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This page was generated on 2025-09-01 11:41 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025)
git_url: https://git.bioconductor.org/packages/BERT
git_branch: RELEASE_3_21
git_last_commit: dedce04
git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BERT on kjohnson1

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

raw results


Summary

Package: BERT
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz
StartedAt: 2025-08-29 13:36:30 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 13:38:05 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 95.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BERT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
BERT 29.247  1.673   23.95
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BERT.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘BERT’ ...
** this is package ‘BERT’ version ‘1.4.0’
** 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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(BERT)
> 
> test_check("BERT")
2025-08-29 13:37:40.281451 INFO::Formatting Data.
2025-08-29 13:37:40.286244 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:40.300282 INFO::Removing potential empty rows and columns
2025-08-29 13:37:40.690108 INFO::Found  0  missing values.
2025-08-29 13:37:40.694633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:40.695407 INFO::Done
2025-08-29 13:37:40.696004 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:40.717492 INFO::Starting hierarchical adjustment
2025-08-29 13:37:40.718687 INFO::Found  3  batches.
2025-08-29 13:37:40.719332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:40.720896 INFO::Using default BPPARAM
2025-08-29 13:37:40.721523 INFO::Processing subtree level 1
2025-08-29 13:37:40.905076 INFO::Adjusting the last 1 batches sequentially
2025-08-29 13:37:40.909042 INFO::Done
2025-08-29 13:37:40.909883 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:40.914384 INFO::ASW Batch was -0.124123027934804 prior to batch effect correction and is now -0.124123027934804 .
2025-08-29 13:37:40.916244 INFO::Total function execution time is  0.636285066604614  s and adjustment time is  0.190582990646362 s ( 29.95 )
2025-08-29 13:37:40.942258 INFO::Formatting Data.
2025-08-29 13:37:40.943315 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:40.944448 INFO::Removing potential empty rows and columns
2025-08-29 13:37:40.94634 INFO::Found  0  missing values.
2025-08-29 13:37:40.947826 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-29 13:37:40.967199 INFO::Formatting Data.
2025-08-29 13:37:40.968422 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:40.969628 INFO::Removing potential empty rows and columns
2025-08-29 13:37:40.97111 INFO::Found  0  missing values.
2025-08-29 13:37:40.972719 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-29 13:37:41.003633 INFO::Formatting Data.
2025-08-29 13:37:41.005491 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:41.007012 INFO::Removing potential empty rows and columns
2025-08-29 13:37:41.0091 INFO::Found  0  missing values.
2025-08-29 13:37:41.010741 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-29 13:37:41.018775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:41.021779 INFO::Done
2025-08-29 13:37:41.022457 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:41.025145 INFO::Starting hierarchical adjustment
2025-08-29 13:37:41.025993 INFO::Found  2  batches.
2025-08-29 13:37:41.026668 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:41.027625 INFO::Using default BPPARAM
2025-08-29 13:37:41.028371 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:41.029676 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 13:37:41.072003 INFO::Done
2025-08-29 13:37:41.07302 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:41.075698 INFO::ASW Batch was -0.0234370033004584 prior to batch effect correction and is now -0.105726418434085 .
2025-08-29 13:37:41.076629 INFO::Total function execution time is  0.0732691287994385  s and adjustment time is  0.0461061000823975 s ( 62.93 )
2025-08-29 13:37:41.080445 INFO::Formatting Data.
2025-08-29 13:37:41.081239 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:41.091297 INFO::Formatting Data.
2025-08-29 13:37:41.092443 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:41.16524 INFO::Removing potential empty rows and columns
2025-08-29 13:37:41.166273 INFO::Found  0  missing values.
2025-08-29 13:37:41.168819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:41.169426 INFO::Done
2025-08-29 13:37:41.169946 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:41.173651 INFO::Starting hierarchical adjustment
2025-08-29 13:37:41.174778 INFO::Found  2  batches.
2025-08-29 13:37:41.175672 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:41.176399 INFO::Using default BPPARAM
2025-08-29 13:37:41.176908 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:41.17784 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 13:37:41.199234 INFO::Done
2025-08-29 13:37:41.200461 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:41.203719 INFO::ASW Batch was -0.00802383756604412 prior to batch effect correction and is now -0.100463439508604 .
2025-08-29 13:37:41.205834 INFO::Total function execution time is  0.114164113998413  s and adjustment time is  0.0244998931884766 s ( 21.46 )
2025-08-29 13:37:41.207629 INFO::Formatting Data.
2025-08-29 13:37:41.208798 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:41.209885 INFO::Removing potential empty rows and columns
2025-08-29 13:37:41.210985 INFO::Found  0  missing values.
2025-08-29 13:37:41.21387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:41.21448 INFO::Done
2025-08-29 13:37:41.21505 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:41.217279 INFO::Starting hierarchical adjustment
2025-08-29 13:37:41.218012 INFO::Found  2  batches.
2025-08-29 13:37:41.218537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:41.219153 INFO::Using default BPPARAM
2025-08-29 13:37:41.219647 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:41.220531 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 13:37:41.236521 INFO::Done
2025-08-29 13:37:41.237197 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:41.241704 INFO::ASW Batch was -0.00802383756604412 prior to batch effect correction and is now -0.100463439508604 .
2025-08-29 13:37:41.242702 INFO::Total function execution time is  0.0350828170776367  s and adjustment time is  0.0186271667480469 s ( 53.09 )
2025-08-29 13:37:45.091749 INFO::Formatting Data.
2025-08-29 13:37:45.093198 INFO::Recognized SummarizedExperiment
2025-08-29 13:37:45.093983 INFO::Typecasting input to dataframe.
2025-08-29 13:37:45.135416 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:45.137455 INFO::Removing potential empty rows and columns
2025-08-29 13:37:45.142655 INFO::Found  0  missing values.
2025-08-29 13:37:45.151527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:45.15236 INFO::Done
2025-08-29 13:37:45.152896 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:45.157979 INFO::Starting hierarchical adjustment
2025-08-29 13:37:45.159867 INFO::Found  2  batches.
2025-08-29 13:37:45.16049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:45.162381 INFO::Using default BPPARAM
2025-08-29 13:37:45.163365 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:45.164527 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 13:37:45.225786 INFO::Done
2025-08-29 13:37:45.226598 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:45.231671 INFO::ASW Batch was 0.0014457487655517 prior to batch effect correction and is now -0.0943532759089196 .
2025-08-29 13:37:45.23307 INFO::Total function execution time is  0.141474008560181  s and adjustment time is  0.0662600994110107 s ( 46.84 )
2025-08-29 13:37:45.252216 INFO::Formatting Data.
2025-08-29 13:37:45.253028 INFO::Recognized SummarizedExperiment
2025-08-29 13:37:45.253535 INFO::Typecasting input to dataframe.
2025-08-29 13:37:45.264577 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:45.266471 INFO::Removing potential empty rows and columns
2025-08-29 13:37:45.270012 INFO::Found  0  missing values.
2025-08-29 13:37:45.276764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:45.277449 INFO::Done
2025-08-29 13:37:45.27794 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:45.281755 INFO::Starting hierarchical adjustment
2025-08-29 13:37:45.282539 INFO::Found  2  batches.
2025-08-29 13:37:45.283028 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:45.28357 INFO::Using default BPPARAM
2025-08-29 13:37:45.284399 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:45.286167 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 13:37:45.31372 INFO::Done
2025-08-29 13:37:45.314509 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:45.318331 INFO::ASW Batch was -0.00230614626091571 prior to batch effect correction and is now -0.00230614626091571 .
2025-08-29 13:37:45.31927 INFO::Total function execution time is  0.0670831203460693  s and adjustment time is  0.031257152557373 s ( 46.59 )
2025-08-29 13:37:45.348955 INFO::Formatting Data.
2025-08-29 13:37:45.349773 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:45.350632 INFO::Removing potential empty rows and columns
2025-08-29 13:37:45.351582 INFO::Found  0  missing values.
2025-08-29 13:37:45.354343 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:45.35493 INFO::Done
2025-08-29 13:37:45.355387 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:45.357349 INFO::Starting hierarchical adjustment
2025-08-29 13:37:45.357965 INFO::Found  3  batches.
2025-08-29 13:37:45.358423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:45.358961 INFO::Using default BPPARAM
2025-08-29 13:37:45.359396 INFO::Processing subtree level 1
2025-08-29 13:37:45.812297 INFO::Adjusting the last 1 batches sequentially
2025-08-29 13:37:45.821265 INFO::Done
2025-08-29 13:37:45.82335 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:45.831683 INFO::ASW Batch was -0.115654726852849 prior to batch effect correction and is now -0.162666008944562 .
2025-08-29 13:37:45.834496 INFO::Total function execution time is  0.485254049301147  s and adjustment time is  0.463214874267578 s ( 95.46 )
2025-08-29 13:37:45.989523 INFO::Skipping initial DF formatting
2025-08-29 13:37:45.990938 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:45.995905 INFO::Starting hierarchical adjustment
2025-08-29 13:37:45.997525 INFO::Found  5  batches.
2025-08-29 13:37:45.998112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:45.998841 INFO::Using default BPPARAM
2025-08-29 13:37:45.999312 INFO::Processing subtree level 1
2025-08-29 13:37:46.259412 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:46.263102 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 13:37:46.304734 INFO::Done
2025-08-29 13:37:46.306145 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:46.318593 INFO::ASW Batch was 0.497390154427087 prior to batch effect correction and is now 0.497390154427087 .
2025-08-29 13:37:46.319523 INFO::ASW Label was 0.418429632522678 prior to batch effect correction and is now 0.418429632522678 .
2025-08-29 13:37:46.320881 INFO::Total function execution time is  0.331496000289917  s and adjustment time is  0.307547092437744 s ( 92.78 )
2025-08-29 13:37:46.352714 INFO::Formatting Data.
2025-08-29 13:37:46.353853 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:46.35509 INFO::Removing potential empty rows and columns
2025-08-29 13:37:46.356528 INFO::Found  0  missing values.
2025-08-29 13:37:46.362334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:46.363245 INFO::Done
2025-08-29 13:37:46.364052 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:46.368222 INFO::Starting hierarchical adjustment
2025-08-29 13:37:46.369365 INFO::Found  5  batches.
2025-08-29 13:37:46.370096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:46.370906 INFO::Using default BPPARAM
2025-08-29 13:37:46.371516 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-08-29 13:37:46.560965 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:46.568269 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 13:37:46.594745 INFO::Done
2025-08-29 13:37:46.595415 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:46.599897 INFO::ASW Batch was 0.334161198289749 prior to batch effect correction and is now -0.0882422848757927 .
2025-08-29 13:37:46.600448 INFO::ASW Label was 0.412782943860232 prior to batch effect correction and is now 0.831601395329088 .
2025-08-29 13:37:46.6049 INFO::Total function execution time is  0.250406980514526  s and adjustment time is  0.225606918334961 s ( 90.1 )
2025-08-29 13:37:46.607418 INFO::Formatting Data.
2025-08-29 13:37:46.608459 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:46.609616 INFO::Removing potential empty rows and columns
2025-08-29 13:37:46.610515 INFO::Found  0  missing values.
2025-08-29 13:37:46.612881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:46.61332 INFO::Done
2025-08-29 13:37:46.61365 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:46.616268 INFO::Starting hierarchical adjustment
2025-08-29 13:37:46.616967 INFO::Found  5  batches.
2025-08-29 13:37:46.617464 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:46.618022 INFO::Using default BPPARAM
2025-08-29 13:37:46.618461 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-08-29 13:37:46.817981 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:46.824013 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 13:37:46.852747 INFO::Done
2025-08-29 13:37:46.853892 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:46.859746 INFO::ASW Batch was 0.334161198289749 prior to batch effect correction and is now -0.0882422848757927 .
2025-08-29 13:37:46.860547 INFO::ASW Label was 0.412782943860232 prior to batch effect correction and is now 0.831601395329088 .
2025-08-29 13:37:46.862128 INFO::Total function execution time is  0.254760980606079  s and adjustment time is  0.235781908035278 s ( 92.55 )
2025-08-29 13:37:46.886919 INFO::Formatting Data.
2025-08-29 13:37:46.888417 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:46.88979 INFO::Removing potential empty rows and columns
2025-08-29 13:37:46.89119 INFO::Found  0  missing values.
2025-08-29 13:37:46.896384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:46.897272 INFO::Done
2025-08-29 13:37:46.898057 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:46.902372 INFO::Starting hierarchical adjustment
2025-08-29 13:37:46.903445 INFO::Found  5  batches.
2025-08-29 13:37:46.904208 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:46.907225 INFO::Using default BPPARAM
2025-08-29 13:37:46.908295 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-08-29 13:37:47.132263 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:47.13871 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 13:37:47.167076 INFO::Done
2025-08-29 13:37:47.168397 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:47.1763 INFO::ASW Batch was 0.467196705555969 prior to batch effect correction and is now -0.0639039490839554 .
2025-08-29 13:37:47.177672 INFO::ASW Label was 0.362402363749158 prior to batch effect correction and is now 0.798160857423879 .
2025-08-29 13:37:47.179866 INFO::Total function execution time is  0.293017148971558  s and adjustment time is  0.263782978057861 s ( 90.02 )
2025-08-29 13:37:47.181071 INFO::Formatting Data.
2025-08-29 13:37:47.181893 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:47.18307 INFO::Removing potential empty rows and columns
2025-08-29 13:37:47.184332 INFO::Found  0  missing values.
2025-08-29 13:37:47.188648 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:47.189435 INFO::Done
2025-08-29 13:37:47.190022 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:47.19318 INFO::Starting hierarchical adjustment
2025-08-29 13:37:47.195291 INFO::Found  5  batches.
2025-08-29 13:37:47.196434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:47.198168 INFO::Using default BPPARAM
2025-08-29 13:37:47.198848 INFO::Processing subtree level 1
design matrix of interest not specified. Assuming a one-group experiment.

design matrix of interest not specified. Assuming a one-group experiment.
design matrix of interest not specified. Assuming a one-group experiment.

2025-08-29 13:37:47.370611 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:47.375472 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 13:37:47.408924 INFO::Done
2025-08-29 13:37:47.410182 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:47.41627 INFO::ASW Batch was 0.467196705555969 prior to batch effect correction and is now -0.0639039490839554 .
2025-08-29 13:37:47.417044 INFO::ASW Label was 0.362402363749158 prior to batch effect correction and is now 0.798160857423879 .
2025-08-29 13:37:47.418263 INFO::Total function execution time is  0.237030982971191  s and adjustment time is  0.214022159576416 s ( 90.29 )
2025-08-29 13:37:47.448431 INFO::Formatting Data.
2025-08-29 13:37:47.449945 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:47.45127 INFO::Removing potential empty rows and columns
2025-08-29 13:37:47.452689 INFO::Found  0  missing values.
2025-08-29 13:37:47.456044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:47.45681 INFO::Done
2025-08-29 13:37:47.457509 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:47.461216 INFO::Starting hierarchical adjustment
2025-08-29 13:37:47.462242 INFO::Found  2  batches.
2025-08-29 13:37:47.462945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:47.463808 INFO::Using default BPPARAM
2025-08-29 13:37:47.468815 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:47.470714 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 13:37:47.493258 INFO::Done
2025-08-29 13:37:47.494129 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:47.501639 INFO::ASW Batch was 0.513399903114926 prior to batch effect correction and is now 0.0044014101531447 .
2025-08-29 13:37:47.502816 INFO::ASW Label was 0.52999596086871 prior to batch effect correction and is now 0.928199114921893 .
2025-08-29 13:37:47.50394 INFO::Total function execution time is  0.0556850433349609  s and adjustment time is  0.0312168598175049 s ( 56.06 )
2025-08-29 13:37:47.504942 INFO::Formatting Data.
2025-08-29 13:37:47.505668 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:47.506876 INFO::Removing potential empty rows and columns
2025-08-29 13:37:47.508115 INFO::Found  0  missing values.
2025-08-29 13:37:47.511227 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:47.511824 INFO::Done
2025-08-29 13:37:47.51238 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:47.51567 INFO::Starting hierarchical adjustment
2025-08-29 13:37:47.516535 INFO::Found  2  batches.
2025-08-29 13:37:47.517096 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:47.517768 INFO::Using default BPPARAM
2025-08-29 13:37:47.518259 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:47.519155 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-08-29 13:37:47.543175 INFO::Done
2025-08-29 13:37:47.544101 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:47.547731 INFO::ASW Batch was 0.513399903114926 prior to batch effect correction and is now 0.0044014101531447 .
2025-08-29 13:37:47.548576 INFO::ASW Label was 0.52999596086871 prior to batch effect correction and is now 0.928199114921893 .
2025-08-29 13:37:47.549528 INFO::Total function execution time is  0.044564962387085  s and adjustment time is  0.0267519950866699 s ( 60.03 )
2025-08-29 13:37:47.56623 INFO::Formatting Data.
2025-08-29 13:37:47.567228 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:47.568233 INFO::Removing potential empty rows and columns
2025-08-29 13:37:47.569284 INFO::Found  0  missing values.
2025-08-29 13:37:47.571566 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:47.572151 INFO::Done
2025-08-29 13:37:47.575947 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:47.579789 INFO::Starting hierarchical adjustment
2025-08-29 13:37:47.58085 INFO::Found  2  batches.
2025-08-29 13:37:47.581449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:47.582084 INFO::Using default BPPARAM
2025-08-29 13:37:47.582628 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:47.583771 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 13:37:47.630386 INFO::Done
2025-08-29 13:37:47.631303 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:47.640936 INFO::ASW Batch was -0.139680305637397 prior to batch effect correction and is now -0.172330272612035 .
2025-08-29 13:37:47.642056 INFO::Total function execution time is  0.0759580135345459  s and adjustment time is  0.0496859550476074 s ( 65.41 )
2025-08-29 13:37:47.660252 INFO::Formatting Data.
2025-08-29 13:37:47.662009 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:47.664091 INFO::Removing potential empty rows and columns
2025-08-29 13:37:47.665397 INFO::Found  0  missing values.
2025-08-29 13:37:47.669381 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-29 13:37:47.675263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:47.675996 INFO::Done
2025-08-29 13:37:47.676541 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:47.67977 INFO::Starting hierarchical adjustment
2025-08-29 13:37:47.680554 INFO::Found  2  batches.
2025-08-29 13:37:47.68107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:47.681705 INFO::Using default BPPARAM
2025-08-29 13:37:47.682189 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:47.683179 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 13:37:47.708716 INFO::Done
2025-08-29 13:37:47.709615 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:47.712892 INFO::ASW Batch was 0.353360025504373 prior to batch effect correction and is now 0.0871073878255495 .
2025-08-29 13:37:47.713589 INFO::ASW Label was 0.693725359600736 prior to batch effect correction and is now 0.894324123040764 .
2025-08-29 13:37:47.715487 INFO::Total function execution time is  0.0551390647888184  s and adjustment time is  0.0281028747558594 s ( 50.97 )
2025-08-29 13:37:47.716919 INFO::Formatting Data.
2025-08-29 13:37:47.717657 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:47.719574 INFO::Removing potential empty rows and columns
2025-08-29 13:37:47.720656 INFO::Found  0  missing values.
2025-08-29 13:37:47.721685 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-29 13:37:47.729717 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:47.730602 INFO::Done
2025-08-29 13:37:47.73122 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:47.734491 INFO::Starting hierarchical adjustment
2025-08-29 13:37:47.735311 INFO::Found  2  batches.
2025-08-29 13:37:47.735849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:47.736446 INFO::Using default BPPARAM
2025-08-29 13:37:47.736928 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:47.737915 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 13:37:47.755761 INFO::Done
2025-08-29 13:37:47.756591 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:47.759536 INFO::ASW Batch was 0.353360025504373 prior to batch effect correction and is now 0.0871073878255495 .
2025-08-29 13:37:47.764572 INFO::ASW Label was 0.693725359600736 prior to batch effect correction and is now 0.894324123040764 .
2025-08-29 13:37:47.765715 INFO::Total function execution time is  0.0486891269683838  s and adjustment time is  0.0205609798431396 s ( 42.23 )
2025-08-29 13:37:48.052191 INFO::Formatting Data.
2025-08-29 13:37:48.053708 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:48.054992 INFO::Removing potential empty rows and columns
2025-08-29 13:37:48.0561 INFO::Found  0  missing values.
2025-08-29 13:37:48.058804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:48.059417 INFO::Done
2025-08-29 13:37:48.059925 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:48.065458 INFO::Starting hierarchical adjustment
2025-08-29 13:37:48.06644 INFO::Found  3  batches.
2025-08-29 13:37:48.066996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:48.067587 INFO::Using default BPPARAM
2025-08-29 13:37:48.06806 INFO::Processing subtree level 1
2025-08-29 13:37:48.218392 INFO::Adjusting the last 1 batches sequentially
2025-08-29 13:37:48.220982 INFO::Done
2025-08-29 13:37:48.221652 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:48.226082 INFO::ASW Batch was -0.0910246203234756 prior to batch effect correction and is now -0.0910246203234756 .
2025-08-29 13:37:48.227442 INFO::Total function execution time is  0.175451993942261  s and adjustment time is  0.154725074768066 s ( 88.19 )
2025-08-29 13:37:48.228581 INFO::Formatting Data.
2025-08-29 13:37:48.229571 INFO::Typecasting input to dataframe.
2025-08-29 13:37:48.230241 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:48.231342 INFO::Removing potential empty rows and columns
2025-08-29 13:37:48.232546 INFO::Found  0  missing values.
2025-08-29 13:37:48.240063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:48.241036 INFO::Done
2025-08-29 13:37:48.241633 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:48.244021 INFO::Starting hierarchical adjustment
2025-08-29 13:37:48.244859 INFO::Found  3  batches.
2025-08-29 13:37:48.245389 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:48.246141 INFO::Using default BPPARAM
2025-08-29 13:37:48.246647 INFO::Processing subtree level 1
2025-08-29 13:37:48.387844 INFO::Adjusting the last 1 batches sequentially
2025-08-29 13:37:48.394712 INFO::Done
2025-08-29 13:37:48.395424 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:48.401072 INFO::ASW Batch was -0.0910246203234756 prior to batch effect correction and is now -0.0910246203234756 .
2025-08-29 13:37:48.403834 INFO::Total function execution time is  0.174695014953613  s and adjustment time is  0.149977922439575 s ( 85.85 )
2025-08-29 13:37:48.425626 INFO::Formatting Data.
2025-08-29 13:37:48.426493 INFO::Typecasting input to dataframe.
2025-08-29 13:37:48.427376 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:48.431687 INFO::Removing potential empty rows and columns
2025-08-29 13:37:48.434041 INFO::Found  0  missing values.
2025-08-29 13:37:48.437148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:48.437787 INFO::Done
2025-08-29 13:37:48.438334 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:48.440753 INFO::Starting hierarchical adjustment
2025-08-29 13:37:48.441954 INFO::Found  3  batches.
2025-08-29 13:37:48.442453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:48.443183 INFO::Using default BPPARAM
2025-08-29 13:37:48.443655 INFO::Processing subtree level 1
2025-08-29 13:37:48.599168 INFO::Adjusting the last 1 batches sequentially
2025-08-29 13:37:48.603972 INFO::Done
2025-08-29 13:37:48.605039 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:48.611881 INFO::ASW Batch was -0.047985329608672 prior to batch effect correction and is now -0.047985329608672 .
2025-08-29 13:37:48.61429 INFO::Total function execution time is  0.18831205368042  s and adjustment time is  0.162161111831665 s ( 86.11 )
2025-08-29 13:37:48.874164 INFO::Formatting Data.
2025-08-29 13:37:48.875134 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:48.876324 INFO::Removing potential empty rows and columns
2025-08-29 13:37:48.879369 INFO::Found  1000  missing values.
2025-08-29 13:37:48.903053 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:48.904016 INFO::Done
2025-08-29 13:37:48.904596 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:48.911226 INFO::Starting hierarchical adjustment
2025-08-29 13:37:48.912119 INFO::Found  10  batches.
2025-08-29 13:37:48.912649 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:48.913402 INFO::Using default BPPARAM
2025-08-29 13:37:48.913982 INFO::Processing subtree level 1
2025-08-29 13:37:49.127349 INFO::Processing subtree level 2
2025-08-29 13:37:49.331526 INFO::Adjusting the last 1 batches sequentially
2025-08-29 13:37:49.340621 INFO::Done
2025-08-29 13:37:49.342911 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:49.355566 INFO::ASW Batch was 0.507084078792593 prior to batch effect correction and is now 0.507084078792593 .
2025-08-29 13:37:49.358921 INFO::ASW Label was 0.349985851249618 prior to batch effect correction and is now 0.349985851249618 .
2025-08-29 13:37:49.364966 INFO::Total function execution time is  0.490659952163696  s and adjustment time is  0.428612947463989 s ( 87.35 )
2025-08-29 13:37:49.366317 INFO::Formatting Data.
2025-08-29 13:37:49.36699 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:49.368839 INFO::Removing potential empty rows and columns
2025-08-29 13:37:49.371654 INFO::Found  1000  missing values.
2025-08-29 13:37:49.393822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:49.394918 INFO::Done
2025-08-29 13:37:49.395502 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:49.403843 INFO::Starting hierarchical adjustment
2025-08-29 13:37:49.405221 INFO::Found  10  batches.
2025-08-29 13:37:51.01651 INFO::Set up parallel execution backend with 2 workers
2025-08-29 13:37:51.017358 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-08-29 13:37:52.75564 INFO::Adjusting the last 2 batches sequentially
2025-08-29 13:37:52.757428 INFO::Adjusting sequential tree level 1 with 2 batches
2025-08-29 13:37:52.77427 INFO::Done
2025-08-29 13:37:52.774841 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:52.77912 INFO::ASW Batch was 0.507084078792593 prior to batch effect correction and is now 0.507084078792593 .
2025-08-29 13:37:52.779974 INFO::ASW Label was 0.349985851249618 prior to batch effect correction and is now 0.349985851249618 .
2025-08-29 13:37:52.780925 INFO::Total function execution time is  3.41460919380188  s and adjustment time is  3.36923909187317 s ( 98.67 )
2025-08-29 13:37:52.987481 INFO::Formatting Data.
2025-08-29 13:37:52.988667 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:52.98986 INFO::Removing potential empty rows and columns
2025-08-29 13:37:52.991576 INFO::Found  0  missing values.
2025-08-29 13:37:52.994795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:52.995467 INFO::Done
2025-08-29 13:37:52.995792 INFO::Acquiring quality metrics before batch effect correction.
2025-08-29 13:37:53.000468 INFO::Starting hierarchical adjustment
2025-08-29 13:37:53.001133 INFO::Found  3  batches.
2025-08-29 13:37:53.00148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-08-29 13:37:53.001952 INFO::Using default BPPARAM
2025-08-29 13:37:53.002224 INFO::Processing subtree level 1
2025-08-29 13:37:53.168203 INFO::Adjusting the last 1 batches sequentially
2025-08-29 13:37:53.173004 INFO::Done
2025-08-29 13:37:53.174516 INFO::Acquiring quality metrics after batch effect correction.
2025-08-29 13:37:53.180194 INFO::ASW Batch was 0.176546199177234 prior to batch effect correction and is now -0.139129332498735 .
2025-08-29 13:37:53.180882 INFO::ASW Label was -0.18886013038242 prior to batch effect correction and is now -0.0753826171274834 .
2025-08-29 13:37:53.183662 INFO::Total function execution time is  0.196177005767822  s and adjustment time is  0.171939849853516 s ( 87.65 )
2025-08-29 13:37:53.350376 INFO::Formatting Data.
2025-08-29 13:37:53.35292 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.353971 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.355123 INFO::Found  2  missing values.
2025-08-29 13:37:53.358814 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.359423 INFO::Done
2025-08-29 13:37:53.403144 INFO::Found NA in Reference column
2025-08-29 13:37:53.419856 INFO::Require at least two references per batch.
2025-08-29 13:37:53.455986 INFO::Formatting Data.
2025-08-29 13:37:53.457351 INFO::Recognized SummarizedExperiment
2025-08-29 13:37:53.459266 INFO::Typecasting input to dataframe.
2025-08-29 13:37:53.478175 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.480581 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.487293 INFO::Found  0  missing values.
2025-08-29 13:37:53.496252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.497004 INFO::Done
2025-08-29 13:37:53.519765 INFO::Formatting Data.
2025-08-29 13:37:53.520835 INFO::Recognized SummarizedExperiment
2025-08-29 13:37:53.521488 INFO::Typecasting input to dataframe.
2025-08-29 13:37:53.546544 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.548241 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.554754 INFO::Found  0  missing values.
2025-08-29 13:37:53.5692 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.57028 INFO::Done
2025-08-29 13:37:53.590957 INFO::Formatting Data.
2025-08-29 13:37:53.591956 INFO::Recognized SummarizedExperiment
2025-08-29 13:37:53.59252 INFO::Typecasting input to dataframe.
2025-08-29 13:37:53.611069 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.612417 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.613613 INFO::Found  0  missing values.
2025-08-29 13:37:53.61467 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-29 13:37:53.619382 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.6201 INFO::Done
2025-08-29 13:37:53.637377 INFO::Formatting Data.
2025-08-29 13:37:53.638382 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.639282 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.640346 INFO::Found  0  missing values.
2025-08-29 13:37:53.643182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.643756 INFO::Done
2025-08-29 13:37:53.661481 INFO::Formatting Data.
2025-08-29 13:37:53.662526 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.663505 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.664618 INFO::Found  0  missing values.
2025-08-29 13:37:53.667923 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.668635 INFO::Done
2025-08-29 13:37:53.715746 INFO::Formatting Data.
2025-08-29 13:37:53.716827 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.718085 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.721453 INFO::Found  1  missing values.
2025-08-29 13:37:53.726772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.727879 INFO::Done
2025-08-29 13:37:53.758366 INFO::Formatting Data.
2025-08-29 13:37:53.759596 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.760802 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.762148 INFO::Found  2  missing values.
2025-08-29 13:37:53.763588 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-08-29 13:37:53.766875 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.76775 INFO::Done
2025-08-29 13:37:53.781683 INFO::Formatting Data.
2025-08-29 13:37:53.782741 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.783819 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.784877 INFO::Found  2  missing values.
2025-08-29 13:37:53.786841 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.787767 INFO::Done
2025-08-29 13:37:53.809475 INFO::Formatting Data.
2025-08-29 13:37:53.813223 INFO::Typecasting input to dataframe.
2025-08-29 13:37:53.814994 INFO::Replacing NaNs with NAs.
2025-08-29 13:37:53.816093 INFO::Removing potential empty rows and columns
2025-08-29 13:37:53.81963 INFO::Found  0  missing values.
2025-08-29 13:37:53.82649 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-08-29 13:37:53.827407 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
> 
> proc.time()
   user  system elapsed 
 20.865   5.682  29.090

Example timings

BERT.Rcheck/BERT-Ex.timings

nameusersystemelapsed
BERT29.247 1.67323.950
compute_asw0.0300.0010.033
count_existing0.0160.0010.020
generate_data_covariables0.0160.0010.020
generate_dataset0.0140.0010.016