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This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 163/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.4.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_21
git_last_commit: dedce04
git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on merida1

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

raw results


Summary

Package: BERT
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz
StartedAt: 2025-10-10 00:30:14 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 00:32:37 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 143.1 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 45.322  2.696   35.45
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.4.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BERT)

Tests output

BERT.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-10-10 00:32:00.823585 INFO::Formatting Data.
2025-10-10 00:32:00.831149 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:00.869163 INFO::Removing potential empty rows and columns
2025-10-10 00:32:01.617454 INFO::Found  0  missing values.
2025-10-10 00:32:01.626674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:01.628283 INFO::Done
2025-10-10 00:32:01.629806 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:01.658702 INFO::Starting hierarchical adjustment
2025-10-10 00:32:01.660506 INFO::Found  3  batches.
2025-10-10 00:32:01.66183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:01.664593 INFO::Using default BPPARAM
2025-10-10 00:32:01.666068 INFO::Processing subtree level 1
2025-10-10 00:32:01.95353 INFO::Adjusting the last 1 batches sequentially
2025-10-10 00:32:01.958916 INFO::Done
2025-10-10 00:32:01.960923 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:01.97226 INFO::ASW Batch was -0.0588856031219116 prior to batch effect correction and is now -0.0588856031219116 .
2025-10-10 00:32:01.974757 INFO::Total function execution time is  1.15267705917358  s and adjustment time is  0.298742055892944 s ( 25.92 )
2025-10-10 00:32:02.015073 INFO::Formatting Data.
2025-10-10 00:32:02.016771 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:02.018939 INFO::Removing potential empty rows and columns
2025-10-10 00:32:02.022405 INFO::Found  0  missing values.
2025-10-10 00:32:02.025064 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.
2025-10-10 00:32:02.054473 INFO::Formatting Data.
2025-10-10 00:32:02.05617 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:02.058346 INFO::Removing potential empty rows and columns
2025-10-10 00:32:02.061319 INFO::Found  0  missing values.
2025-10-10 00:32:02.064704 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.
2025-10-10 00:32:02.181435 INFO::Formatting Data.
2025-10-10 00:32:02.183249 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:02.185556 INFO::Removing potential empty rows and columns
2025-10-10 00:32:02.188916 INFO::Found  0  missing values.
2025-10-10 00:32:02.191573 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.
2025-10-10 00:32:02.204899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:02.208029 INFO::Done
2025-10-10 00:32:02.209575 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:02.21441 INFO::Starting hierarchical adjustment
2025-10-10 00:32:02.218815 INFO::Found  2  batches.
2025-10-10 00:32:02.220422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:02.222187 INFO::Using default BPPARAM
2025-10-10 00:32:02.234031 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:02.23667 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 00:32:02.293348 INFO::Done
2025-10-10 00:32:02.29494 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:02.299959 INFO::ASW Batch was -0.0501245691974225 prior to batch effect correction and is now -0.116594738489639 .
2025-10-10 00:32:02.302057 INFO::Total function execution time is  0.120660066604614  s and adjustment time is  0.075127124786377 s ( 62.26 )
2025-10-10 00:32:02.308759 INFO::Formatting Data.
2025-10-10 00:32:02.310486 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:02.335611 INFO::Formatting Data.
2025-10-10 00:32:02.39171 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:02.394052 INFO::Removing potential empty rows and columns
2025-10-10 00:32:02.396784 INFO::Found  0  missing values.
2025-10-10 00:32:02.404756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:02.406202 INFO::Done
2025-10-10 00:32:02.407479 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:02.412092 INFO::Starting hierarchical adjustment
2025-10-10 00:32:02.413916 INFO::Found  2  batches.
2025-10-10 00:32:02.415235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:02.416747 INFO::Using default BPPARAM
2025-10-10 00:32:02.418104 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:02.420379 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 00:32:02.457261 INFO::Done
2025-10-10 00:32:02.458656 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:02.463066 INFO::ASW Batch was -0.0319222723491968 prior to batch effect correction and is now -0.127522991087951 .
2025-10-10 00:32:02.464838 INFO::Total function execution time is  0.129552125930786  s and adjustment time is  0.0436890125274658 s ( 33.72 )
2025-10-10 00:32:02.467325 INFO::Formatting Data.
2025-10-10 00:32:02.468773 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:02.470807 INFO::Removing potential empty rows and columns
2025-10-10 00:32:02.473335 INFO::Found  0  missing values.
2025-10-10 00:32:02.481146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:02.482608 INFO::Done
2025-10-10 00:32:02.484026 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:02.488851 INFO::Starting hierarchical adjustment
2025-10-10 00:32:02.490738 INFO::Found  2  batches.
2025-10-10 00:32:02.492059 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:02.493771 INFO::Using default BPPARAM
2025-10-10 00:32:02.495199 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:02.497477 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 00:32:02.53764 INFO::Done
2025-10-10 00:32:02.539123 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:02.543986 INFO::ASW Batch was -0.0319222723491968 prior to batch effect correction and is now -0.127522991087951 .
2025-10-10 00:32:02.545928 INFO::Total function execution time is  0.07859206199646  s and adjustment time is  0.0472559928894043 s ( 60.13 )
2025-10-10 00:32:09.296554 INFO::Formatting Data.
2025-10-10 00:32:09.298609 INFO::Recognized SummarizedExperiment
2025-10-10 00:32:09.300528 INFO::Typecasting input to dataframe.
2025-10-10 00:32:09.377764 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:09.380335 INFO::Removing potential empty rows and columns
2025-10-10 00:32:09.390288 INFO::Found  0  missing values.
2025-10-10 00:32:09.412405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:09.414163 INFO::Done
2025-10-10 00:32:09.416797 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:09.426914 INFO::Starting hierarchical adjustment
2025-10-10 00:32:09.428864 INFO::Found  2  batches.
2025-10-10 00:32:09.430192 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:09.432888 INFO::Using default BPPARAM
2025-10-10 00:32:09.434227 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:09.436527 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 00:32:09.593728 INFO::Done
2025-10-10 00:32:09.595468 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:09.605479 INFO::ASW Batch was -0.00846679762315869 prior to batch effect correction and is now -0.0908212638990353 .
2025-10-10 00:32:09.607646 INFO::Total function execution time is  0.311879873275757  s and adjustment time is  0.165218114852905 s ( 52.97 )
2025-10-10 00:32:09.657707 INFO::Formatting Data.
2025-10-10 00:32:09.65938 INFO::Recognized SummarizedExperiment
2025-10-10 00:32:09.660743 INFO::Typecasting input to dataframe.
2025-10-10 00:32:09.683963 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:09.686558 INFO::Removing potential empty rows and columns
2025-10-10 00:32:09.699613 INFO::Found  0  missing values.
2025-10-10 00:32:09.724025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:09.725586 INFO::Done
2025-10-10 00:32:09.726997 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:09.740333 INFO::Starting hierarchical adjustment
2025-10-10 00:32:09.742233 INFO::Found  2  batches.
2025-10-10 00:32:09.744907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:09.746554 INFO::Using default BPPARAM
2025-10-10 00:32:09.747915 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:09.750386 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 00:32:09.824463 INFO::Done
2025-10-10 00:32:09.825945 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:09.835196 INFO::ASW Batch was 0.0120036232386158 prior to batch effect correction and is now 0.0120036232386158 .
2025-10-10 00:32:09.837214 INFO::Total function execution time is  0.179484844207764  s and adjustment time is  0.0825760364532471 s ( 46.01 )
2025-10-10 00:32:09.884571 INFO::Formatting Data.
2025-10-10 00:32:09.88637 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:09.888588 INFO::Removing potential empty rows and columns
2025-10-10 00:32:09.891267 INFO::Found  0  missing values.
2025-10-10 00:32:09.899207 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:09.900751 INFO::Done
2025-10-10 00:32:09.902121 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:09.907029 INFO::Starting hierarchical adjustment
2025-10-10 00:32:09.90894 INFO::Found  3  batches.
2025-10-10 00:32:09.910337 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:09.911911 INFO::Using default BPPARAM
2025-10-10 00:32:09.913266 INFO::Processing subtree level 1
2025-10-10 00:32:10.596867 INFO::Adjusting the last 1 batches sequentially
2025-10-10 00:32:10.604872 INFO::Done
2025-10-10 00:32:10.609819 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:10.648195 INFO::ASW Batch was -0.0493219704995437 prior to batch effect correction and is now -0.171535597368166 .
2025-10-10 00:32:10.658325 INFO::Total function execution time is  0.772193908691406  s and adjustment time is  0.696105003356934 s ( 90.15 )
2025-10-10 00:32:10.818355 INFO::Skipping initial DF formatting
2025-10-10 00:32:10.819932 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:10.829216 INFO::Starting hierarchical adjustment
2025-10-10 00:32:10.831152 INFO::Found  5  batches.
2025-10-10 00:32:10.832486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:10.833856 INFO::Using default BPPARAM
2025-10-10 00:32:10.835216 INFO::Processing subtree level 1
2025-10-10 00:32:11.320531 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:11.328869 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 00:32:11.407035 INFO::Done
2025-10-10 00:32:11.408576 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:11.419774 INFO::ASW Batch was 0.52590671332054 prior to batch effect correction and is now 0.52590671332054 .
2025-10-10 00:32:11.42222 INFO::ASW Label was 0.344752884310296 prior to batch effect correction and is now 0.344752884310296 .
2025-10-10 00:32:11.424873 INFO::Total function execution time is  0.606510162353516  s and adjustment time is  0.576246976852417 s ( 95.01 )
2025-10-10 00:32:11.475892 INFO::Formatting Data.
2025-10-10 00:32:11.477551 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:11.479662 INFO::Removing potential empty rows and columns
2025-10-10 00:32:11.482826 INFO::Found  0  missing values.
2025-10-10 00:32:11.496199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:11.498052 INFO::Done
2025-10-10 00:32:11.499772 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:11.507809 INFO::Starting hierarchical adjustment
2025-10-10 00:32:11.509862 INFO::Found  5  batches.
2025-10-10 00:32:11.511272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:11.513168 INFO::Using default BPPARAM
2025-10-10 00:32:11.514669 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.

2025-10-10 00:32:11.863752 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:11.874451 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 00:32:11.93533 INFO::Done
2025-10-10 00:32:11.937038 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:11.945584 INFO::ASW Batch was 0.206748841708064 prior to batch effect correction and is now -0.0526187537017712 .
2025-10-10 00:32:11.947409 INFO::ASW Label was 0.621989735972235 prior to batch effect correction and is now 0.799052734102571 .
2025-10-10 00:32:11.949828 INFO::Total function execution time is  0.473904848098755  s and adjustment time is  0.425894021987915 s ( 89.87 )
2025-10-10 00:32:11.952183 INFO::Formatting Data.
2025-10-10 00:32:11.954218 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:11.957046 INFO::Removing potential empty rows and columns
2025-10-10 00:32:11.96101 INFO::Found  0  missing values.
2025-10-10 00:32:11.97363 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:11.975459 INFO::Done
2025-10-10 00:32:11.977071 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:11.984845 INFO::Starting hierarchical adjustment
2025-10-10 00:32:11.98701 INFO::Found  5  batches.
2025-10-10 00:32:11.988808 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:11.990684 INFO::Using default BPPARAM
2025-10-10 00:32:11.992308 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.

2025-10-10 00:32:12.366185 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:12.38273 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 00:32:12.447481 INFO::Done
2025-10-10 00:32:12.44912 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:12.457168 INFO::ASW Batch was 0.206748841708064 prior to batch effect correction and is now -0.0526187537017712 .
2025-10-10 00:32:12.458836 INFO::ASW Label was 0.621989735972235 prior to batch effect correction and is now 0.799052734102571 .
2025-10-10 00:32:12.46091 INFO::Total function execution time is  0.508768081665039  s and adjustment time is  0.460916042327881 s ( 90.59 )
2025-10-10 00:32:12.499999 INFO::Formatting Data.
2025-10-10 00:32:12.502142 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:12.50469 INFO::Removing potential empty rows and columns
2025-10-10 00:32:12.507571 INFO::Found  0  missing values.
2025-10-10 00:32:12.520955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:12.522883 INFO::Done
2025-10-10 00:32:12.52446 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:12.532432 INFO::Starting hierarchical adjustment
2025-10-10 00:32:12.53464 INFO::Found  5  batches.
2025-10-10 00:32:12.536099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:12.537714 INFO::Using default BPPARAM
2025-10-10 00:32:12.53928 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.

2025-10-10 00:32:12.90258 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:12.913145 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 00:32:12.990071 INFO::Done
2025-10-10 00:32:12.992569 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:13.0009 INFO::ASW Batch was 0.304220115284493 prior to batch effect correction and is now -0.0822120177830661 .
2025-10-10 00:32:13.002667 INFO::ASW Label was 0.455350774978271 prior to batch effect correction and is now 0.842168949027759 .
2025-10-10 00:32:13.004946 INFO::Total function execution time is  0.504971981048584  s and adjustment time is  0.455877065658569 s ( 90.28 )
2025-10-10 00:32:13.007556 INFO::Formatting Data.
2025-10-10 00:32:13.009294 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:13.011714 INFO::Removing potential empty rows and columns
2025-10-10 00:32:13.014779 INFO::Found  0  missing values.
2025-10-10 00:32:13.02607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:13.027721 INFO::Done
2025-10-10 00:32:13.029287 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:13.036932 INFO::Starting hierarchical adjustment
2025-10-10 00:32:13.038883 INFO::Found  5  batches.
2025-10-10 00:32:13.040644 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:13.04255 INFO::Using default BPPARAM
2025-10-10 00:32:13.044209 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.

2025-10-10 00:32:13.376091 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:13.388959 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 00:32:13.447468 INFO::Done
2025-10-10 00:32:13.449202 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:13.457329 INFO::ASW Batch was 0.304220115284493 prior to batch effect correction and is now -0.0822120177830661 .
2025-10-10 00:32:13.45899 INFO::ASW Label was 0.455350774978271 prior to batch effect correction and is now 0.842168949027759 .
2025-10-10 00:32:13.462725 INFO::Total function execution time is  0.45518684387207  s and adjustment time is  0.408974170684814 s ( 89.85 )
2025-10-10 00:32:13.503183 INFO::Formatting Data.
2025-10-10 00:32:13.505067 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:13.508546 INFO::Removing potential empty rows and columns
2025-10-10 00:32:13.511401 INFO::Found  0  missing values.
2025-10-10 00:32:13.519463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:13.521005 INFO::Done
2025-10-10 00:32:13.522361 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:13.530694 INFO::Starting hierarchical adjustment
2025-10-10 00:32:13.532817 INFO::Found  2  batches.
2025-10-10 00:32:13.535032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:13.536734 INFO::Using default BPPARAM
2025-10-10 00:32:13.538143 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:13.540579 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 00:32:13.579616 INFO::Done
2025-10-10 00:32:13.581217 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:13.589202 INFO::ASW Batch was 0.462703688938169 prior to batch effect correction and is now -0.0243609199658107 .
2025-10-10 00:32:13.590997 INFO::ASW Label was 0.616452221185078 prior to batch effect correction and is now 0.915191127631062 .
2025-10-10 00:32:13.592968 INFO::Total function execution time is  0.0899322032928467  s and adjustment time is  0.0471580028533936 s ( 52.44 )
2025-10-10 00:32:13.594952 INFO::Formatting Data.
2025-10-10 00:32:13.596469 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:13.598597 INFO::Removing potential empty rows and columns
2025-10-10 00:32:13.602768 INFO::Found  0  missing values.
2025-10-10 00:32:13.612797 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:13.614913 INFO::Done
2025-10-10 00:32:13.616487 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:13.625699 INFO::Starting hierarchical adjustment
2025-10-10 00:32:13.627779 INFO::Found  2  batches.
2025-10-10 00:32:13.629345 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:13.631237 INFO::Using default BPPARAM
2025-10-10 00:32:13.632707 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:13.635654 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-10 00:32:13.678626 INFO::Done
2025-10-10 00:32:13.681044 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:13.688807 INFO::ASW Batch was 0.462703688938169 prior to batch effect correction and is now -0.0243609199658107 .
2025-10-10 00:32:13.690686 INFO::ASW Label was 0.616452221185078 prior to batch effect correction and is now 0.915191127631062 .
2025-10-10 00:32:13.694059 INFO::Total function execution time is  0.0991649627685547  s and adjustment time is  0.0512490272521973 s ( 51.68 )
2025-10-10 00:32:13.728804 INFO::Formatting Data.
2025-10-10 00:32:13.730909 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:13.733342 INFO::Removing potential empty rows and columns
2025-10-10 00:32:13.736494 INFO::Found  0  missing values.
2025-10-10 00:32:13.742888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:13.744517 INFO::Done
2025-10-10 00:32:13.746215 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:13.751753 INFO::Starting hierarchical adjustment
2025-10-10 00:32:13.753941 INFO::Found  2  batches.
2025-10-10 00:32:13.755607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:13.757504 INFO::Using default BPPARAM
2025-10-10 00:32:13.759132 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:13.762256 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 00:32:13.865692 INFO::Done
2025-10-10 00:32:13.867206 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:13.872301 INFO::ASW Batch was 0.00560131112421892 prior to batch effect correction and is now -0.211935660709033 .
2025-10-10 00:32:13.875688 INFO::Total function execution time is  0.146989107131958  s and adjustment time is  0.112068891525269 s ( 76.24 )
2025-10-10 00:32:13.917494 INFO::Formatting Data.
2025-10-10 00:32:13.920167 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:13.923132 INFO::Removing potential empty rows and columns
2025-10-10 00:32:13.926372 INFO::Found  0  missing values.
2025-10-10 00:32:13.929476 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.
2025-10-10 00:32:13.94288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:13.944361 INFO::Done
2025-10-10 00:32:13.945662 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:13.953201 INFO::Starting hierarchical adjustment
2025-10-10 00:32:13.955017 INFO::Found  2  batches.
2025-10-10 00:32:13.95662 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:13.959334 INFO::Using default BPPARAM
2025-10-10 00:32:13.960921 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:13.964043 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 00:32:14.015707 INFO::Done
2025-10-10 00:32:14.017422 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:14.025299 INFO::ASW Batch was 0.124820911915921 prior to batch effect correction and is now -0.0369040527598465 .
2025-10-10 00:32:14.026826 INFO::ASW Label was 0.820550049869225 prior to batch effect correction and is now 0.938487617445931 .
2025-10-10 00:32:14.028593 INFO::Total function execution time is  0.11142110824585  s and adjustment time is  0.0610229969024658 s ( 54.77 )
2025-10-10 00:32:14.030508 INFO::Formatting Data.
2025-10-10 00:32:14.032021 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:14.035247 INFO::Removing potential empty rows and columns
2025-10-10 00:32:14.038014 INFO::Found  0  missing values.
2025-10-10 00:32:14.040582 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.
2025-10-10 00:32:14.053386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:14.05491 INFO::Done
2025-10-10 00:32:14.056366 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:14.065161 INFO::Starting hierarchical adjustment
2025-10-10 00:32:14.067295 INFO::Found  2  batches.
2025-10-10 00:32:14.068941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:14.070587 INFO::Using default BPPARAM
2025-10-10 00:32:14.071946 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:14.074458 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 00:32:14.120959 INFO::Done
2025-10-10 00:32:14.122559 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:14.130298 INFO::ASW Batch was 0.124820911915921 prior to batch effect correction and is now -0.0369040527598465 .
2025-10-10 00:32:14.131725 INFO::ASW Label was 0.820550049869225 prior to batch effect correction and is now 0.938487617445931 .
2025-10-10 00:32:14.133483 INFO::Total function execution time is  0.103060007095337  s and adjustment time is  0.0541090965270996 s ( 52.5 )
2025-10-10 00:32:14.741134 INFO::Formatting Data.
2025-10-10 00:32:14.742919 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:14.745129 INFO::Removing potential empty rows and columns
2025-10-10 00:32:14.74786 INFO::Found  0  missing values.
2025-10-10 00:32:14.757014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:14.758484 INFO::Done
2025-10-10 00:32:14.759755 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:14.765974 INFO::Starting hierarchical adjustment
2025-10-10 00:32:14.768063 INFO::Found  3  batches.
2025-10-10 00:32:14.76952 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:14.77102 INFO::Using default BPPARAM
2025-10-10 00:32:14.772351 INFO::Processing subtree level 1
2025-10-10 00:32:15.013454 INFO::Adjusting the last 1 batches sequentially
2025-10-10 00:32:15.024305 INFO::Done
2025-10-10 00:32:15.027786 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:15.037733 INFO::ASW Batch was 0.017377682941134 prior to batch effect correction and is now 0.017377682941134 .
2025-10-10 00:32:15.042919 INFO::Total function execution time is  0.301663160324097  s and adjustment time is  0.256599903106689 s ( 85.06 )
2025-10-10 00:32:15.047562 INFO::Formatting Data.
2025-10-10 00:32:15.052042 INFO::Typecasting input to dataframe.
2025-10-10 00:32:15.053994 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:15.056194 INFO::Removing potential empty rows and columns
2025-10-10 00:32:15.058757 INFO::Found  0  missing values.
2025-10-10 00:32:15.066775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:15.068929 INFO::Done
2025-10-10 00:32:15.070483 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:15.075771 INFO::Starting hierarchical adjustment
2025-10-10 00:32:15.077688 INFO::Found  3  batches.
2025-10-10 00:32:15.079067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:15.08073 INFO::Using default BPPARAM
2025-10-10 00:32:15.082125 INFO::Processing subtree level 1
2025-10-10 00:32:15.324246 INFO::Adjusting the last 1 batches sequentially
2025-10-10 00:32:15.333726 INFO::Done
2025-10-10 00:32:15.336303 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:15.345215 INFO::ASW Batch was 0.017377682941134 prior to batch effect correction and is now 0.017377682941134 .
2025-10-10 00:32:15.350862 INFO::Total function execution time is  0.303270816802979  s and adjustment time is  0.256386995315552 s ( 84.54 )
2025-10-10 00:32:15.403232 INFO::Formatting Data.
2025-10-10 00:32:15.407352 INFO::Typecasting input to dataframe.
2025-10-10 00:32:15.410096 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:15.413517 INFO::Removing potential empty rows and columns
2025-10-10 00:32:15.417818 INFO::Found  0  missing values.
2025-10-10 00:32:15.426674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:15.428594 INFO::Done
2025-10-10 00:32:15.430096 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:15.435195 INFO::Starting hierarchical adjustment
2025-10-10 00:32:15.438139 INFO::Found  3  batches.
2025-10-10 00:32:15.439827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:15.442067 INFO::Using default BPPARAM
2025-10-10 00:32:15.443636 INFO::Processing subtree level 1
2025-10-10 00:32:15.644758 INFO::Adjusting the last 1 batches sequentially
2025-10-10 00:32:15.650607 INFO::Done
2025-10-10 00:32:15.652264 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:15.659844 INFO::ASW Batch was -0.0703532793301655 prior to batch effect correction and is now -0.0703532793301655 .
2025-10-10 00:32:15.662751 INFO::Total function execution time is  0.262288093566895  s and adjustment time is  0.2137610912323 s ( 81.5 )
2025-10-10 00:32:16.012173 INFO::Formatting Data.
2025-10-10 00:32:16.014102 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:16.017187 INFO::Removing potential empty rows and columns
2025-10-10 00:32:16.025922 INFO::Found  1000  missing values.
2025-10-10 00:32:16.089009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:16.090682 INFO::Done
2025-10-10 00:32:16.092006 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:16.104885 INFO::Starting hierarchical adjustment
2025-10-10 00:32:16.107047 INFO::Found  10  batches.
2025-10-10 00:32:16.108657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:16.110398 INFO::Using default BPPARAM
2025-10-10 00:32:16.111982 INFO::Processing subtree level 1
2025-10-10 00:32:16.408951 INFO::Processing subtree level 2
2025-10-10 00:32:16.89657 INFO::Adjusting the last 1 batches sequentially
2025-10-10 00:32:16.909426 INFO::Done
2025-10-10 00:32:16.913428 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:16.936287 INFO::ASW Batch was 0.510324757586946 prior to batch effect correction and is now 0.510324757586946 .
2025-10-10 00:32:16.938184 INFO::ASW Label was 0.317499399794672 prior to batch effect correction and is now 0.317499399794672 .
2025-10-10 00:32:16.944526 INFO::Total function execution time is  0.932224035263062  s and adjustment time is  0.802824974060059 s ( 86.12 )
2025-10-10 00:32:16.948251 INFO::Formatting Data.
2025-10-10 00:32:16.950811 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:16.957025 INFO::Removing potential empty rows and columns
2025-10-10 00:32:16.966201 INFO::Found  1000  missing values.
2025-10-10 00:32:17.031392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:17.033232 INFO::Done
2025-10-10 00:32:17.035695 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:17.052425 INFO::Starting hierarchical adjustment
2025-10-10 00:32:17.054564 INFO::Found  10  batches.
2025-10-10 00:32:18.629165 INFO::Set up parallel execution backend with 2 workers
2025-10-10 00:32:18.63057 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-10 00:32:20.491621 INFO::Adjusting the last 2 batches sequentially
2025-10-10 00:32:20.49416 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-10 00:32:20.539745 INFO::Done
2025-10-10 00:32:20.541081 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:20.553872 INFO::ASW Batch was 0.510324757586946 prior to batch effect correction and is now 0.510324757586946 .
2025-10-10 00:32:20.555213 INFO::ASW Label was 0.317499399794672 prior to batch effect correction and is now 0.317499399794672 .
2025-10-10 00:32:20.556829 INFO::Total function execution time is  3.6089141368866  s and adjustment time is  3.48566794395447 s ( 96.58 )
2025-10-10 00:32:21.018918 INFO::Formatting Data.
2025-10-10 00:32:21.020748 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:21.024069 INFO::Removing potential empty rows and columns
2025-10-10 00:32:21.027123 INFO::Found  0  missing values.
2025-10-10 00:32:21.037854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:21.03935 INFO::Done
2025-10-10 00:32:21.040727 INFO::Acquiring quality metrics before batch effect correction.
2025-10-10 00:32:21.047722 INFO::Starting hierarchical adjustment
2025-10-10 00:32:21.049599 INFO::Found  3  batches.
2025-10-10 00:32:21.050955 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-10 00:32:21.052471 INFO::Using default BPPARAM
2025-10-10 00:32:21.053828 INFO::Processing subtree level 1
2025-10-10 00:32:21.358188 INFO::Adjusting the last 1 batches sequentially
2025-10-10 00:32:21.372002 INFO::Done
2025-10-10 00:32:21.374622 INFO::Acquiring quality metrics after batch effect correction.
2025-10-10 00:32:21.388578 INFO::ASW Batch was 0.266645341961298 prior to batch effect correction and is now -0.12892611649431 .
2025-10-10 00:32:21.391174 INFO::ASW Label was -0.228093322819888 prior to batch effect correction and is now 0.0067404181437111 .
2025-10-10 00:32:21.397457 INFO::Total function execution time is  0.377564907073975  s and adjustment time is  0.322735071182251 s ( 85.48 )
2025-10-10 00:32:21.737242 INFO::Formatting Data.
2025-10-10 00:32:21.739095 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:21.741589 INFO::Removing potential empty rows and columns
2025-10-10 00:32:21.745174 INFO::Found  2  missing values.
2025-10-10 00:32:21.754357 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:21.756231 INFO::Done
2025-10-10 00:32:21.844138 INFO::Found NA in Reference column
2025-10-10 00:32:21.878331 INFO::Require at least two references per batch.
2025-10-10 00:32:21.942026 INFO::Formatting Data.
2025-10-10 00:32:21.943611 INFO::Recognized SummarizedExperiment
2025-10-10 00:32:21.944966 INFO::Typecasting input to dataframe.
2025-10-10 00:32:21.975337 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:21.978067 INFO::Removing potential empty rows and columns
2025-10-10 00:32:21.989807 INFO::Found  0  missing values.
2025-10-10 00:32:22.013035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.0178 INFO::Done
2025-10-10 00:32:22.065224 INFO::Formatting Data.
2025-10-10 00:32:22.066861 INFO::Recognized SummarizedExperiment
2025-10-10 00:32:22.068256 INFO::Typecasting input to dataframe.
2025-10-10 00:32:22.121266 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:22.124732 INFO::Removing potential empty rows and columns
2025-10-10 00:32:22.137243 INFO::Found  0  missing values.
2025-10-10 00:32:22.177807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.179204 INFO::Done
2025-10-10 00:32:22.223341 INFO::Formatting Data.
2025-10-10 00:32:22.224847 INFO::Recognized SummarizedExperiment
2025-10-10 00:32:22.226101 INFO::Typecasting input to dataframe.
2025-10-10 00:32:22.272878 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:22.275115 INFO::Removing potential empty rows and columns
2025-10-10 00:32:22.277885 INFO::Found  0  missing values.
2025-10-10 00:32:22.281741 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.
2025-10-10 00:32:22.295227 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.297602 INFO::Done
2025-10-10 00:32:22.32616 INFO::Formatting Data.
2025-10-10 00:32:22.327938 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:22.330096 INFO::Removing potential empty rows and columns
2025-10-10 00:32:22.332643 INFO::Found  0  missing values.
2025-10-10 00:32:22.340868 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.342402 INFO::Done
2025-10-10 00:32:22.372728 INFO::Formatting Data.
2025-10-10 00:32:22.37453 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:22.377155 INFO::Removing potential empty rows and columns
2025-10-10 00:32:22.380134 INFO::Found  0  missing values.
2025-10-10 00:32:22.388478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.390056 INFO::Done
2025-10-10 00:32:22.484938 INFO::Formatting Data.
2025-10-10 00:32:22.486878 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:22.489308 INFO::Removing potential empty rows and columns
2025-10-10 00:32:22.492662 INFO::Found  1  missing values.
2025-10-10 00:32:22.500645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.502256 INFO::Done
2025-10-10 00:32:22.562707 INFO::Formatting Data.
2025-10-10 00:32:22.564762 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:22.567063 INFO::Removing potential empty rows and columns
2025-10-10 00:32:22.569645 INFO::Found  2  missing values.
2025-10-10 00:32:22.57231 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.
2025-10-10 00:32:22.582559 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.584211 INFO::Done
2025-10-10 00:32:22.616217 INFO::Formatting Data.
2025-10-10 00:32:22.618223 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:22.620826 INFO::Removing potential empty rows and columns
2025-10-10 00:32:22.623544 INFO::Found  2  missing values.
2025-10-10 00:32:22.62807 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.62981 INFO::Done
2025-10-10 00:32:22.663014 INFO::Formatting Data.
2025-10-10 00:32:22.665884 INFO::Typecasting input to dataframe.
2025-10-10 00:32:22.668283 INFO::Replacing NaNs with NAs.
2025-10-10 00:32:22.670757 INFO::Removing potential empty rows and columns
2025-10-10 00:32:22.673903 INFO::Found  0  missing values.
2025-10-10 00:32:22.683431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-10 00:32:22.685058 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 35.734   7.132  45.262

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT45.322 2.69635.450
compute_asw0.0560.0030.060
count_existing0.0280.0010.029
generate_data_covariables0.0270.0020.030
generate_dataset0.0250.0030.033