 53.18 )
2025-08-07 20:24:47.173282 INFO::Formatting Data.
2025-08-07 20:24:47.173908 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:47.174807 INFO::Removing potential empty rows and columns
2025-08-07 20:24:47.175847 INFO::Found  0  missing values.
2025-08-07 20:24:47.178636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:47.179198 INFO::Done
2025-08-07 20:24:47.17971 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:47.182803 INFO::Starting hierarchical adjustment
2025-08-07 20:24:47.183541 INFO::Found  2  batches.
2025-08-07 20:24:47.184069 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:47.1847 INFO::Using default BPPARAM
2025-08-07 20:24:47.185239 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:47.186187 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-07 20:24:47.201238 INFO::Done
2025-08-07 20:24:47.201847 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.204783 INFO::ASW Batch was 0.494331662607473 prior to batch effect correction and is now -0.0193727954162693 .
2025-08-07 20:24:47.205346 INFO::ASW Label was 0.57472234908802 prior to batch effect correction and is now 0.950773191820959 .
2025-08-07 20:24:47.206123 INFO::Total function execution time is  0.0328657627105713  s and adjustment time is  0.0178453922271729 s ( 54.3 )
2025-08-07 20:24:47.216995 INFO::Formatting Data.
2025-08-07 20:24:47.217827 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:47.218734 INFO::Removing potential empty rows and columns
2025-08-07 20:24:47.219645 INFO::Found  0  missing values.
2025-08-07 20:24:47.22166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:47.222204 INFO::Done
2025-08-07 20:24:47.222706 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:47.224675 INFO::Starting hierarchical adjustment
2025-08-07 20:24:47.225384 INFO::Found  2  batches.
2025-08-07 20:24:47.225897 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:47.226501 INFO::Using default BPPARAM
2025-08-07 20:24:47.227002 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:47.227878 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-07 20:24:47.259451 INFO::Done
2025-08-07 20:24:47.260208 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.262341 INFO::ASW Batch was -0.000450182927443449 prior to batch effect correction and is now -0.145067547987886 .
2025-08-07 20:24:47.263202 INFO::Total function execution time is  0.0462605953216553  s and adjustment time is  0.0341708660125732 s ( 73.87 )
2025-08-07 20:24:47.275138 INFO::Formatting Data.
2025-08-07 20:24:47.275897 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:47.276785 INFO::Removing potential empty rows and columns
2025-08-07 20:24:47.277823 INFO::Found  0  missing values.
2025-08-07 20:24:47.278971 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.
2025-08-07 20:24:47.283605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:47.284174 INFO::Done
2025-08-07 20:24:47.284679 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:47.287742 INFO::Starting hierarchical adjustment
2025-08-07 20:24:47.288452 INFO::Found  2  batches.
2025-08-07 20:24:47.288968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:47.289593 INFO::Using default BPPARAM
2025-08-07 20:24:47.290118 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:47.291023 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-07 20:24:47.308221 INFO::Done
2025-08-07 20:24:47.308913 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.311928 INFO::ASW Batch was 0.594905959576295 prior to batch effect correction and is now -0.0326171624559283 .
2025-08-07 20:24:47.312525 INFO::ASW Label was 0.443642015631996 prior to batch effect correction and is now 0.874565428192485 .
2025-08-07 20:24:47.313313 INFO::Total function execution time is  0.0382890701293945  s and adjustment time is  0.0198616981506348 s ( 51.87 )
2025-08-07 20:24:47.314116 INFO::Formatting Data.
2025-08-07 20:24:47.314721 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:47.315653 INFO::Removing potential empty rows and columns
2025-08-07 20:24:47.316686 INFO::Found  0  missing values.
2025-08-07 20:24:47.317642 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.
2025-08-07 20:24:47.322196 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:47.322756 INFO::Done
2025-08-07 20:24:47.323284 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:47.326272 INFO::Starting hierarchical adjustment
2025-08-07 20:24:47.326958 INFO::Found  2  batches.
2025-08-07 20:24:47.327488 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:47.328081 INFO::Using default BPPARAM
2025-08-07 20:24:47.328591 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:47.329504 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-07 20:24:47.346908 INFO::Done
2025-08-07 20:24:47.347746 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.350989 INFO::ASW Batch was 0.594905959576295 prior to batch effect correction and is now -0.0326171624559283 .
2025-08-07 20:24:47.351646 INFO::ASW Label was 0.443642015631996 prior to batch effect correction and is now 0.874565428192485 .
2025-08-07 20:24:47.352475 INFO::Total function execution time is  0.0383856296539307  s and adjustment time is  0.0200259685516357 s ( 52.17 )
2025-08-07 20:24:47.573899 INFO::Formatting Data.
2025-08-07 20:24:47.574778 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:47.575716 INFO::Removing potential empty rows and columns
2025-08-07 20:24:47.576783 INFO::Found  0  missing values.
2025-08-07 20:24:47.579834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:47.580394 INFO::Done
2025-08-07 20:24:47.580916 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:47.583062 INFO::Starting hierarchical adjustment
2025-08-07 20:24:47.583775 INFO::Found  3  batches.
2025-08-07 20:24:47.584317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:47.584932 INFO::Using default BPPARAM
2025-08-07 20:24:47.585465 INFO::Processing subtree level 1
2025-08-07 20:24:47.674463 INFO::Adjusting the last 1 batches sequentially
2025-08-07 20:24:47.676235 INFO::Done
2025-08-07 20:24:47.67691 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.679562 INFO::ASW Batch was 0.0661713310905968 prior to batch effect correction and is now 0.0661713310905968 .
2025-08-07 20:24:47.680538 INFO::Total function execution time is  0.106720209121704  s and adjustment time is  0.0925846099853516 s ( 86.75 )
2025-08-07 20:24:47.68169 INFO::Formatting Data.
2025-08-07 20:24:47.682383 INFO::Typecasting input to dataframe.
2025-08-07 20:24:47.683193 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:47.684144 INFO::Removing potential empty rows and columns
2025-08-07 20:24:47.685271 INFO::Found  0  missing values.
2025-08-07 20:24:47.688406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:47.688964 INFO::Done
2025-08-07 20:24:47.689533 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:47.691645 INFO::Starting hierarchical adjustment
2025-08-07 20:24:47.692388 INFO::Found  3  batches.
2025-08-07 20:24:47.692918 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:47.693571 INFO::Using default BPPARAM
2025-08-07 20:24:47.694128 INFO::Processing subtree level 1
2025-08-07 20:24:47.781758 INFO::Adjusting the last 1 batches sequentially
2025-08-07 20:24:47.783511 INFO::Done
2025-08-07 20:24:47.784166 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.786662 INFO::ASW Batch was 0.0661713310905968 prior to batch effect correction and is now 0.0661713310905968 .
2025-08-07 20:24:47.787604 INFO::Total function execution time is  0.105914115905762  s and adjustment time is  0.0912582874298096 s ( 86.16 )
2025-08-07 20:24:47.800447 INFO::Formatting Data.
2025-08-07 20:24:47.801344 INFO::Typecasting input to dataframe.
2025-08-07 20:24:47.802224 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:47.803165 INFO::Removing potential empty rows and columns
2025-08-07 20:24:47.804242 INFO::Found  0  missing values.
2025-08-07 20:24:47.807232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:47.807757 INFO::Done
2025-08-07 20:24:47.808297 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:47.81056 INFO::Starting hierarchical adjustment
2025-08-07 20:24:47.811276 INFO::Found  3  batches.
2025-08-07 20:24:47.811807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:47.81246 INFO::Using default BPPARAM
2025-08-07 20:24:47.812985 INFO::Processing subtree level 1
2025-08-07 20:24:47.899253 INFO::Adjusting the last 1 batches sequentially
2025-08-07 20:24:47.901199 INFO::Done
2025-08-07 20:24:47.901896 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:47.904492 INFO::ASW Batch was -0.110512218447241 prior to batch effect correction and is now -0.110512218447241 .
2025-08-07 20:24:47.905429 INFO::Total function execution time is  0.105061292648315  s and adjustment time is  0.0900266170501709 s ( 85.69 )
2025-08-07 20:24:48.04458 INFO::Formatting Data.
2025-08-07 20:24:48.045468 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:48.04663 INFO::Removing potential empty rows and columns
2025-08-07 20:24:48.049416 INFO::Found  1000  missing values.
2025-08-07 20:24:48.06839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:48.069194 INFO::Done
2025-08-07 20:24:48.069799 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:48.0755 INFO::Starting hierarchical adjustment
2025-08-07 20:24:48.076313 INFO::Found  10  batches.
2025-08-07 20:24:48.076864 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:48.07752 INFO::Using default BPPARAM
2025-08-07 20:24:48.078053 INFO::Processing subtree level 1
2025-08-07 20:24:48.227342 INFO::Processing subtree level 2
2025-08-07 20:24:48.372977 INFO::Adjusting the last 1 batches sequentially
2025-08-07 20:24:48.374973 INFO::Done
2025-08-07 20:24:48.375667 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:48.38138 INFO::ASW Batch was 0.504420857332661 prior to batch effect correction and is now 0.504420857332661 .
2025-08-07 20:24:48.382029 INFO::ASW Label was 0.338256019670117 prior to batch effect correction and is now 0.338256019670117 .
2025-08-07 20:24:48.38298 INFO::Total function execution time is  0.338456869125366  s and adjustment time is  0.29882025718689 s ( 88.29 )
2025-08-07 20:24:48.383846 INFO::Formatting Data.
2025-08-07 20:24:48.384516 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:48.385732 INFO::Removing potential empty rows and columns
2025-08-07 20:24:48.388566 INFO::Found  1000  missing values.
2025-08-07 20:24:48.40767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:48.408449 INFO::Done
2025-08-07 20:24:48.409005 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:48.414552 INFO::Starting hierarchical adjustment
2025-08-07 20:24:48.415359 INFO::Found  10  batches.
2025-08-07 20:24:49.745634 INFO::Set up parallel execution backend with 2 workers
2025-08-07 20:24:49.749127 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-07 20:24:51.047773 INFO::Adjusting the last 2 batches sequentially
2025-08-07 20:24:51.049591 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-07 20:24:51.065618 INFO::Done
2025-08-07 20:24:51.066301 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:51.07078 INFO::ASW Batch was 0.504420857332661 prior to batch effect correction and is now 0.504420857332661 .
2025-08-07 20:24:51.07135 INFO::ASW Label was 0.338256019670117 prior to batch effect correction and is now 0.338256019670117 .
2025-08-07 20:24:51.07206 INFO::Total function execution time is  2.68824863433838  s and adjustment time is  2.65042734146118 s ( 98.59 )
2025-08-07 20:24:51.21869 INFO::Formatting Data.
2025-08-07 20:24:51.219483 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.220378 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.221458 INFO::Found  0  missing values.
2025-08-07 20:24:51.225008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.225548 INFO::Done
2025-08-07 20:24:51.226047 INFO::Acquiring quality metrics before batch effect correction.
2025-08-07 20:24:51.228839 INFO::Starting hierarchical adjustment
2025-08-07 20:24:51.229538 INFO::Found  3  batches.
2025-08-07 20:24:51.230053 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-07 20:24:51.230663 INFO::Using default BPPARAM
2025-08-07 20:24:51.231202 INFO::Processing subtree level 1
2025-08-07 20:24:51.33408 INFO::Adjusting the last 1 batches sequentially
2025-08-07 20:24:51.335843 INFO::Done
2025-08-07 20:24:51.336486 INFO::Acquiring quality metrics after batch effect correction.
2025-08-07 20:24:51.339662 INFO::ASW Batch was 0.181747353866083 prior to batch effect correction and is now -0.163797028073338 .
2025-08-07 20:24:51.340272 INFO::ASW Label was -0.231898908314556 prior to batch effect correction and is now -0.111026301219261 .
2025-08-07 20:24:51.341177 INFO::Total function execution time is  0.122514963150024  s and adjustment time is  0.106428146362305 s ( 86.87 )
2025-08-07 20:24:51.453384 INFO::Formatting Data.
2025-08-07 20:24:51.454286 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.455259 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.456344 INFO::Found  2  missing values.
2025-08-07 20:24:51.459191 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.459738 INFO::Done
2025-08-07 20:24:51.485648 INFO::Found NA in Reference column
2025-08-07 20:24:51.494809 INFO::Require at least two references per batch.
2025-08-07 20:24:51.514629 INFO::Formatting Data.
2025-08-07 20:24:51.515503 INFO::Recognized SummarizedExperiment
2025-08-07 20:24:51.516016 INFO::Typecasting input to dataframe.
2025-08-07 20:24:51.525549 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.52672 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.530042 INFO::Found  0  missing values.
2025-08-07 20:24:51.536402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.536963 INFO::Done
2025-08-07 20:24:51.552107 INFO::Formatting Data.
2025-08-07 20:24:51.552798 INFO::Recognized SummarizedExperiment
2025-08-07 20:24:51.5533 INFO::Typecasting input to dataframe.
2025-08-07 20:24:51.569487 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.570666 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.57394 INFO::Found  0  missing values.
2025-08-07 20:24:51.583862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.584506 INFO::Done
2025-08-07 20:24:51.600049 INFO::Formatting Data.
2025-08-07 20:24:51.600777 INFO::Recognized SummarizedExperiment
2025-08-07 20:24:51.601295 INFO::Typecasting input to dataframe.
2025-08-07 20:24:51.618073 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.619196 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.620322 INFO::Found  0  missing values.
2025-08-07 20:24:51.621268 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.
2025-08-07 20:24:51.625603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.626148 INFO::Done
2025-08-07 20:24:51.636453 INFO::Formatting Data.
2025-08-07 20:24:51.63716 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.638001 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.638986 INFO::Found  0  missing values.
2025-08-07 20:24:51.64178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.642303 INFO::Done
2025-08-07 20:24:51.652881 INFO::Formatting Data.
2025-08-07 20:24:51.653662 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.654485 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.655457 INFO::Found  0  missing values.
2025-08-07 20:24:51.658244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.658753 INFO::Done
2025-08-07 20:24:51.68632 INFO::Formatting Data.
2025-08-07 20:24:51.687154 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.68818 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.689332 INFO::Found  1  missing values.
2025-08-07 20:24:51.691887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.69243 INFO::Done
2025-08-07 20:24:51.710725 INFO::Formatting Data.
2025-08-07 20:24:51.711596 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.712475 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.713424 INFO::Found  2  missing values.
2025-08-07 20:24:51.714318 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.
2025-08-07 20:24:51.716594 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.717142 INFO::Done
2025-08-07 20:24:51.726652 INFO::Formatting Data.
2025-08-07 20:24:51.727514 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.728363 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.729292 INFO::Found  2  missing values.
2025-08-07 20:24:51.730865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.731412 INFO::Done
2025-08-07 20:24:51.741592 INFO::Formatting Data.
2025-08-07 20:24:51.742295 INFO::Typecasting input to dataframe.
2025-08-07 20:24:51.743039 INFO::Replacing NaNs with NAs.
2025-08-07 20:24:51.743857 INFO::Removing potential empty rows and columns
2025-08-07 20:24:51.744819 INFO::Found  0  missing values.
2025-08-07 20:24:51.747512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-07 20:24:51.748008 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 18.294   3.916  21.837 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT22.699 1.36716.497
compute_asw0.0270.0000.027
count_existing0.0140.0030.017
generate_data_covariables0.0130.0010.014
generate_dataset0.0130.0000.013