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

This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 162/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.5.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 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 kjohnson3

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: /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_1.5.0.tar.gz
StartedAt: 2025-08-08 18:16:46 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 18:17:16 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 30.4 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 9.671  0.396   6.894
* 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-arm64/Resources/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-08-08 18:17:09.023184 INFO::Formatting Data.
2025-08-08 18:17:09.024644 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:09.028539 INFO::Removing potential empty rows and columns
2025-08-08 18:17:09.129123 INFO::Found  0  missing values.
2025-08-08 18:17:09.130438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:09.130668 INFO::Done
2025-08-08 18:17:09.130862 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:09.136722 INFO::Starting hierarchical adjustment
2025-08-08 18:17:09.137099 INFO::Found  3  batches.
2025-08-08 18:17:09.137307 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:09.137736 INFO::Using default BPPARAM
2025-08-08 18:17:09.137928 INFO::Processing subtree level 1
2025-08-08 18:17:09.191514 INFO::Adjusting the last 1 batches sequentially
2025-08-08 18:17:09.192966 INFO::Done
2025-08-08 18:17:09.193737 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:09.195521 INFO::ASW Batch was -0.0911865939391904 prior to batch effect correction and is now -0.0911865939391904 .
2025-08-08 18:17:09.196063 INFO::Total function execution time is  0.173130035400391  s and adjustment time is  0.0559380054473877 s ( 32.31 )
2025-08-08 18:17:09.204823 INFO::Formatting Data.
2025-08-08 18:17:09.205092 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:09.205406 INFO::Removing potential empty rows and columns
2025-08-08 18:17:09.205839 INFO::Found  0  missing values.
2025-08-08 18:17:09.206169 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.
2025-08-08 18:17:09.210375 INFO::Formatting Data.
2025-08-08 18:17:09.210631 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:09.210932 INFO::Removing potential empty rows and columns
2025-08-08 18:17:09.211306 INFO::Found  0  missing values.
2025-08-08 18:17:09.211626 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.
2025-08-08 18:17:09.217473 INFO::Formatting Data.
2025-08-08 18:17:09.217722 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:09.218021 INFO::Removing potential empty rows and columns
2025-08-08 18:17:09.218357 INFO::Found  0  missing values.
2025-08-08 18:17:09.218671 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.
2025-08-08 18:17:09.220128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:09.220325 INFO::Done
2025-08-08 18:17:09.220513 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:09.221277 INFO::Starting hierarchical adjustment
2025-08-08 18:17:09.221503 INFO::Found  2  batches.
2025-08-08 18:17:09.221717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:09.221995 INFO::Using default BPPARAM
2025-08-08 18:17:09.222186 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:09.222504 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-08 18:17:09.233758 INFO::Done
2025-08-08 18:17:09.234031 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:09.234754 INFO::ASW Batch was -0.0214848729563446 prior to batch effect correction and is now -0.10261136935066 .
2025-08-08 18:17:09.235027 INFO::Total function execution time is  0.0175650119781494  s and adjustment time is  0.0122749805450439 s ( 69.88 )
2025-08-08 18:17:09.236094 INFO::Formatting Data.
2025-08-08 18:17:09.236316 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:09.239431 INFO::Formatting Data.
2025-08-08 18:17:09.239672 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:09.239968 INFO::Removing potential empty rows and columns
2025-08-08 18:17:09.240311 INFO::Found  0  missing values.
2025-08-08 18:17:09.241244 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:09.241416 INFO::Done
2025-08-08 18:17:09.241602 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:09.242295 INFO::Starting hierarchical adjustment
2025-08-08 18:17:09.242537 INFO::Found  2  batches.
2025-08-08 18:17:09.24281 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:09.243117 INFO::Using default BPPARAM
2025-08-08 18:17:09.243322 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:09.243667 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-08 18:17:09.272252 INFO::Done
2025-08-08 18:17:09.272522 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:09.273242 INFO::ASW Batch was 0.0754462434373444 prior to batch effect correction and is now -0.117563501973463 .
2025-08-08 18:17:09.273514 INFO::Total function execution time is  0.034080982208252  s and adjustment time is  0.0297620296478271 s ( 87.33 )
2025-08-08 18:17:09.273848 INFO::Formatting Data.
2025-08-08 18:17:09.274033 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:09.27433 INFO::Removing potential empty rows and columns
2025-08-08 18:17:09.274661 INFO::Found  0  missing values.
2025-08-08 18:17:09.275557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:09.275722 INFO::Done
2025-08-08 18:17:09.275881 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:09.276527 INFO::Starting hierarchical adjustment
2025-08-08 18:17:09.276744 INFO::Found  2  batches.
2025-08-08 18:17:09.276913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:09.277115 INFO::Using default BPPARAM
2025-08-08 18:17:09.277292 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:09.277584 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-08 18:17:09.282808 INFO::Done
2025-08-08 18:17:09.28301 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:09.283668 INFO::ASW Batch was 0.0754462434373444 prior to batch effect correction and is now -0.117563501973463 .
2025-08-08 18:17:09.283933 INFO::Total function execution time is  0.0100760459899902  s and adjustment time is  0.00610184669494629 s ( 60.56 )
2025-08-08 18:17:10.459183 INFO::Formatting Data.
2025-08-08 18:17:10.459493 INFO::Recognized SummarizedExperiment
2025-08-08 18:17:10.459674 INFO::Typecasting input to dataframe.
2025-08-08 18:17:10.470218 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:10.470619 INFO::Removing potential empty rows and columns
2025-08-08 18:17:10.471777 INFO::Found  0  missing values.
2025-08-08 18:17:10.473898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:10.474104 INFO::Done
2025-08-08 18:17:10.474265 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:10.47547 INFO::Starting hierarchical adjustment
2025-08-08 18:17:10.475686 INFO::Found  2  batches.
2025-08-08 18:17:10.475837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:10.47614 INFO::Using default BPPARAM
2025-08-08 18:17:10.476292 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:10.476574 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-08 18:17:10.493619 INFO::Done
2025-08-08 18:17:10.493855 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:10.495034 INFO::ASW Batch was -0.0199471959103296 prior to batch effect correction and is now -0.0992534940982004 .
2025-08-08 18:17:10.495284 INFO::Total function execution time is  0.0362100601196289  s and adjustment time is  0.017970085144043 s ( 49.63 )
2025-08-08 18:17:10.511047 INFO::Formatting Data.
2025-08-08 18:17:10.511311 INFO::Recognized SummarizedExperiment
2025-08-08 18:17:10.511481 INFO::Typecasting input to dataframe.
2025-08-08 18:17:10.514461 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:10.514835 INFO::Removing potential empty rows and columns
2025-08-08 18:17:10.515975 INFO::Found  0  missing values.
2025-08-08 18:17:10.518068 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:10.518277 INFO::Done
2025-08-08 18:17:10.518432 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:10.519624 INFO::Starting hierarchical adjustment
2025-08-08 18:17:10.519841 INFO::Found  2  batches.
2025-08-08 18:17:10.519992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:10.520167 INFO::Using default BPPARAM
2025-08-08 18:17:10.520305 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:10.520588 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-08 18:17:10.528359 INFO::Done
2025-08-08 18:17:10.528577 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:10.529729 INFO::ASW Batch was 0.0142048124358971 prior to batch effect correction and is now 0.0142048124358971 .
2025-08-08 18:17:10.52999 INFO::Total function execution time is  0.0189549922943115  s and adjustment time is  0.00854897499084473 s ( 45.1 )
2025-08-08 18:17:10.536275 INFO::Formatting Data.
2025-08-08 18:17:10.536512 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:10.536787 INFO::Removing potential empty rows and columns
2025-08-08 18:17:10.537099 INFO::Found  0  missing values.
2025-08-08 18:17:10.537925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:10.538091 INFO::Done
2025-08-08 18:17:10.538246 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:10.538835 INFO::Starting hierarchical adjustment
2025-08-08 18:17:10.539046 INFO::Found  3  batches.
2025-08-08 18:17:10.539192 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:10.539369 INFO::Using default BPPARAM
2025-08-08 18:17:10.539512 INFO::Processing subtree level 1
2025-08-08 18:17:10.596192 INFO::Adjusting the last 1 batches sequentially
2025-08-08 18:17:10.597474 INFO::Done
2025-08-08 18:17:10.597741 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:10.599757 INFO::ASW Batch was -0.0656766200460145 prior to batch effect correction and is now -0.159388217776751 .
2025-08-08 18:17:10.600665 INFO::Total function execution time is  0.0643689632415771  s and adjustment time is  0.0584771633148193 s ( 90.85 )
2025-08-08 18:17:10.60778 INFO::Skipping initial DF formatting
2025-08-08 18:17:10.608036 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:10.609478 INFO::Starting hierarchical adjustment
2025-08-08 18:17:10.609731 INFO::Found  5  batches.
2025-08-08 18:17:10.609907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:10.610125 INFO::Using default BPPARAM
2025-08-08 18:17:10.610289 INFO::Processing subtree level 1
2025-08-08 18:17:10.710104 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:10.715218 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-08 18:17:10.724212 INFO::Done
2025-08-08 18:17:10.724735 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:10.761165 INFO::ASW Batch was 0.498226808417275 prior to batch effect correction and is now 0.498226808417275 .
2025-08-08 18:17:10.761456 INFO::ASW Label was 0.363330665545483 prior to batch effect correction and is now 0.363330665545483 .
2025-08-08 18:17:10.762027 INFO::Total function execution time is  0.154125928878784  s and adjustment time is  0.114526033401489 s ( 74.31 )
2025-08-08 18:17:10.769279 INFO::Formatting Data.
2025-08-08 18:17:10.769528 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:10.769833 INFO::Removing potential empty rows and columns
2025-08-08 18:17:10.770196 INFO::Found  0  missing values.
2025-08-08 18:17:10.771777 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:10.771978 INFO::Done
2025-08-08 18:17:10.772257 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:10.773479 INFO::Starting hierarchical adjustment
2025-08-08 18:17:10.773859 INFO::Found  5  batches.
2025-08-08 18:17:10.774042 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:10.774289 INFO::Using default BPPARAM
2025-08-08 18:17:10.774465 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.

2025-08-08 18:17:10.856242 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:10.858116 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-08 18:17:10.868435 INFO::Done
2025-08-08 18:17:10.868813 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:10.870731 INFO::ASW Batch was 0.484699781399638 prior to batch effect correction and is now -0.00407786415045454 .
2025-08-08 18:17:10.871091 INFO::ASW Label was 0.38035346424044 prior to batch effect correction and is now 0.694609232416613 .
2025-08-08 18:17:10.871556 INFO::Total function execution time is  0.102275133132935  s and adjustment time is  0.0946590900421143 s ( 92.55 )
2025-08-08 18:17:10.872 INFO::Formatting Data.
2025-08-08 18:17:10.872329 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:10.872788 INFO::Removing potential empty rows and columns
2025-08-08 18:17:10.873324 INFO::Found  0  missing values.
2025-08-08 18:17:10.875132 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:10.875365 INFO::Done
2025-08-08 18:17:10.875612 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:10.876839 INFO::Starting hierarchical adjustment
2025-08-08 18:17:10.877279 INFO::Found  5  batches.
2025-08-08 18:17:10.877495 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:10.877787 INFO::Using default BPPARAM
2025-08-08 18:17:10.878002 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.

2025-08-08 18:17:10.940335 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:10.941771 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-08 18:17:10.951719 INFO::Done
2025-08-08 18:17:10.952064 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:10.953901 INFO::ASW Batch was 0.484699781399638 prior to batch effect correction and is now -0.00407786415045454 .
2025-08-08 18:17:10.954144 INFO::ASW Label was 0.38035346424044 prior to batch effect correction and is now 0.694609232416613 .
2025-08-08 18:17:10.95464 INFO::Total function execution time is  0.0826139450073242  s and adjustment time is  0.0746269226074219 s ( 90.33 )
2025-08-08 18:17:10.962585 INFO::Formatting Data.
2025-08-08 18:17:10.962849 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:10.963184 INFO::Removing potential empty rows and columns
2025-08-08 18:17:10.96354 INFO::Found  0  missing values.
2025-08-08 18:17:10.964919 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:10.965104 INFO::Done
2025-08-08 18:17:10.965274 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:10.966356 INFO::Starting hierarchical adjustment
2025-08-08 18:17:10.966598 INFO::Found  5  batches.
2025-08-08 18:17:10.96676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:10.966995 INFO::Using default BPPARAM
2025-08-08 18:17:10.967336 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.

2025-08-08 18:17:11.018116 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:11.019349 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-08 18:17:11.02746 INFO::Done
2025-08-08 18:17:11.027762 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.029186 INFO::ASW Batch was 0.375108034228136 prior to batch effect correction and is now -0.0258208528193616 .
2025-08-08 18:17:11.029396 INFO::ASW Label was 0.508729525641939 prior to batch effect correction and is now 0.691649962267798 .
2025-08-08 18:17:11.029929 INFO::Total function execution time is  0.0672440528869629  s and adjustment time is  0.0609090328216553 s ( 90.58 )
2025-08-08 18:17:11.030223 INFO::Formatting Data.
2025-08-08 18:17:11.030416 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.030703 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.031036 INFO::Found  0  missing values.
2025-08-08 18:17:11.032324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.032503 INFO::Done
2025-08-08 18:17:11.032673 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.033617 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.033865 INFO::Found  5  batches.
2025-08-08 18:17:11.034042 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.034277 INFO::Using default BPPARAM
2025-08-08 18:17:11.034579 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.

2025-08-08 18:17:11.086164 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:11.087439 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-08 18:17:11.097137 INFO::Done
2025-08-08 18:17:11.097867 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.09951 INFO::ASW Batch was 0.375108034228136 prior to batch effect correction and is now -0.0258208528193616 .
2025-08-08 18:17:11.099716 INFO::ASW Label was 0.508729525641939 prior to batch effect correction and is now 0.691649962267798 .
2025-08-08 18:17:11.100276 INFO::Total function execution time is  0.070019006729126  s and adjustment time is  0.0632519721984863 s ( 90.34 )
2025-08-08 18:17:11.106265 INFO::Formatting Data.
2025-08-08 18:17:11.106519 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.106827 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.107155 INFO::Found  0  missing values.
2025-08-08 18:17:11.107998 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.108172 INFO::Done
2025-08-08 18:17:11.108337 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.109256 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.109475 INFO::Found  2  batches.
2025-08-08 18:17:11.109637 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.109843 INFO::Using default BPPARAM
2025-08-08 18:17:11.110004 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:11.110265 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-08 18:17:11.114947 INFO::Done
2025-08-08 18:17:11.115125 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.115989 INFO::ASW Batch was 0.323857690842417 prior to batch effect correction and is now 0.00177874968880474 .
2025-08-08 18:17:11.116165 INFO::ASW Label was 0.659960078789625 prior to batch effect correction and is now 0.91892088368425 .
2025-08-08 18:17:11.116389 INFO::Total function execution time is  0.0101568698883057  s and adjustment time is  0.00551486015319824 s ( 54.3 )
2025-08-08 18:17:11.116609 INFO::Formatting Data.
2025-08-08 18:17:11.116775 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.117015 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.11729 INFO::Found  0  missing values.
2025-08-08 18:17:11.118086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.118239 INFO::Done
2025-08-08 18:17:11.118384 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.119185 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.119516 INFO::Found  2  batches.
2025-08-08 18:17:11.119659 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.119831 INFO::Using default BPPARAM
2025-08-08 18:17:11.119977 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:11.120211 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-08 18:17:11.124529 INFO::Done
2025-08-08 18:17:11.124713 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.125579 INFO::ASW Batch was 0.323857690842417 prior to batch effect correction and is now 0.00177874968880474 .
2025-08-08 18:17:11.125737 INFO::ASW Label was 0.659960078789625 prior to batch effect correction and is now 0.91892088368425 .
2025-08-08 18:17:11.125967 INFO::Total function execution time is  0.00935220718383789  s and adjustment time is  0.00505208969116211 s ( 54.02 )
2025-08-08 18:17:11.130088 INFO::Formatting Data.
2025-08-08 18:17:11.130297 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.13057 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.13086 INFO::Found  0  missing values.
2025-08-08 18:17:11.131467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.13162 INFO::Done
2025-08-08 18:17:11.131767 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.132305 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.13251 INFO::Found  2  batches.
2025-08-08 18:17:11.132664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.132832 INFO::Using default BPPARAM
2025-08-08 18:17:11.132986 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:11.133245 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-08 18:17:11.144167 INFO::Done
2025-08-08 18:17:11.144398 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.145055 INFO::ASW Batch was -0.0865711540250348 prior to batch effect correction and is now -0.157587588807162 .
2025-08-08 18:17:11.145345 INFO::Total function execution time is  0.015265941619873  s and adjustment time is  0.011685848236084 s ( 76.55 )
2025-08-08 18:17:11.150521 INFO::Formatting Data.
2025-08-08 18:17:11.150734 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.150994 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.151292 INFO::Found  0  missing values.
2025-08-08 18:17:11.15168 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.
2025-08-08 18:17:11.153016 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.153193 INFO::Done
2025-08-08 18:17:11.153344 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.154187 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.154386 INFO::Found  2  batches.
2025-08-08 18:17:11.154537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.154707 INFO::Using default BPPARAM
2025-08-08 18:17:11.154852 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:11.155104 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-08 18:17:11.160108 INFO::Done
2025-08-08 18:17:11.1603 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.161151 INFO::ASW Batch was 0.878996607891111 prior to batch effect correction and is now 0.000148347827486245 .
2025-08-08 18:17:11.161317 INFO::ASW Label was 0.0858137640373267 prior to batch effect correction and is now 0.675989759172987 .
2025-08-08 18:17:11.161539 INFO::Total function execution time is  0.0110340118408203  s and adjustment time is  0.00575494766235352 s ( 52.16 )
2025-08-08 18:17:11.161762 INFO::Formatting Data.
2025-08-08 18:17:11.161932 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.162186 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.162462 INFO::Found  0  missing values.
2025-08-08 18:17:11.162709 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.
2025-08-08 18:17:11.163929 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.164096 INFO::Done
2025-08-08 18:17:11.164246 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.165047 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.16525 INFO::Found  2  batches.
2025-08-08 18:17:11.165395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.165566 INFO::Using default BPPARAM
2025-08-08 18:17:11.165714 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:11.165965 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-08 18:17:11.170784 INFO::Done
2025-08-08 18:17:11.170977 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.171822 INFO::ASW Batch was 0.878996607891111 prior to batch effect correction and is now 0.000148347827486245 .
2025-08-08 18:17:11.171997 INFO::ASW Label was 0.0858137640373267 prior to batch effect correction and is now 0.675989759172987 .
2025-08-08 18:17:11.172231 INFO::Total function execution time is  0.0104601383209229  s and adjustment time is  0.00557303428649902 s ( 53.28 )
2025-08-08 18:17:11.23626 INFO::Formatting Data.
2025-08-08 18:17:11.236508 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.23679 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.237104 INFO::Found  0  missing values.
2025-08-08 18:17:11.237972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.238139 INFO::Done
2025-08-08 18:17:11.238303 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.238931 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.239138 INFO::Found  3  batches.
2025-08-08 18:17:11.239279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.239457 INFO::Using default BPPARAM
2025-08-08 18:17:11.2396 INFO::Processing subtree level 1
2025-08-08 18:17:11.281528 INFO::Adjusting the last 1 batches sequentially
2025-08-08 18:17:11.282633 INFO::Done
2025-08-08 18:17:11.283041 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.284965 INFO::ASW Batch was -0.116018442551123 prior to batch effect correction and is now -0.116018442551123 .
2025-08-08 18:17:11.285662 INFO::Total function execution time is  0.0494289398193359  s and adjustment time is  0.0435349941253662 s ( 88.08 )
2025-08-08 18:17:11.286207 INFO::Formatting Data.
2025-08-08 18:17:11.286388 INFO::Typecasting input to dataframe.
2025-08-08 18:17:11.286599 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.286881 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.28723 INFO::Found  0  missing values.
2025-08-08 18:17:11.288098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.28826 INFO::Done
2025-08-08 18:17:11.288415 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.288992 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.2892 INFO::Found  3  batches.
2025-08-08 18:17:11.289356 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.289557 INFO::Using default BPPARAM
2025-08-08 18:17:11.289707 INFO::Processing subtree level 1
2025-08-08 18:17:11.325796 INFO::Adjusting the last 1 batches sequentially
2025-08-08 18:17:11.326999 INFO::Done
2025-08-08 18:17:11.327208 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.32916 INFO::ASW Batch was -0.116018442551123 prior to batch effect correction and is now -0.116018442551123 .
2025-08-08 18:17:11.330021 INFO::Total function execution time is  0.0439579486846924  s and adjustment time is  0.037837028503418 s ( 86.08 )
2025-08-08 18:17:11.33679 INFO::Formatting Data.
2025-08-08 18:17:11.337053 INFO::Typecasting input to dataframe.
2025-08-08 18:17:11.337321 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.33763 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.338027 INFO::Found  0  missing values.
2025-08-08 18:17:11.338937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.339111 INFO::Done
2025-08-08 18:17:11.33927 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.339959 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.340171 INFO::Found  3  batches.
2025-08-08 18:17:11.340332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.340558 INFO::Using default BPPARAM
2025-08-08 18:17:11.340717 INFO::Processing subtree level 1
2025-08-08 18:17:11.378931 INFO::Adjusting the last 1 batches sequentially
2025-08-08 18:17:11.380027 INFO::Done
2025-08-08 18:17:11.380232 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.382055 INFO::ASW Batch was 0.0300466290382846 prior to batch effect correction and is now 0.0300466290382846 .
2025-08-08 18:17:11.38273 INFO::Total function execution time is  0.0461370944976807  s and adjustment time is  0.0399022102355957 s ( 86.49 )
2025-08-08 18:17:11.446583 INFO::Formatting Data.
2025-08-08 18:17:11.446839 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.447219 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.44812 INFO::Found  1000  missing values.
2025-08-08 18:17:11.453772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.453984 INFO::Done
2025-08-08 18:17:11.454154 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.456094 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.456328 INFO::Found  10  batches.
2025-08-08 18:17:11.456494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:11.456722 INFO::Using default BPPARAM
2025-08-08 18:17:11.456879 INFO::Processing subtree level 1
2025-08-08 18:17:11.521793 INFO::Processing subtree level 2
2025-08-08 18:17:11.585423 INFO::Adjusting the last 1 batches sequentially
2025-08-08 18:17:11.587224 INFO::Done
2025-08-08 18:17:11.58745 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:11.590692 INFO::ASW Batch was 0.484269377373541 prior to batch effect correction and is now 0.484269377373541 .
2025-08-08 18:17:11.591112 INFO::ASW Label was 0.333338800151016 prior to batch effect correction and is now 0.333338800151016 .
2025-08-08 18:17:11.591954 INFO::Total function execution time is  0.145334005355835  s and adjustment time is  0.130807876586914 s ( 90.01 )
2025-08-08 18:17:11.592307 INFO::Formatting Data.
2025-08-08 18:17:11.592512 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:11.593006 INFO::Removing potential empty rows and columns
2025-08-08 18:17:11.594075 INFO::Found  1000  missing values.
2025-08-08 18:17:11.599824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:11.600068 INFO::Done
2025-08-08 18:17:11.600254 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:11.602249 INFO::Starting hierarchical adjustment
2025-08-08 18:17:11.602521 INFO::Found  10  batches.
2025-08-08 18:17:12.054546 INFO::Set up parallel execution backend with 2 workers
2025-08-08 18:17:12.05484 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-08 18:17:12.538626 INFO::Adjusting the last 2 batches sequentially
2025-08-08 18:17:12.539208 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-08 18:17:12.544674 INFO::Done
2025-08-08 18:17:12.544878 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:12.546752 INFO::ASW Batch was 0.484269377373541 prior to batch effect correction and is now 0.484269377373541 .
2025-08-08 18:17:12.546919 INFO::ASW Label was 0.333338800151016 prior to batch effect correction and is now 0.333338800151016 .
2025-08-08 18:17:12.54715 INFO::Total function execution time is  0.954848051071167  s and adjustment time is  0.942214012145996 s ( 98.68 )
2025-08-08 18:17:12.620005 INFO::Formatting Data.
2025-08-08 18:17:12.620365 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.6208 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.621731 INFO::Found  0  missing values.
2025-08-08 18:17:12.623513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.623863 INFO::Done
2025-08-08 18:17:12.624222 INFO::Acquiring quality metrics before batch effect correction.
2025-08-08 18:17:12.626239 INFO::Starting hierarchical adjustment
2025-08-08 18:17:12.626985 INFO::Found  3  batches.
2025-08-08 18:17:12.627308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-08 18:17:12.627874 INFO::Using default BPPARAM
2025-08-08 18:17:12.628209 INFO::Processing subtree level 1
2025-08-08 18:17:12.686512 INFO::Adjusting the last 1 batches sequentially
2025-08-08 18:17:12.687869 INFO::Done
2025-08-08 18:17:12.688105 INFO::Acquiring quality metrics after batch effect correction.
2025-08-08 18:17:12.690413 INFO::ASW Batch was 0.18549953092305 prior to batch effect correction and is now -0.108999777128199 .
2025-08-08 18:17:12.690636 INFO::ASW Label was -0.154596307520024 prior to batch effect correction and is now 0.0214572256352693 .
2025-08-08 18:17:12.691581 INFO::Total function execution time is  0.0715129375457764  s and adjustment time is  0.0610330104827881 s ( 85.35 )
2025-08-08 18:17:12.739561 INFO::Formatting Data.
2025-08-08 18:17:12.739959 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.740364 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.740883 INFO::Found  2  missing values.
2025-08-08 18:17:12.742067 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.742274 INFO::Done
2025-08-08 18:17:12.752067 INFO::Found NA in Reference column
2025-08-08 18:17:12.755349 INFO::Require at least two references per batch.
2025-08-08 18:17:12.763104 INFO::Formatting Data.
2025-08-08 18:17:12.763346 INFO::Recognized SummarizedExperiment
2025-08-08 18:17:12.763513 INFO::Typecasting input to dataframe.
2025-08-08 18:17:12.767111 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.767475 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.76865 INFO::Found  0  missing values.
2025-08-08 18:17:12.770888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.771074 INFO::Done
2025-08-08 18:17:12.776457 INFO::Formatting Data.
2025-08-08 18:17:12.776694 INFO::Recognized SummarizedExperiment
2025-08-08 18:17:12.77688 INFO::Typecasting input to dataframe.
2025-08-08 18:17:12.782567 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.782974 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.784212 INFO::Found  0  missing values.
2025-08-08 18:17:12.787941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.78813 INFO::Done
2025-08-08 18:17:12.793679 INFO::Formatting Data.
2025-08-08 18:17:12.793914 INFO::Recognized SummarizedExperiment
2025-08-08 18:17:12.79408 INFO::Typecasting input to dataframe.
2025-08-08 18:17:12.799229 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.799543 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.799887 INFO::Found  0  missing values.
2025-08-08 18:17:12.800173 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.
2025-08-08 18:17:12.801557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.80173 INFO::Done
2025-08-08 18:17:12.805736 INFO::Formatting Data.
2025-08-08 18:17:12.805964 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.806242 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.806558 INFO::Found  0  missing values.
2025-08-08 18:17:12.807452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.807613 INFO::Done
2025-08-08 18:17:12.811619 INFO::Formatting Data.
2025-08-08 18:17:12.811834 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.812082 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.812416 INFO::Found  0  missing values.
2025-08-08 18:17:12.813365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.813548 INFO::Done
2025-08-08 18:17:12.825836 INFO::Formatting Data.
2025-08-08 18:17:12.826163 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.826564 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.82709 INFO::Found  1  missing values.
2025-08-08 18:17:12.828323 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.828536 INFO::Done
2025-08-08 18:17:12.836581 INFO::Formatting Data.
2025-08-08 18:17:12.836863 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.837156 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.837464 INFO::Found  2  missing values.
2025-08-08 18:17:12.837748 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.
2025-08-08 18:17:12.838458 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.838649 INFO::Done
2025-08-08 18:17:12.842539 INFO::Formatting Data.
2025-08-08 18:17:12.842759 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.843011 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.843283 INFO::Found  2  missing values.
2025-08-08 18:17:12.843757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.843921 INFO::Done
2025-08-08 18:17:12.847772 INFO::Formatting Data.
2025-08-08 18:17:12.847981 INFO::Typecasting input to dataframe.
2025-08-08 18:17:12.848218 INFO::Replacing NaNs with NAs.
2025-08-08 18:17:12.848464 INFO::Removing potential empty rows and columns
2025-08-08 18:17:12.84876 INFO::Found  0  missing values.
2025-08-08 18:17:12.849587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-08 18:17:12.849742 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
  6.619   1.545   8.358 

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT9.6710.3966.894
compute_asw0.0100.0010.011
count_existing0.0060.0010.006
generate_data_covariables0.0050.0000.006
generate_dataset0.0040.0000.005