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This page was generated on 2025-03-20 12:04 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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 159/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BERT 1.2.0  (landing page)
Yannis Schumann
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_20
git_last_commit: 9764e3f
git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on nebbiolo2

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

raw results


Summary

Package: BERT
Version: 1.2.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz
StartedAt: 2025-03-17 20:57:55 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 20:59:24 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 88.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* 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 23.642  1.234  17.285
* 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-3.20-bioc/R/bin/R CMD INSTALL BERT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘BERT’ ...
** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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")
2025-03-17 20:58:45.701344 INFO::Formatting Data.
2025-03-17 20:58:45.702896 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:45.714788 INFO::Removing potential empty rows and columns
2025-03-17 20:58:46.01279 INFO::Found  0  missing values.
2025-03-17 20:58:46.016511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:46.017185 INFO::Done
2025-03-17 20:58:46.017695 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:46.029925 INFO::Starting hierarchical adjustment
2025-03-17 20:58:46.030826 INFO::Found  3  batches.
2025-03-17 20:58:46.031338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:46.032551 INFO::Using default BPPARAM
2025-03-17 20:58:46.033068 INFO::Processing subtree level 1
2025-03-17 20:58:46.135475 INFO::Adjusting the last 1 batches sequentially
2025-03-17 20:58:46.137185 INFO::Done
2025-03-17 20:58:46.1378 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:46.14025 INFO::ASW Batch was -0.00646355670458852 prior to batch effect correction and is now -0.00646355670458852 .
2025-03-17 20:58:46.141291 INFO::Total function execution time is  0.440812587738037  s and adjustment time is  0.106558322906494 s ( 24.17 )
2025-03-17 20:58:46.154911 INFO::Formatting Data.
2025-03-17 20:58:46.155594 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:46.156443 INFO::Removing potential empty rows and columns
2025-03-17 20:58:46.157437 INFO::Found  0  missing values.
2025-03-17 20:58:46.158309 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.
2025-03-17 20:58:46.168481 INFO::Formatting Data.
2025-03-17 20:58:46.169265 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:46.170064 INFO::Removing potential empty rows and columns
2025-03-17 20:58:46.171016 INFO::Found  0  missing values.
2025-03-17 20:58:46.171855 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.
2025-03-17 20:58:46.186615 INFO::Formatting Data.
2025-03-17 20:58:46.187306 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:46.188114 INFO::Removing potential empty rows and columns
2025-03-17 20:58:46.189071 INFO::Found  0  missing values.
2025-03-17 20:58:46.189932 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.
2025-03-17 20:58:46.194148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:46.194641 INFO::Done
2025-03-17 20:58:46.19511 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:46.197032 INFO::Starting hierarchical adjustment
2025-03-17 20:58:46.197698 INFO::Found  2  batches.
2025-03-17 20:58:46.198203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:46.198809 INFO::Using default BPPARAM
2025-03-17 20:58:46.199313 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:46.200201 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:46.222937 INFO::Done
2025-03-17 20:58:46.223656 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:46.225667 INFO::ASW Batch was -0.115988184797091 prior to batch effect correction and is now -0.135413518109673 .
2025-03-17 20:58:46.226446 INFO::Total function execution time is  0.0399100780487061  s and adjustment time is  0.0251140594482422 s ( 62.93 )
2025-03-17 20:58:46.229212 INFO::Formatting Data.
2025-03-17 20:58:46.229819 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:46.238583 INFO::Formatting Data.
2025-03-17 20:58:46.239312 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:46.240201 INFO::Removing potential empty rows and columns
2025-03-17 20:58:46.241221 INFO::Found  0  missing values.
2025-03-17 20:58:46.244073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:46.244589 INFO::Done
2025-03-17 20:58:46.24509 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:46.247087 INFO::Starting hierarchical adjustment
2025-03-17 20:58:46.247786 INFO::Found  2  batches.
2025-03-17 20:58:46.248301 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:46.248949 INFO::Using default BPPARAM
2025-03-17 20:58:46.249481 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:46.250423 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:46.265536 INFO::Done
2025-03-17 20:58:46.266229 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:46.268172 INFO::ASW Batch was 0.0800492365066735 prior to batch effect correction and is now -0.0859783386800543 .
2025-03-17 20:58:46.268961 INFO::Total function execution time is  0.0304429531097412  s and adjustment time is  0.0178728103637695 s ( 58.71 )
2025-03-17 20:58:46.269984 INFO::Formatting Data.
2025-03-17 20:58:46.270545 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:46.271361 INFO::Removing potential empty rows and columns
2025-03-17 20:58:46.272336 INFO::Found  0  missing values.
2025-03-17 20:58:46.275117 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:46.275618 INFO::Done
2025-03-17 20:58:46.276104 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:46.278009 INFO::Starting hierarchical adjustment
2025-03-17 20:58:46.278672 INFO::Found  2  batches.
2025-03-17 20:58:46.279164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:46.279728 INFO::Using default BPPARAM
2025-03-17 20:58:46.280209 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:46.281046 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:46.2963 INFO::Done
2025-03-17 20:58:46.297026 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:46.299021 INFO::ASW Batch was 0.0800492365066735 prior to batch effect correction and is now -0.0859783386800543 .
2025-03-17 20:58:46.299829 INFO::Total function execution time is  0.0298395156860352  s and adjustment time is  0.0177385807037354 s ( 59.45 )
2025-03-17 20:58:49.356824 INFO::Formatting Data.
2025-03-17 20:58:49.357532 INFO::Recognized SummarizedExperiment
2025-03-17 20:58:49.357991 INFO::Typecasting input to dataframe.
2025-03-17 20:58:49.386014 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:49.387107 INFO::Removing potential empty rows and columns
2025-03-17 20:58:49.390146 INFO::Found  0  missing values.
2025-03-17 20:58:49.395793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:49.396274 INFO::Done
2025-03-17 20:58:49.396721 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:49.399634 INFO::Starting hierarchical adjustment
2025-03-17 20:58:49.400246 INFO::Found  2  batches.
2025-03-17 20:58:49.400687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:49.401587 INFO::Using default BPPARAM
2025-03-17 20:58:49.402046 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:49.402867 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:49.449229 INFO::Done
2025-03-17 20:58:49.449882 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:49.452852 INFO::ASW Batch was -0.0140590028890762 prior to batch effect correction and is now -0.0889910031198881 .
2025-03-17 20:58:49.45357 INFO::Total function execution time is  0.0970404148101807  s and adjustment time is  0.0490715503692627 s ( 50.57 )
2025-03-17 20:58:49.469397 INFO::Formatting Data.
2025-03-17 20:58:49.470073 INFO::Recognized SummarizedExperiment
2025-03-17 20:58:49.47052 INFO::Typecasting input to dataframe.
2025-03-17 20:58:49.478579 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:49.479773 INFO::Removing potential empty rows and columns
2025-03-17 20:58:49.483486 INFO::Found  0  missing values.
2025-03-17 20:58:49.490693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:49.491349 INFO::Done
2025-03-17 20:58:49.491886 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:49.495404 INFO::Starting hierarchical adjustment
2025-03-17 20:58:49.496112 INFO::Found  2  batches.
2025-03-17 20:58:49.496607 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:49.497185 INFO::Using default BPPARAM
2025-03-17 20:58:49.497671 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:49.498584 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:49.522987 INFO::Done
2025-03-17 20:58:49.523662 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:49.527041 INFO::ASW Batch was -0.0133242438472856 prior to batch effect correction and is now -0.0133242438472856 .
2025-03-17 20:58:49.527847 INFO::Total function execution time is  0.0584278106689453  s and adjustment time is  0.0269927978515625 s ( 46.2 )
2025-03-17 20:58:49.544962 INFO::Formatting Data.
2025-03-17 20:58:49.545691 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:49.546513 INFO::Removing potential empty rows and columns
2025-03-17 20:58:49.547473 INFO::Found  0  missing values.
2025-03-17 20:58:49.550388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:49.55089 INFO::Done
2025-03-17 20:58:49.551356 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:49.553216 INFO::Starting hierarchical adjustment
2025-03-17 20:58:49.553869 INFO::Found  3  batches.
2025-03-17 20:58:49.554349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:49.55491 INFO::Using default BPPARAM
2025-03-17 20:58:49.555387 INFO::Processing subtree level 1
2025-03-17 20:58:49.6903 INFO::Adjusting the last 1 batches sequentially
2025-03-17 20:58:49.692097 INFO::Done
2025-03-17 20:58:49.692735 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:49.695165 INFO::ASW Batch was -0.0561075866510398 prior to batch effect correction and is now -0.152897885728787 .
2025-03-17 20:58:49.696086 INFO::Total function execution time is  0.151125907897949  s and adjustment time is  0.138342380523682 s ( 91.54 )
2025-03-17 20:58:49.710626 INFO::Skipping initial DF formatting
2025-03-17 20:58:49.711385 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:49.715458 INFO::Starting hierarchical adjustment
2025-03-17 20:58:49.716248 INFO::Found  5  batches.
2025-03-17 20:58:49.716771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:49.717362 INFO::Using default BPPARAM
2025-03-17 20:58:49.717876 INFO::Processing subtree level 1
2025-03-17 20:58:49.847819 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:49.84978 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:49.871543 INFO::Done
2025-03-17 20:58:49.872436 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:49.877253 INFO::ASW Batch was 0.502546746238446 prior to batch effect correction and is now 0.502546746238446 .
2025-03-17 20:58:49.87796 INFO::ASW Label was 0.358582456802692 prior to batch effect correction and is now 0.358582456802692 .
2025-03-17 20:58:49.878852 INFO::Total function execution time is  0.168331623077393  s and adjustment time is  0.155397176742554 s ( 92.32 )
2025-03-17 20:58:49.896878 INFO::Formatting Data.
2025-03-17 20:58:49.897733 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:49.898637 INFO::Removing potential empty rows and columns
2025-03-17 20:58:49.899623 INFO::Found  0  missing values.
2025-03-17 20:58:49.903602 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:49.904125 INFO::Done
2025-03-17 20:58:49.904622 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:49.907598 INFO::Starting hierarchical adjustment
2025-03-17 20:58:49.908295 INFO::Found  5  batches.
2025-03-17 20:58:49.908822 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:49.909396 INFO::Using default BPPARAM
2025-03-17 20:58:49.909904 INFO::Processing subtree level 1
2025-03-17 20:58:50.025692 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.027567 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.044287 INFO::Done
2025-03-17 20:58:50.045089 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.048205 INFO::ASW Batch was 0.503786599750347 prior to batch effect correction and is now -0.0604883054859265 .
2025-03-17 20:58:50.048816 INFO::ASW Label was 0.251359149513754 prior to batch effect correction and is now 0.833085148319239 .
2025-03-17 20:58:50.049601 INFO::Total function execution time is  0.152884960174561  s and adjustment time is  0.136089563369751 s ( 89.01 )
2025-03-17 20:58:50.050417 INFO::Formatting Data.
2025-03-17 20:58:50.051009 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:50.051848 INFO::Removing potential empty rows and columns
2025-03-17 20:58:50.052782 INFO::Found  0  missing values.
2025-03-17 20:58:50.056685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:50.057187 INFO::Done
2025-03-17 20:58:50.057674 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:50.060455 INFO::Starting hierarchical adjustment
2025-03-17 20:58:50.061131 INFO::Found  5  batches.
2025-03-17 20:58:50.061616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:50.062211 INFO::Using default BPPARAM
2025-03-17 20:58:50.062708 INFO::Processing subtree level 1
2025-03-17 20:58:50.175302 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.177083 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.193537 INFO::Done
2025-03-17 20:58:50.194341 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.197716 INFO::ASW Batch was 0.503786599750347 prior to batch effect correction and is now -0.0604883054859265 .
2025-03-17 20:58:50.198395 INFO::ASW Label was 0.251359149513754 prior to batch effect correction and is now 0.833085148319239 .
2025-03-17 20:58:50.199266 INFO::Total function execution time is  0.148800611495972  s and adjustment time is  0.13247537612915 s ( 89.03 )
2025-03-17 20:58:50.213065 INFO::Formatting Data.
2025-03-17 20:58:50.213905 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:50.214818 INFO::Removing potential empty rows and columns
2025-03-17 20:58:50.215802 INFO::Found  0  missing values.
2025-03-17 20:58:50.219765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:50.22028 INFO::Done
2025-03-17 20:58:50.220787 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:50.223805 INFO::Starting hierarchical adjustment
2025-03-17 20:58:50.224497 INFO::Found  5  batches.
2025-03-17 20:58:50.225011 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:50.225583 INFO::Using default BPPARAM
2025-03-17 20:58:50.22609 INFO::Processing subtree level 1
2025-03-17 20:58:50.341398 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.343265 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.373206 INFO::Done
2025-03-17 20:58:50.374218 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.377556 INFO::ASW Batch was 0.307117264943852 prior to batch effect correction and is now -0.042006558960864 .
2025-03-17 20:58:50.378136 INFO::ASW Label was 0.49794327784252 prior to batch effect correction and is now 0.821008512340974 .
2025-03-17 20:58:50.378921 INFO::Total function execution time is  0.165991306304932  s and adjustment time is  0.148805141448975 s ( 89.65 )
2025-03-17 20:58:50.379745 INFO::Formatting Data.
2025-03-17 20:58:50.38034 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:50.381198 INFO::Removing potential empty rows and columns
2025-03-17 20:58:50.38217 INFO::Found  0  missing values.
2025-03-17 20:58:50.386137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:50.386646 INFO::Done
2025-03-17 20:58:50.387147 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:50.389928 INFO::Starting hierarchical adjustment
2025-03-17 20:58:50.390595 INFO::Found  5  batches.
2025-03-17 20:58:50.391098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:50.391761 INFO::Using default BPPARAM
2025-03-17 20:58:50.392254 INFO::Processing subtree level 1
2025-03-17 20:58:50.507853 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.509563 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.525177 INFO::Done
2025-03-17 20:58:50.525944 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.529117 INFO::ASW Batch was 0.307117264943852 prior to batch effect correction and is now -0.042006558960864 .
2025-03-17 20:58:50.529717 INFO::ASW Label was 0.49794327784252 prior to batch effect correction and is now 0.821008512340974 .
2025-03-17 20:58:50.530535 INFO::Total function execution time is  0.150763034820557  s and adjustment time is  0.134688377380371 s ( 89.34 )
2025-03-17 20:58:50.545069 INFO::Formatting Data.
2025-03-17 20:58:50.54588 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:50.546799 INFO::Removing potential empty rows and columns
2025-03-17 20:58:50.547825 INFO::Found  0  missing values.
2025-03-17 20:58:50.550582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:50.551102 INFO::Done
2025-03-17 20:58:50.551587 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:50.554532 INFO::Starting hierarchical adjustment
2025-03-17 20:58:50.555237 INFO::Found  2  batches.
2025-03-17 20:58:50.555748 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:50.55633 INFO::Using default BPPARAM
2025-03-17 20:58:50.556834 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.557717 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.572033 INFO::Done
2025-03-17 20:58:50.572713 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.575568 INFO::ASW Batch was 0.576846136232515 prior to batch effect correction and is now 0.0270932002790834 .
2025-03-17 20:58:50.576162 INFO::ASW Label was 0.486222919489187 prior to batch effect correction and is now 0.895780241541434 .
2025-03-17 20:58:50.57692 INFO::Total function execution time is  0.0319807529449463  s and adjustment time is  0.0169467926025391 s ( 52.99 )
2025-03-17 20:58:50.577683 INFO::Formatting Data.
2025-03-17 20:58:50.578258 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:50.579082 INFO::Removing potential empty rows and columns
2025-03-17 20:58:50.580024 INFO::Found  0  missing values.
2025-03-17 20:58:50.582621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:50.583122 INFO::Done
2025-03-17 20:58:50.583598 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:50.586433 INFO::Starting hierarchical adjustment
2025-03-17 20:58:50.587114 INFO::Found  2  batches.
2025-03-17 20:58:50.587599 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:50.588173 INFO::Using default BPPARAM
2025-03-17 20:58:50.588664 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.589523 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.604666 INFO::Done
2025-03-17 20:58:50.605332 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.608162 INFO::ASW Batch was 0.576846136232515 prior to batch effect correction and is now 0.0270932002790834 .
2025-03-17 20:58:50.608726 INFO::ASW Label was 0.486222919489187 prior to batch effect correction and is now 0.895780241541434 .
2025-03-17 20:58:50.609438 INFO::Total function execution time is  0.031782865524292  s and adjustment time is  0.0176601409912109 s ( 55.56 )
2025-03-17 20:58:50.620205 INFO::Formatting Data.
2025-03-17 20:58:50.620902 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:50.621757 INFO::Removing potential empty rows and columns
2025-03-17 20:58:50.622613 INFO::Found  0  missing values.
2025-03-17 20:58:50.624669 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:50.62517 INFO::Done
2025-03-17 20:58:50.625646 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:50.62748 INFO::Starting hierarchical adjustment
2025-03-17 20:58:50.628144 INFO::Found  2  batches.
2025-03-17 20:58:50.628623 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:50.629199 INFO::Using default BPPARAM
2025-03-17 20:58:50.629693 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.630539 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.66142 INFO::Done
2025-03-17 20:58:50.662151 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.664067 INFO::ASW Batch was -0.0711646668261683 prior to batch effect correction and is now -0.148479868427243 .
2025-03-17 20:58:50.664868 INFO::Total function execution time is  0.0447368621826172  s and adjustment time is  0.0333766937255859 s ( 74.61 )
2025-03-17 20:58:50.676366 INFO::Formatting Data.
2025-03-17 20:58:50.677115 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:50.677975 INFO::Removing potential empty rows and columns
2025-03-17 20:58:50.678936 INFO::Found  0  missing values.
2025-03-17 20:58:50.680087 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.
2025-03-17 20:58:50.684568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:50.685186 INFO::Done
2025-03-17 20:58:50.685689 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:50.688493 INFO::Starting hierarchical adjustment
2025-03-17 20:58:50.689183 INFO::Found  2  batches.
2025-03-17 20:58:50.689682 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:50.690238 INFO::Using default BPPARAM
2025-03-17 20:58:50.690721 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.691631 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.707809 INFO::Done
2025-03-17 20:58:50.708483 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.711292 INFO::ASW Batch was 0.616634543295191 prior to batch effect correction and is now 0.0760312604341029 .
2025-03-17 20:58:50.711867 INFO::ASW Label was 0.410176493607189 prior to batch effect correction and is now 0.754537800369065 .
2025-03-17 20:58:50.712582 INFO::Total function execution time is  0.0363121032714844  s and adjustment time is  0.0187275409698486 s ( 51.57 )
2025-03-17 20:58:50.713315 INFO::Formatting Data.
2025-03-17 20:58:50.713895 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:50.714767 INFO::Removing potential empty rows and columns
2025-03-17 20:58:50.715711 INFO::Found  0  missing values.
2025-03-17 20:58:50.71657 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.
2025-03-17 20:58:50.720975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:50.72153 INFO::Done
2025-03-17 20:58:50.722032 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:50.724819 INFO::Starting hierarchical adjustment
2025-03-17 20:58:50.725485 INFO::Found  2  batches.
2025-03-17 20:58:50.725981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:50.726537 INFO::Using default BPPARAM
2025-03-17 20:58:50.727033 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:50.727934 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:50.744148 INFO::Done
2025-03-17 20:58:50.74485 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:50.74769 INFO::ASW Batch was 0.616634543295191 prior to batch effect correction and is now 0.0760312604341029 .
2025-03-17 20:58:50.748267 INFO::ASW Label was 0.410176493607189 prior to batch effect correction and is now 0.754537800369065 .
2025-03-17 20:58:50.749018 INFO::Total function execution time is  0.0356960296630859  s and adjustment time is  0.0187888145446777 s ( 52.64 )
2025-03-17 20:58:50.999093 INFO::Formatting Data.
2025-03-17 20:58:50.999821 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:51.000627 INFO::Removing potential empty rows and columns
2025-03-17 20:58:51.001561 INFO::Found  0  missing values.
2025-03-17 20:58:51.004316 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:51.004818 INFO::Done
2025-03-17 20:58:51.005275 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:51.007116 INFO::Starting hierarchical adjustment
2025-03-17 20:58:51.007752 INFO::Found  3  batches.
2025-03-17 20:58:51.008214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:51.008761 INFO::Using default BPPARAM
2025-03-17 20:58:51.009218 INFO::Processing subtree level 1
2025-03-17 20:58:51.11261 INFO::Adjusting the last 1 batches sequentially
2025-03-17 20:58:51.114351 INFO::Done
2025-03-17 20:58:51.114967 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:51.117345 INFO::ASW Batch was -0.0472697304095006 prior to batch effect correction and is now -0.0472697304095006 .
2025-03-17 20:58:51.11827 INFO::Total function execution time is  0.119192838668823  s and adjustment time is  0.10672664642334 s ( 89.54 )
2025-03-17 20:58:51.119339 INFO::Formatting Data.
2025-03-17 20:58:51.120034 INFO::Typecasting input to dataframe.
2025-03-17 20:58:51.120879 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:51.121816 INFO::Removing potential empty rows and columns
2025-03-17 20:58:51.122928 INFO::Found  0  missing values.
2025-03-17 20:58:51.125838 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:51.126334 INFO::Done
2025-03-17 20:58:51.126847 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:51.138254 INFO::Starting hierarchical adjustment
2025-03-17 20:58:51.139305 INFO::Found  3  batches.
2025-03-17 20:58:51.139879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:51.140516 INFO::Using default BPPARAM
2025-03-17 20:58:51.141048 INFO::Processing subtree level 1
2025-03-17 20:58:51.243711 INFO::Adjusting the last 1 batches sequentially
2025-03-17 20:58:51.2456 INFO::Done
2025-03-17 20:58:51.246258 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:51.248779 INFO::ASW Batch was -0.0472697304095006 prior to batch effect correction and is now -0.0472697304095006 .
2025-03-17 20:58:51.249778 INFO::Total function execution time is  0.130390644073486  s and adjustment time is  0.106490612030029 s ( 81.67 )
2025-03-17 20:58:51.263425 INFO::Formatting Data.
2025-03-17 20:58:51.264199 INFO::Typecasting input to dataframe.
2025-03-17 20:58:51.265104 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:51.266077 INFO::Removing potential empty rows and columns
2025-03-17 20:58:51.267248 INFO::Found  0  missing values.
2025-03-17 20:58:51.27063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:51.271232 INFO::Done
2025-03-17 20:58:51.27177 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:51.273838 INFO::Starting hierarchical adjustment
2025-03-17 20:58:51.274573 INFO::Found  3  batches.
2025-03-17 20:58:51.275105 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:51.275698 INFO::Using default BPPARAM
2025-03-17 20:58:51.27619 INFO::Processing subtree level 1
2025-03-17 20:58:51.376192 INFO::Adjusting the last 1 batches sequentially
2025-03-17 20:58:51.378382 INFO::Done
2025-03-17 20:58:51.379056 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:51.381505 INFO::ASW Batch was -0.114845910746569 prior to batch effect correction and is now -0.114845910746569 .
2025-03-17 20:58:51.382421 INFO::Total function execution time is  0.119093656539917  s and adjustment time is  0.103894948959351 s ( 87.24 )
2025-03-17 20:58:51.526192 INFO::Formatting Data.
2025-03-17 20:58:51.527011 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:51.528144 INFO::Removing potential empty rows and columns
2025-03-17 20:58:51.530947 INFO::Found  1000  missing values.
2025-03-17 20:58:51.549502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:51.550179 INFO::Done
2025-03-17 20:58:51.550708 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:51.555947 INFO::Starting hierarchical adjustment
2025-03-17 20:58:51.556686 INFO::Found  10  batches.
2025-03-17 20:58:51.557191 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:51.557771 INFO::Using default BPPARAM
2025-03-17 20:58:51.558265 INFO::Processing subtree level 1
2025-03-17 20:58:51.718149 INFO::Processing subtree level 2
2025-03-17 20:58:51.897584 INFO::Adjusting the last 1 batches sequentially
2025-03-17 20:58:51.900697 INFO::Done
2025-03-17 20:58:51.901886 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:51.90812 INFO::ASW Batch was 0.521682811240246 prior to batch effect correction and is now 0.521682811240246 .
2025-03-17 20:58:51.908901 INFO::ASW Label was 0.303575634863267 prior to batch effect correction and is now 0.303575634863267 .
2025-03-17 20:58:51.90994 INFO::Total function execution time is  0.383782148361206  s and adjustment time is  0.344080209732056 s ( 89.66 )
2025-03-17 20:58:51.910946 INFO::Formatting Data.
2025-03-17 20:58:51.911624 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:51.913175 INFO::Removing potential empty rows and columns
2025-03-17 20:58:51.916221 INFO::Found  1000  missing values.
2025-03-17 20:58:51.936253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:51.937174 INFO::Done
2025-03-17 20:58:51.93783 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:51.943835 INFO::Starting hierarchical adjustment
2025-03-17 20:58:51.944745 INFO::Found  10  batches.
2025-03-17 20:58:53.034618 INFO::Set up parallel execution backend with 2 workers
2025-03-17 20:58:53.036525 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-17 20:58:54.224911 INFO::Adjusting the last 2 batches sequentially
2025-03-17 20:58:54.226901 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 20:58:54.241928 INFO::Done
2025-03-17 20:58:54.242513 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:54.246732 INFO::ASW Batch was 0.521682811240246 prior to batch effect correction and is now 0.521682811240246 .
2025-03-17 20:58:54.247239 INFO::ASW Label was 0.303575634863267 prior to batch effect correction and is now 0.303575634863267 .
2025-03-17 20:58:54.247908 INFO::Total function execution time is  2.33703589439392  s and adjustment time is  2.29739737510681 s ( 98.3 )
2025-03-17 20:58:54.391486 INFO::Formatting Data.
2025-03-17 20:58:54.392401 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.393377 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.394544 INFO::Found  0  missing values.
2025-03-17 20:58:54.410567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.41136 INFO::Done
2025-03-17 20:58:54.411922 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 20:58:54.414824 INFO::Starting hierarchical adjustment
2025-03-17 20:58:54.415534 INFO::Found  3  batches.
2025-03-17 20:58:54.416067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 20:58:54.416692 INFO::Using default BPPARAM
2025-03-17 20:58:54.417239 INFO::Processing subtree level 1
2025-03-17 20:58:54.529665 INFO::Adjusting the last 1 batches sequentially
2025-03-17 20:58:54.531568 INFO::Done
2025-03-17 20:58:54.532276 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 20:58:54.535753 INFO::ASW Batch was 0.113803934169954 prior to batch effect correction and is now -0.183998655956736 .
2025-03-17 20:58:54.536423 INFO::ASW Label was -0.104067220160116 prior to batch effect correction and is now 0.136430856044075 .
2025-03-17 20:58:54.537405 INFO::Total function execution time is  0.146017074584961  s and adjustment time is  0.116145133972168 s ( 79.54 )
2025-03-17 20:58:54.662385 INFO::Formatting Data.
2025-03-17 20:58:54.663195 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.66407 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.66512 INFO::Found  2  missing values.
2025-03-17 20:58:54.668063 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.668581 INFO::Done
2025-03-17 20:58:54.697047 INFO::Found NA in Reference column
2025-03-17 20:58:54.706989 INFO::Require at least two references per batch.
2025-03-17 20:58:54.728064 INFO::Formatting Data.
2025-03-17 20:58:54.728889 INFO::Recognized SummarizedExperiment
2025-03-17 20:58:54.729397 INFO::Typecasting input to dataframe.
2025-03-17 20:58:54.739443 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.740764 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.74454 INFO::Found  0  missing values.
2025-03-17 20:58:54.751826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.752527 INFO::Done
2025-03-17 20:58:54.768599 INFO::Formatting Data.
2025-03-17 20:58:54.769432 INFO::Recognized SummarizedExperiment
2025-03-17 20:58:54.769986 INFO::Typecasting input to dataframe.
2025-03-17 20:58:54.789469 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.790845 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.794757 INFO::Found  0  missing values.
2025-03-17 20:58:54.806938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.807729 INFO::Done
2025-03-17 20:58:54.826096 INFO::Formatting Data.
2025-03-17 20:58:54.826987 INFO::Recognized SummarizedExperiment
2025-03-17 20:58:54.827569 INFO::Typecasting input to dataframe.
2025-03-17 20:58:54.846707 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.848011 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.849262 INFO::Found  0  missing values.
2025-03-17 20:58:54.850318 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.
2025-03-17 20:58:54.854947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.855495 INFO::Done
2025-03-17 20:58:54.865761 INFO::Formatting Data.
2025-03-17 20:58:54.866465 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.86728 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.868221 INFO::Found  0  missing values.
2025-03-17 20:58:54.871097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.87161 INFO::Done
2025-03-17 20:58:54.882427 INFO::Formatting Data.
2025-03-17 20:58:54.883211 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.884056 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.88502 INFO::Found  0  missing values.
2025-03-17 20:58:54.88778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.888258 INFO::Done
2025-03-17 20:58:54.915488 INFO::Formatting Data.
2025-03-17 20:58:54.916264 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.917263 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.918491 INFO::Found  1  missing values.
2025-03-17 20:58:54.920963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.921474 INFO::Done
2025-03-17 20:58:54.938971 INFO::Formatting Data.
2025-03-17 20:58:54.939762 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.940573 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.941471 INFO::Found  2  missing values.
2025-03-17 20:58:54.942307 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.
2025-03-17 20:58:54.944422 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.944906 INFO::Done
2025-03-17 20:58:54.95401 INFO::Formatting Data.
2025-03-17 20:58:54.954744 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.95556 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.956416 INFO::Found  2  missing values.
2025-03-17 20:58:54.957922 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.958424 INFO::Done
2025-03-17 20:58:54.967962 INFO::Formatting Data.
2025-03-17 20:58:54.968669 INFO::Typecasting input to dataframe.
2025-03-17 20:58:54.969428 INFO::Replacing NaNs with NAs.
2025-03-17 20:58:54.970233 INFO::Removing potential empty rows and columns
2025-03-17 20:58:54.971174 INFO::Found  0  missing values.
2025-03-17 20:58:54.973854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 20:58:54.974348 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 16.597   3.761  19.946

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT23.642 1.23417.285
compute_asw0.0220.0010.023
count_existing0.0120.0010.013
generate_data_covariables0.0100.0010.011
generate_dataset0.0110.0000.011