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This page was generated on 2025-10-16 11:37 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 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: 2025-10-13 13:40 -0400 (Mon, 13 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 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.4.0.tar.gz
StartedAt: 2025-10-15 21:06:34 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 21:08:04 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 90.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 25.746  1.794  18.902
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-10-15 21:07:28.139831 INFO::Formatting Data.
2025-10-15 21:07:28.141385 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:28.153637 INFO::Removing potential empty rows and columns
2025-10-15 21:07:28.410339 INFO::Found  0  missing values.
2025-10-15 21:07:28.41408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:28.414802 INFO::Done
2025-10-15 21:07:28.415391 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:28.427476 INFO::Starting hierarchical adjustment
2025-10-15 21:07:28.428404 INFO::Found  3  batches.
2025-10-15 21:07:28.428991 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:28.430162 INFO::Using default BPPARAM
2025-10-15 21:07:28.430782 INFO::Processing subtree level 1
2025-10-15 21:07:28.535523 INFO::Adjusting the last 1 batches sequentially
2025-10-15 21:07:28.537741 INFO::Done
2025-10-15 21:07:28.538478 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:28.54133 INFO::ASW Batch was -0.0853361392466832 prior to batch effect correction and is now -0.0853361392466832 .
2025-10-15 21:07:28.542563 INFO::Total function execution time is  0.403481721878052  s and adjustment time is  0.109466552734375 s ( 27.13 )
2025-10-15 21:07:28.556767 INFO::Formatting Data.
2025-10-15 21:07:28.557593 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:28.55856 INFO::Removing potential empty rows and columns
2025-10-15 21:07:28.559791 INFO::Found  0  missing values.
2025-10-15 21:07:28.560844 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.
2025-10-15 21:07:28.572828 INFO::Formatting Data.
2025-10-15 21:07:28.573565 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:28.574476 INFO::Removing potential empty rows and columns
2025-10-15 21:07:28.575513 INFO::Found  0  missing values.
2025-10-15 21:07:28.576465 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.
2025-10-15 21:07:28.592219 INFO::Formatting Data.
2025-10-15 21:07:28.592968 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:28.593843 INFO::Removing potential empty rows and columns
2025-10-15 21:07:28.59487 INFO::Found  0  missing values.
2025-10-15 21:07:28.595774 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.
2025-10-15 21:07:28.600053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:28.600589 INFO::Done
2025-10-15 21:07:28.60112 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:28.603098 INFO::Starting hierarchical adjustment
2025-10-15 21:07:28.603796 INFO::Found  2  batches.
2025-10-15 21:07:28.60433 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:28.605015 INFO::Using default BPPARAM
2025-10-15 21:07:28.605562 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:28.606501 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-15 21:07:28.628553 INFO::Done
2025-10-15 21:07:28.629288 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:28.63139 INFO::ASW Batch was -0.0818020679431234 prior to batch effect correction and is now -0.129292678992886 .
2025-10-15 21:07:28.632228 INFO::Total function execution time is  0.0400586128234863  s and adjustment time is  0.0248749256134033 s ( 62.1 )
2025-10-15 21:07:28.634957 INFO::Formatting Data.
2025-10-15 21:07:28.635597 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:28.644419 INFO::Formatting Data.
2025-10-15 21:07:28.645161 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:28.667976 INFO::Removing potential empty rows and columns
2025-10-15 21:07:28.669096 INFO::Found  0  missing values.
2025-10-15 21:07:28.671688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:28.67223 INFO::Done
2025-10-15 21:07:28.672742 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:28.674662 INFO::Starting hierarchical adjustment
2025-10-15 21:07:28.675335 INFO::Found  2  batches.
2025-10-15 21:07:28.675848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:28.676435 INFO::Using default BPPARAM
2025-10-15 21:07:28.676941 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:28.677775 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-15 21:07:28.691045 INFO::Done
2025-10-15 21:07:28.691677 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:28.693529 INFO::ASW Batch was 0.093768754337511 prior to batch effect correction and is now -0.120157169263906 .
2025-10-15 21:07:28.694321 INFO::Total function execution time is  0.0499494075775146  s and adjustment time is  0.0158340930938721 s ( 31.7 )
2025-10-15 21:07:28.695289 INFO::Formatting Data.
2025-10-15 21:07:28.695857 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:28.696651 INFO::Removing potential empty rows and columns
2025-10-15 21:07:28.697579 INFO::Found  0  missing values.
2025-10-15 21:07:28.701191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:28.701779 INFO::Done
2025-10-15 21:07:28.702276 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:28.704171 INFO::Starting hierarchical adjustment
2025-10-15 21:07:28.704851 INFO::Found  2  batches.
2025-10-15 21:07:28.705345 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:28.70592 INFO::Using default BPPARAM
2025-10-15 21:07:28.706415 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:28.70728 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-15 21:07:28.72094 INFO::Done
2025-10-15 21:07:28.721587 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:28.723493 INFO::ASW Batch was 0.093768754337511 prior to batch effect correction and is now -0.120157169263906 .
2025-10-15 21:07:28.724236 INFO::Total function execution time is  0.0289430618286133  s and adjustment time is  0.0162112712860107 s ( 56.01 )
2025-10-15 21:07:31.769076 INFO::Formatting Data.
2025-10-15 21:07:31.76987 INFO::Recognized SummarizedExperiment
2025-10-15 21:07:31.770393 INFO::Typecasting input to dataframe.
2025-10-15 21:07:31.802102 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:31.803254 INFO::Removing potential empty rows and columns
2025-10-15 21:07:31.80645 INFO::Found  0  missing values.
2025-10-15 21:07:31.813502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:31.81412 INFO::Done
2025-10-15 21:07:31.814656 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:31.818222 INFO::Starting hierarchical adjustment
2025-10-15 21:07:31.818935 INFO::Found  2  batches.
2025-10-15 21:07:31.819455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:31.820529 INFO::Using default BPPARAM
2025-10-15 21:07:31.821088 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:31.82212 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-15 21:07:31.879122 INFO::Done
2025-10-15 21:07:31.879918 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:31.883638 INFO::ASW Batch was 0.0168189165885933 prior to batch effect correction and is now -0.0828871333565347 .
2025-10-15 21:07:31.884504 INFO::Total function execution time is  0.115715980529785  s and adjustment time is  0.0602996349334717 s ( 52.11 )
2025-10-15 21:07:31.90363 INFO::Formatting Data.
2025-10-15 21:07:31.904351 INFO::Recognized SummarizedExperiment
2025-10-15 21:07:31.904906 INFO::Typecasting input to dataframe.
2025-10-15 21:07:31.914445 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:31.9156 INFO::Removing potential empty rows and columns
2025-10-15 21:07:31.919436 INFO::Found  0  missing values.
2025-10-15 21:07:31.926558 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:31.927141 INFO::Done
2025-10-15 21:07:31.927711 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:31.931314 INFO::Starting hierarchical adjustment
2025-10-15 21:07:31.932042 INFO::Found  2  batches.
2025-10-15 21:07:31.932577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:31.93318 INFO::Using default BPPARAM
2025-10-15 21:07:31.93372 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:31.93472 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-15 21:07:31.960285 INFO::Done
2025-10-15 21:07:31.961031 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:31.964821 INFO::ASW Batch was -0.00140225985030536 prior to batch effect correction and is now -0.00140225985030536 .
2025-10-15 21:07:31.965682 INFO::Total function execution time is  0.0620353221893311  s and adjustment time is  0.0283479690551758 s ( 45.7 )
2025-10-15 21:07:31.983968 INFO::Formatting Data.
2025-10-15 21:07:31.984773 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:31.985714 INFO::Removing potential empty rows and columns
2025-10-15 21:07:31.986742 INFO::Found  0  missing values.
2025-10-15 21:07:31.989689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:31.990219 INFO::Done
2025-10-15 21:07:31.990746 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:31.992761 INFO::Starting hierarchical adjustment
2025-10-15 21:07:31.993456 INFO::Found  3  batches.
2025-10-15 21:07:31.994005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:31.994595 INFO::Using default BPPARAM
2025-10-15 21:07:31.995122 INFO::Processing subtree level 1
2025-10-15 21:07:32.260091 INFO::Adjusting the last 1 batches sequentially
2025-10-15 21:07:32.262009 INFO::Done
2025-10-15 21:07:32.26271 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:32.265241 INFO::ASW Batch was -0.066770375238349 prior to batch effect correction and is now -0.131224540119547 .
2025-10-15 21:07:32.266202 INFO::Total function execution time is  0.28226900100708  s and adjustment time is  0.26866602897644 s ( 95.18 )
2025-10-15 21:07:32.474147 INFO::Skipping initial DF formatting
2025-10-15 21:07:32.475008 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:32.479136 INFO::Starting hierarchical adjustment
2025-10-15 21:07:32.479988 INFO::Found  5  batches.
2025-10-15 21:07:32.480588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:32.481252 INFO::Using default BPPARAM
2025-10-15 21:07:32.481821 INFO::Processing subtree level 1
2025-10-15 21:07:32.666075 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:32.66854 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-15 21:07:32.693798 INFO::Done
2025-10-15 21:07:32.694582 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:32.699559 INFO::ASW Batch was 0.510901032556976 prior to batch effect correction and is now 0.510901032556976 .
2025-10-15 21:07:32.700334 INFO::ASW Label was 0.356456111119911 prior to batch effect correction and is now 0.356456111119911 .
2025-10-15 21:07:32.701392 INFO::Total function execution time is  0.227437973022461  s and adjustment time is  0.213966369628906 s ( 94.08 )
2025-10-15 21:07:32.722701 INFO::Formatting Data.
2025-10-15 21:07:32.723652 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:32.724783 INFO::Removing potential empty rows and columns
2025-10-15 21:07:32.725981 INFO::Found  0  missing values.
2025-10-15 21:07:32.73073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:32.731366 INFO::Done
2025-10-15 21:07:32.731979 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:32.735584 INFO::Starting hierarchical adjustment
2025-10-15 21:07:32.736547 INFO::Found  5  batches.
2025-10-15 21:07:32.737254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:32.737974 INFO::Using default BPPARAM
2025-10-15 21:07:32.738613 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.

2025-10-15 21:07:32.880054 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:32.881898 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-15 21:07:32.900639 INFO::Done
2025-10-15 21:07:32.901587 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:32.905412 INFO::ASW Batch was 0.393625869641963 prior to batch effect correction and is now -0.0585183118637373 .
2025-10-15 21:07:32.906172 INFO::ASW Label was 0.312538695693202 prior to batch effect correction and is now 0.79097202057538 .
2025-10-15 21:07:32.907181 INFO::Total function execution time is  0.184632301330566  s and adjustment time is  0.164243459701538 s ( 88.96 )
2025-10-15 21:07:32.908143 INFO::Formatting Data.
2025-10-15 21:07:32.908889 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:32.909883 INFO::Removing potential empty rows and columns
2025-10-15 21:07:32.910989 INFO::Found  0  missing values.
2025-10-15 21:07:32.915303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:32.91592 INFO::Done
2025-10-15 21:07:32.916534 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:32.919865 INFO::Starting hierarchical adjustment
2025-10-15 21:07:32.920641 INFO::Found  5  batches.
2025-10-15 21:07:32.921209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:32.921891 INFO::Using default BPPARAM
2025-10-15 21:07:32.922466 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.

2025-10-15 21:07:33.069324 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:33.071234 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-15 21:07:33.087594 INFO::Done
2025-10-15 21:07:33.088408 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.091908 INFO::ASW Batch was 0.393625869641963 prior to batch effect correction and is now -0.0585183118637373 .
2025-10-15 21:07:33.092563 INFO::ASW Label was 0.312538695693202 prior to batch effect correction and is now 0.79097202057538 .
2025-10-15 21:07:33.093435 INFO::Total function execution time is  0.185303211212158  s and adjustment time is  0.167094230651855 s ( 90.17 )
2025-10-15 21:07:33.107291 INFO::Formatting Data.
2025-10-15 21:07:33.108131 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.109103 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.110156 INFO::Found  0  missing values.
2025-10-15 21:07:33.114285 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.114883 INFO::Done
2025-10-15 21:07:33.115441 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.118515 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.119284 INFO::Found  5  batches.
2025-10-15 21:07:33.119861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.120533 INFO::Using default BPPARAM
2025-10-15 21:07:33.121119 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.

2025-10-15 21:07:33.251563 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:33.253325 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-15 21:07:33.270417 INFO::Done
2025-10-15 21:07:33.271318 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.275028 INFO::ASW Batch was 0.47649084592058 prior to batch effect correction and is now 0.0329564518908365 .
2025-10-15 21:07:33.275773 INFO::ASW Label was 0.375907104003623 prior to batch effect correction and is now 0.708222240346283 .
2025-10-15 21:07:33.276713 INFO::Total function execution time is  0.169438600540161  s and adjustment time is  0.151228666305542 s ( 89.25 )
2025-10-15 21:07:33.277642 INFO::Formatting Data.
2025-10-15 21:07:33.278314 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.279275 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.280347 INFO::Found  0  missing values.
2025-10-15 21:07:33.284613 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.285201 INFO::Done
2025-10-15 21:07:33.285754 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.288902 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.289613 INFO::Found  5  batches.
2025-10-15 21:07:33.290168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.290815 INFO::Using default BPPARAM
2025-10-15 21:07:33.291355 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.

2025-10-15 21:07:33.406382 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:33.408062 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-15 21:07:33.423994 INFO::Done
2025-10-15 21:07:33.424742 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.428005 INFO::ASW Batch was 0.47649084592058 prior to batch effect correction and is now 0.0329564518908365 .
2025-10-15 21:07:33.428636 INFO::ASW Label was 0.375907104003623 prior to batch effect correction and is now 0.708222240346283 .
2025-10-15 21:07:33.42948 INFO::Total function execution time is  0.151860952377319  s and adjustment time is  0.134504795074463 s ( 88.57 )
2025-10-15 21:07:33.443191 INFO::Formatting Data.
2025-10-15 21:07:33.444016 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.444982 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.446043 INFO::Found  0  missing values.
2025-10-15 21:07:33.448802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.449355 INFO::Done
2025-10-15 21:07:33.449899 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.452881 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.45361 INFO::Found  2  batches.
2025-10-15 21:07:33.454179 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.454833 INFO::Using default BPPARAM
2025-10-15 21:07:33.455367 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:33.456306 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-15 21:07:33.47085 INFO::Done
2025-10-15 21:07:33.471528 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.47442 INFO::ASW Batch was 0.534851155587392 prior to batch effect correction and is now -0.0359903031480019 .
2025-10-15 21:07:33.475026 INFO::ASW Label was 0.551722055335537 prior to batch effect correction and is now 0.939656588608329 .
2025-10-15 21:07:33.475796 INFO::Total function execution time is  0.0327017307281494  s and adjustment time is  0.0173847675323486 s ( 53.16 )
2025-10-15 21:07:33.476614 INFO::Formatting Data.
2025-10-15 21:07:33.477244 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.478112 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.479083 INFO::Found  0  missing values.
2025-10-15 21:07:33.48172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.482271 INFO::Done
2025-10-15 21:07:33.482798 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.485577 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.486271 INFO::Found  2  batches.
2025-10-15 21:07:33.486811 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.4874 INFO::Using default BPPARAM
2025-10-15 21:07:33.487937 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:33.488825 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-10-15 21:07:33.503522 INFO::Done
2025-10-15 21:07:33.504206 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.507315 INFO::ASW Batch was 0.534851155587392 prior to batch effect correction and is now -0.0359903031480019 .
2025-10-15 21:07:33.507925 INFO::ASW Label was 0.551722055335537 prior to batch effect correction and is now 0.939656588608329 .
2025-10-15 21:07:33.508731 INFO::Total function execution time is  0.0321168899536133  s and adjustment time is  0.0173707008361816 s ( 54.09 )
2025-10-15 21:07:33.519363 INFO::Formatting Data.
2025-10-15 21:07:33.52012 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.521007 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.521926 INFO::Found  0  missing values.
2025-10-15 21:07:33.524111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.524667 INFO::Done
2025-10-15 21:07:33.525193 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.527215 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.527949 INFO::Found  2  batches.
2025-10-15 21:07:33.528497 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.529167 INFO::Using default BPPARAM
2025-10-15 21:07:33.529703 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:33.530604 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-15 21:07:33.560491 INFO::Done
2025-10-15 21:07:33.5612 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.563182 INFO::ASW Batch was -0.0128755101444047 prior to batch effect correction and is now -0.17979113199292 .
2025-10-15 21:07:33.564004 INFO::Total function execution time is  0.0446953773498535  s and adjustment time is  0.0326647758483887 s ( 73.08 )
2025-10-15 21:07:33.575438 INFO::Formatting Data.
2025-10-15 21:07:33.576206 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.577103 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.578047 INFO::Found  0  missing values.
2025-10-15 21:07:33.579143 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.
2025-10-15 21:07:33.58344 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.583978 INFO::Done
2025-10-15 21:07:33.584506 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.587264 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.587938 INFO::Found  2  batches.
2025-10-15 21:07:33.58845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.589033 INFO::Using default BPPARAM
2025-10-15 21:07:33.589534 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:33.590429 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-15 21:07:33.605705 INFO::Done
2025-10-15 21:07:33.606368 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.609168 INFO::ASW Batch was 0.542264392569938 prior to batch effect correction and is now -0.0238996166490365 .
2025-10-15 21:07:33.60975 INFO::ASW Label was 0.558823582305588 prior to batch effect correction and is now 0.924378867565364 .
2025-10-15 21:07:33.610505 INFO::Total function execution time is  0.0351533889770508  s and adjustment time is  0.0178604125976562 s ( 50.81 )
2025-10-15 21:07:33.611304 INFO::Formatting Data.
2025-10-15 21:07:33.611911 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.612781 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.613712 INFO::Found  0  missing values.
2025-10-15 21:07:33.614567 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.
2025-10-15 21:07:33.618759 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.619289 INFO::Done
2025-10-15 21:07:33.619785 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.622451 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.623117 INFO::Found  2  batches.
2025-10-15 21:07:33.623632 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.624208 INFO::Using default BPPARAM
2025-10-15 21:07:33.624734 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:33.625633 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-15 21:07:33.640937 INFO::Done
2025-10-15 21:07:33.64158 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.644365 INFO::ASW Batch was 0.542264392569938 prior to batch effect correction and is now -0.0238996166490365 .
2025-10-15 21:07:33.644938 INFO::ASW Label was 0.558823582305588 prior to batch effect correction and is now 0.924378867565364 .
2025-10-15 21:07:33.645729 INFO::Total function execution time is  0.0344324111938477  s and adjustment time is  0.0179271697998047 s ( 52.06 )
2025-10-15 21:07:33.848827 INFO::Formatting Data.
2025-10-15 21:07:33.849607 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.850505 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.851526 INFO::Found  0  missing values.
2025-10-15 21:07:33.85452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.85509 INFO::Done
2025-10-15 21:07:33.85564 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.857668 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.858378 INFO::Found  3  batches.
2025-10-15 21:07:33.858913 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.859525 INFO::Using default BPPARAM
2025-10-15 21:07:33.86006 INFO::Processing subtree level 1
2025-10-15 21:07:33.943055 INFO::Adjusting the last 1 batches sequentially
2025-10-15 21:07:33.944779 INFO::Done
2025-10-15 21:07:33.945422 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:33.947881 INFO::ASW Batch was -0.0783677275863025 prior to batch effect correction and is now -0.0783677275863025 .
2025-10-15 21:07:33.948807 INFO::Total function execution time is  0.100048542022705  s and adjustment time is  0.0865311622619629 s ( 86.49 )
2025-10-15 21:07:33.949927 INFO::Formatting Data.
2025-10-15 21:07:33.950587 INFO::Typecasting input to dataframe.
2025-10-15 21:07:33.951368 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:33.952307 INFO::Removing potential empty rows and columns
2025-10-15 21:07:33.953389 INFO::Found  0  missing values.
2025-10-15 21:07:33.956432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:33.957018 INFO::Done
2025-10-15 21:07:33.957551 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:33.959562 INFO::Starting hierarchical adjustment
2025-10-15 21:07:33.960437 INFO::Found  3  batches.
2025-10-15 21:07:33.961005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:33.961633 INFO::Using default BPPARAM
2025-10-15 21:07:33.962173 INFO::Processing subtree level 1
2025-10-15 21:07:34.050079 INFO::Adjusting the last 1 batches sequentially
2025-10-15 21:07:34.05209 INFO::Done
2025-10-15 21:07:34.052858 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:34.055549 INFO::ASW Batch was -0.0783677275863025 prior to batch effect correction and is now -0.0783677275863025 .
2025-10-15 21:07:34.056575 INFO::Total function execution time is  0.106605291366577  s and adjustment time is  0.091883659362793 s ( 86.19 )
2025-10-15 21:07:34.070593 INFO::Formatting Data.
2025-10-15 21:07:34.071526 INFO::Typecasting input to dataframe.
2025-10-15 21:07:34.073079 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:34.074242 INFO::Removing potential empty rows and columns
2025-10-15 21:07:34.075405 INFO::Found  0  missing values.
2025-10-15 21:07:34.078444 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:34.079025 INFO::Done
2025-10-15 21:07:34.079563 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:34.081834 INFO::Starting hierarchical adjustment
2025-10-15 21:07:34.082576 INFO::Found  3  batches.
2025-10-15 21:07:34.083148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:34.083799 INFO::Using default BPPARAM
2025-10-15 21:07:34.084361 INFO::Processing subtree level 1
2025-10-15 21:07:34.171481 INFO::Adjusting the last 1 batches sequentially
2025-10-15 21:07:34.17344 INFO::Done
2025-10-15 21:07:34.174116 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:34.176682 INFO::ASW Batch was -0.0152260231466913 prior to batch effect correction and is now -0.0152260231466913 .
2025-10-15 21:07:34.177715 INFO::Total function execution time is  0.107205629348755  s and adjustment time is  0.0910015106201172 s ( 84.89 )
2025-10-15 21:07:34.320522 INFO::Formatting Data.
2025-10-15 21:07:34.32145 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:34.322617 INFO::Removing potential empty rows and columns
2025-10-15 21:07:34.325482 INFO::Found  1000  missing values.
2025-10-15 21:07:34.344352 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:34.345145 INFO::Done
2025-10-15 21:07:34.345742 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:34.351272 INFO::Starting hierarchical adjustment
2025-10-15 21:07:34.352071 INFO::Found  10  batches.
2025-10-15 21:07:34.352633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:34.353266 INFO::Using default BPPARAM
2025-10-15 21:07:34.353851 INFO::Processing subtree level 1
2025-10-15 21:07:34.487924 INFO::Processing subtree level 2
2025-10-15 21:07:34.634389 INFO::Adjusting the last 1 batches sequentially
2025-10-15 21:07:34.636559 INFO::Done
2025-10-15 21:07:34.637271 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:34.643046 INFO::ASW Batch was 0.451709367354822 prior to batch effect correction and is now 0.451709367354822 .
2025-10-15 21:07:34.643727 INFO::ASW Label was 0.364647332775764 prior to batch effect correction and is now 0.364647332775764 .
2025-10-15 21:07:34.644716 INFO::Total function execution time is  0.324297189712524  s and adjustment time is  0.284638404846191 s ( 87.77 )
2025-10-15 21:07:34.645591 INFO::Formatting Data.
2025-10-15 21:07:34.646271 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:34.647544 INFO::Removing potential empty rows and columns
2025-10-15 21:07:34.650452 INFO::Found  1000  missing values.
2025-10-15 21:07:34.669273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:34.670105 INFO::Done
2025-10-15 21:07:34.670744 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:34.676297 INFO::Starting hierarchical adjustment
2025-10-15 21:07:34.677097 INFO::Found  10  batches.
2025-10-15 21:07:35.728316 INFO::Set up parallel execution backend with 2 workers
2025-10-15 21:07:35.730353 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-10-15 21:07:36.832173 INFO::Adjusting the last 2 batches sequentially
2025-10-15 21:07:36.834105 INFO::Adjusting sequential tree level 1 with 2 batches
2025-10-15 21:07:36.851812 INFO::Done
2025-10-15 21:07:36.8525 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:36.857345 INFO::ASW Batch was 0.451709367354822 prior to batch effect correction and is now 0.451709367354822 .
2025-10-15 21:07:36.85798 INFO::ASW Label was 0.364647332775764 prior to batch effect correction and is now 0.364647332775764 .
2025-10-15 21:07:36.858778 INFO::Total function execution time is  2.21320223808289  s and adjustment time is  2.17485070228577 s ( 98.27 )
2025-10-15 21:07:37.009558 INFO::Formatting Data.
2025-10-15 21:07:37.010361 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.011284 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.012353 INFO::Found  0  missing values.
2025-10-15 21:07:37.016007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.016571 INFO::Done
2025-10-15 21:07:37.01713 INFO::Acquiring quality metrics before batch effect correction.
2025-10-15 21:07:37.01985 INFO::Starting hierarchical adjustment
2025-10-15 21:07:37.020553 INFO::Found  3  batches.
2025-10-15 21:07:37.021086 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-10-15 21:07:37.021711 INFO::Using default BPPARAM
2025-10-15 21:07:37.022234 INFO::Processing subtree level 1
2025-10-15 21:07:37.124459 INFO::Adjusting the last 1 batches sequentially
2025-10-15 21:07:37.1262 INFO::Done
2025-10-15 21:07:37.126852 INFO::Acquiring quality metrics after batch effect correction.
2025-10-15 21:07:37.129976 INFO::ASW Batch was 0.113895834156012 prior to batch effect correction and is now -0.140513133614125 .
2025-10-15 21:07:37.130587 INFO::ASW Label was -0.180834638638869 prior to batch effect correction and is now -0.053579120701705 .
2025-10-15 21:07:37.13148 INFO::Total function execution time is  0.121992111206055  s and adjustment time is  0.105769634246826 s ( 86.7 )
2025-10-15 21:07:37.246881 INFO::Formatting Data.
2025-10-15 21:07:37.247686 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.248576 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.249603 INFO::Found  2  missing values.
2025-10-15 21:07:37.252402 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.252946 INFO::Done
2025-10-15 21:07:37.279427 INFO::Found NA in Reference column
2025-10-15 21:07:37.288651 INFO::Require at least two references per batch.
2025-10-15 21:07:37.308662 INFO::Formatting Data.
2025-10-15 21:07:37.309425 INFO::Recognized SummarizedExperiment
2025-10-15 21:07:37.309983 INFO::Typecasting input to dataframe.
2025-10-15 21:07:37.319505 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.320709 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.324248 INFO::Found  0  missing values.
2025-10-15 21:07:37.331013 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.331734 INFO::Done
2025-10-15 21:07:37.346965 INFO::Formatting Data.
2025-10-15 21:07:37.347696 INFO::Recognized SummarizedExperiment
2025-10-15 21:07:37.348223 INFO::Typecasting input to dataframe.
2025-10-15 21:07:37.365633 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.366842 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.370332 INFO::Found  0  missing values.
2025-10-15 21:07:37.381027 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.381755 INFO::Done
2025-10-15 21:07:37.397276 INFO::Formatting Data.
2025-10-15 21:07:37.398037 INFO::Recognized SummarizedExperiment
2025-10-15 21:07:37.398574 INFO::Typecasting input to dataframe.
2025-10-15 21:07:37.415063 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.416125 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.417202 INFO::Found  0  missing values.
2025-10-15 21:07:37.418128 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.
2025-10-15 21:07:37.42248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.423076 INFO::Done
2025-10-15 21:07:37.432826 INFO::Formatting Data.
2025-10-15 21:07:37.43361 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.434512 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.43551 INFO::Found  0  missing values.
2025-10-15 21:07:37.438394 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.438962 INFO::Done
2025-10-15 21:07:37.44971 INFO::Formatting Data.
2025-10-15 21:07:37.450441 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.451302 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.452309 INFO::Found  0  missing values.
2025-10-15 21:07:37.455188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.455762 INFO::Done
2025-10-15 21:07:37.483613 INFO::Formatting Data.
2025-10-15 21:07:37.484395 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.485404 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.486614 INFO::Found  1  missing values.
2025-10-15 21:07:37.489118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.489617 INFO::Done
2025-10-15 21:07:37.506967 INFO::Formatting Data.
2025-10-15 21:07:37.507765 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.508668 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.509603 INFO::Found  2  missing values.
2025-10-15 21:07:37.510476 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.
2025-10-15 21:07:37.512666 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.513163 INFO::Done
2025-10-15 21:07:37.522418 INFO::Formatting Data.
2025-10-15 21:07:37.523187 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.524051 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.524971 INFO::Found  2  missing values.
2025-10-15 21:07:37.526552 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.527105 INFO::Done
2025-10-15 21:07:37.537425 INFO::Formatting Data.
2025-10-15 21:07:37.538205 INFO::Typecasting input to dataframe.
2025-10-15 21:07:37.539023 INFO::Replacing NaNs with NAs.
2025-10-15 21:07:37.539878 INFO::Removing potential empty rows and columns
2025-10-15 21:07:37.540866 INFO::Found  0  missing values.
2025-10-15 21:07:37.543717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-10-15 21:07:37.544236 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 17.503   3.589  20.749

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT25.746 1.79418.902
compute_asw0.0230.0040.028
count_existing0.0130.0040.017
generate_data_covariables0.0110.0040.015
generate_dataset0.0110.0040.015