Yannis Schumann
| Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 3fb455b |
| git_last_commit_date: 2025-06-06 07:20:51 -0400 (Fri, 06 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-29 12:04 -0400 (Mon, 29 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4833 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4621 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4566 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
| 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 163/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.5.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: BERT |
| Version: 1.5.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz |
| StartedAt: 2025-09-28 19:40:57 -0400 (Sun, 28 Sep 2025) |
| EndedAt: 2025-09-28 19:42:25 -0400 (Sun, 28 Sep 2025) |
| EllapsedTime: 87.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BERT.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 29.019 1.661 20.617
* 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
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.5.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-09-28 19:42:02.86302 INFO::Formatting Data.
2025-09-28 19:42:02.867547 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:02.881358 INFO::Removing potential empty rows and columns
2025-09-28 19:42:03.210057 INFO::Found 0 missing values.
2025-09-28 19:42:03.214326 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:03.215144 INFO::Done
2025-09-28 19:42:03.215912 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:03.232441 INFO::Starting hierarchical adjustment
2025-09-28 19:42:03.233384 INFO::Found 3 batches.
2025-09-28 19:42:03.23399 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:03.235061 INFO::Using default BPPARAM
2025-09-28 19:42:03.235582 INFO::Processing subtree level 1
2025-09-28 19:42:03.407865 INFO::Adjusting the last 1 batches sequentially
2025-09-28 19:42:03.414003 INFO::Done
2025-09-28 19:42:03.415817 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:03.421891 INFO::ASW Batch was -0.023815394108686 prior to batch effect correction and is now -0.023815394108686 .
2025-09-28 19:42:03.425959 INFO::Total function execution time is 0.562955141067505 s and adjustment time is 0.180794954299927 s ( 32.12 )
2025-09-28 19:42:03.45059 INFO::Formatting Data.
2025-09-28 19:42:03.451755 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:03.452838 INFO::Removing potential empty rows and columns
2025-09-28 19:42:03.455606 INFO::Found 0 missing values.
2025-09-28 19:42:03.456608 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.
2025-09-28 19:42:03.468267 INFO::Formatting Data.
2025-09-28 19:42:03.469399 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:03.470372 INFO::Removing potential empty rows and columns
2025-09-28 19:42:03.471373 INFO::Found 0 missing values.
2025-09-28 19:42:03.47227 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.
2025-09-28 19:42:03.49166 INFO::Formatting Data.
2025-09-28 19:42:03.492936 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:03.494004 INFO::Removing potential empty rows and columns
2025-09-28 19:42:03.49506 INFO::Found 0 missing values.
2025-09-28 19:42:03.495987 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.
2025-09-28 19:42:03.501405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:03.502287 INFO::Done
2025-09-28 19:42:03.503101 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:03.505582 INFO::Starting hierarchical adjustment
2025-09-28 19:42:03.506284 INFO::Found 2 batches.
2025-09-28 19:42:03.50679 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:03.5074 INFO::Using default BPPARAM
2025-09-28 19:42:03.507898 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:03.508794 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-28 19:42:03.534191 INFO::Done
2025-09-28 19:42:03.535241 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:03.538275 INFO::ASW Batch was 0.0629833913658777 prior to batch effect correction and is now -0.110594261216579 .
2025-09-28 19:42:03.539448 INFO::Total function execution time is 0.0479590892791748 s and adjustment time is 0.0278699398040771 s ( 58.11 )
2025-09-28 19:42:03.542398 INFO::Formatting Data.
2025-09-28 19:42:03.543177 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:03.553137 INFO::Formatting Data.
2025-09-28 19:42:03.553951 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:03.555459 INFO::Removing potential empty rows and columns
2025-09-28 19:42:03.557177 INFO::Found 0 missing values.
2025-09-28 19:42:03.561202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:03.562036 INFO::Done
2025-09-28 19:42:03.562757 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:03.565939 INFO::Starting hierarchical adjustment
2025-09-28 19:42:03.566927 INFO::Found 2 batches.
2025-09-28 19:42:03.567676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:03.568751 INFO::Using default BPPARAM
2025-09-28 19:42:03.569548 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:03.570888 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-28 19:42:03.628861 INFO::Done
2025-09-28 19:42:03.629862 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:03.632732 INFO::ASW Batch was -0.0614800734458223 prior to batch effect correction and is now -0.111972806930167 .
2025-09-28 19:42:03.633914 INFO::Total function execution time is 0.0807759761810303 s and adjustment time is 0.0620889663696289 s ( 76.87 )
2025-09-28 19:42:03.635204 INFO::Formatting Data.
2025-09-28 19:42:03.635798 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:03.636584 INFO::Removing potential empty rows and columns
2025-09-28 19:42:03.637475 INFO::Found 0 missing values.
2025-09-28 19:42:03.640684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:03.64144 INFO::Done
2025-09-28 19:42:03.642156 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:03.645041 INFO::Starting hierarchical adjustment
2025-09-28 19:42:03.64605 INFO::Found 2 batches.
2025-09-28 19:42:03.646804 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:03.647656 INFO::Using default BPPARAM
2025-09-28 19:42:03.648388 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:03.649711 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-28 19:42:03.668475 INFO::Done
2025-09-28 19:42:03.669404 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:03.671909 INFO::ASW Batch was -0.0614800734458223 prior to batch effect correction and is now -0.111972806930167 .
2025-09-28 19:42:03.672958 INFO::Total function execution time is 0.0376629829406738 s and adjustment time is 0.0226261615753174 s ( 60.08 )
2025-09-28 19:42:07.178329 INFO::Formatting Data.
2025-09-28 19:42:07.179326 INFO::Recognized SummarizedExperiment
2025-09-28 19:42:07.180105 INFO::Typecasting input to dataframe.
2025-09-28 19:42:07.21754 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:07.219367 INFO::Removing potential empty rows and columns
2025-09-28 19:42:07.223758 INFO::Found 0 missing values.
2025-09-28 19:42:07.231794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:07.23274 INFO::Done
2025-09-28 19:42:07.233493 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:07.238264 INFO::Starting hierarchical adjustment
2025-09-28 19:42:07.23921 INFO::Found 2 batches.
2025-09-28 19:42:07.240073 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:07.241659 INFO::Using default BPPARAM
2025-09-28 19:42:07.242426 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:07.243958 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-28 19:42:07.31174 INFO::Done
2025-09-28 19:42:07.312481 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:07.31753 INFO::ASW Batch was -0.0171739438337642 prior to batch effect correction and is now -0.0961138611805345 .
2025-09-28 19:42:07.318765 INFO::Total function execution time is 0.140825986862183 s and adjustment time is 0.0727639198303223 s ( 51.67 )
2025-09-28 19:42:07.344893 INFO::Formatting Data.
2025-09-28 19:42:07.345978 INFO::Recognized SummarizedExperiment
2025-09-28 19:42:07.346971 INFO::Typecasting input to dataframe.
2025-09-28 19:42:07.360864 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:07.362646 INFO::Removing potential empty rows and columns
2025-09-28 19:42:07.367929 INFO::Found 0 missing values.
2025-09-28 19:42:07.376861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:07.377845 INFO::Done
2025-09-28 19:42:07.378663 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:07.383861 INFO::Starting hierarchical adjustment
2025-09-28 19:42:07.384938 INFO::Found 2 batches.
2025-09-28 19:42:07.385715 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:07.386583 INFO::Using default BPPARAM
2025-09-28 19:42:07.387314 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:07.388746 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-28 19:42:07.417245 INFO::Done
2025-09-28 19:42:07.418169 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:07.422314 INFO::ASW Batch was 0.00585560379801729 prior to batch effect correction and is now 0.00585560379801729 .
2025-09-28 19:42:07.423477 INFO::Total function execution time is 0.0785629749298096 s and adjustment time is 0.0324950218200684 s ( 41.36 )
2025-09-28 19:42:07.451597 INFO::Formatting Data.
2025-09-28 19:42:07.45283 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:07.454207 INFO::Removing potential empty rows and columns
2025-09-28 19:42:07.455718 INFO::Found 0 missing values.
2025-09-28 19:42:07.459443 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:07.460007 INFO::Done
2025-09-28 19:42:07.460478 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:07.462832 INFO::Starting hierarchical adjustment
2025-09-28 19:42:07.463697 INFO::Found 3 batches.
2025-09-28 19:42:07.464485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:07.465305 INFO::Using default BPPARAM
2025-09-28 19:42:07.466021 INFO::Processing subtree level 1
2025-09-28 19:42:07.677839 INFO::Adjusting the last 1 batches sequentially
2025-09-28 19:42:07.693219 INFO::Done
2025-09-28 19:42:07.695711 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:07.706479 INFO::ASW Batch was -0.0450371623652 prior to batch effect correction and is now -0.179775946364256 .
2025-09-28 19:42:07.712753 INFO::Total function execution time is 0.261167049407959 s and adjustment time is 0.229744911193848 s ( 87.97 )
2025-09-28 19:42:07.74109 INFO::Skipping initial DF formatting
2025-09-28 19:42:07.741902 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:07.746479 INFO::Starting hierarchical adjustment
2025-09-28 19:42:07.747382 INFO::Found 5 batches.
2025-09-28 19:42:07.748111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:07.748877 INFO::Using default BPPARAM
2025-09-28 19:42:07.749428 INFO::Processing subtree level 1
2025-09-28 19:42:08.124827 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:08.128248 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-28 19:42:08.186859 INFO::Done
2025-09-28 19:42:08.190104 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:08.20188 INFO::ASW Batch was 0.507283807876273 prior to batch effect correction and is now 0.507283807876273 .
2025-09-28 19:42:08.202818 INFO::ASW Label was 0.372441745147555 prior to batch effect correction and is now 0.372441745147555 .
2025-09-28 19:42:08.206522 INFO::Total function execution time is 0.464232206344604 s and adjustment time is 0.439543008804321 s ( 94.68 )
2025-09-28 19:42:08.331735 INFO::Formatting Data.
2025-09-28 19:42:08.332871 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:08.334221 INFO::Removing potential empty rows and columns
2025-09-28 19:42:08.335607 INFO::Found 0 missing values.
2025-09-28 19:42:08.340335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:08.341118 INFO::Done
2025-09-28 19:42:08.341651 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:08.345932 INFO::Starting hierarchical adjustment
2025-09-28 19:42:08.34707 INFO::Found 5 batches.
2025-09-28 19:42:08.347861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:08.348696 INFO::Using default BPPARAM
2025-09-28 19:42:08.349413 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.
2025-09-28 19:42:08.581702 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:08.594031 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-28 19:42:08.632752 INFO::Done
2025-09-28 19:42:08.633919 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:08.641017 INFO::ASW Batch was 0.452950824569368 prior to batch effect correction and is now -0.109907612818017 .
2025-09-28 19:42:08.642031 INFO::ASW Label was 0.281646460172883 prior to batch effect correction and is now 0.898767049086776 .
2025-09-28 19:42:08.643474 INFO::Total function execution time is 0.311826944351196 s and adjustment time is 0.285887002944946 s ( 91.68 )
2025-09-28 19:42:08.644768 INFO::Formatting Data.
2025-09-28 19:42:08.645671 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:08.647072 INFO::Removing potential empty rows and columns
2025-09-28 19:42:08.648718 INFO::Found 0 missing values.
2025-09-28 19:42:08.655595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:08.656293 INFO::Done
2025-09-28 19:42:08.657151 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:08.661217 INFO::Starting hierarchical adjustment
2025-09-28 19:42:08.661985 INFO::Found 5 batches.
2025-09-28 19:42:08.662508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:08.663193 INFO::Using default BPPARAM
2025-09-28 19:42:08.664348 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.
2025-09-28 19:42:08.852363 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:08.890064 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-28 19:42:08.931252 INFO::Done
2025-09-28 19:42:08.934644 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:08.943255 INFO::ASW Batch was 0.452950824569368 prior to batch effect correction and is now -0.109907612818017 .
2025-09-28 19:42:08.944023 INFO::ASW Label was 0.281646460172883 prior to batch effect correction and is now 0.898767049086776 .
2025-09-28 19:42:08.945583 INFO::Total function execution time is 0.300544023513794 s and adjustment time is 0.269344091415405 s ( 89.62 )
2025-09-28 19:42:08.969194 INFO::Formatting Data.
2025-09-28 19:42:08.970341 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:08.97152 INFO::Removing potential empty rows and columns
2025-09-28 19:42:08.972712 INFO::Found 0 missing values.
2025-09-28 19:42:08.978526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:08.979389 INFO::Done
2025-09-28 19:42:08.979973 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:08.983781 INFO::Starting hierarchical adjustment
2025-09-28 19:42:08.984908 INFO::Found 5 batches.
2025-09-28 19:42:08.985663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:08.98651 INFO::Using default BPPARAM
2025-09-28 19:42:08.987312 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.
2025-09-28 19:42:09.173568 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:09.199723 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-28 19:42:09.255187 INFO::Done
2025-09-28 19:42:09.256939 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:09.264846 INFO::ASW Batch was 0.464127060115774 prior to batch effect correction and is now -0.0822461439120328 .
2025-09-28 19:42:09.266375 INFO::ASW Label was 0.295052821226082 prior to batch effect correction and is now 0.846041393980425 .
2025-09-28 19:42:09.267723 INFO::Total function execution time is 0.298532009124756 s and adjustment time is 0.270449876785278 s ( 90.59 )
2025-09-28 19:42:09.269093 INFO::Formatting Data.
2025-09-28 19:42:09.270205 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:09.272424 INFO::Removing potential empty rows and columns
2025-09-28 19:42:09.274106 INFO::Found 0 missing values.
2025-09-28 19:42:09.279802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:09.281391 INFO::Done
2025-09-28 19:42:09.282403 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:09.287025 INFO::Starting hierarchical adjustment
2025-09-28 19:42:09.288179 INFO::Found 5 batches.
2025-09-28 19:42:09.289097 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:09.290059 INFO::Using default BPPARAM
2025-09-28 19:42:09.290736 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.
2025-09-28 19:42:09.499495 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:09.529097 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-28 19:42:09.575494 INFO::Done
2025-09-28 19:42:09.577199 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:09.582931 INFO::ASW Batch was 0.464127060115774 prior to batch effect correction and is now -0.0822461439120328 .
2025-09-28 19:42:09.584153 INFO::ASW Label was 0.295052821226082 prior to batch effect correction and is now 0.846041393980425 .
2025-09-28 19:42:09.585824 INFO::Total function execution time is 0.316591024398804 s and adjustment time is 0.287508010864258 s ( 90.81 )
2025-09-28 19:42:09.608922 INFO::Formatting Data.
2025-09-28 19:42:09.609756 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:09.611513 INFO::Removing potential empty rows and columns
2025-09-28 19:42:09.613045 INFO::Found 0 missing values.
2025-09-28 19:42:09.61644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:09.617058 INFO::Done
2025-09-28 19:42:09.617794 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:09.621984 INFO::Starting hierarchical adjustment
2025-09-28 19:42:09.62277 INFO::Found 2 batches.
2025-09-28 19:42:09.623407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:09.624185 INFO::Using default BPPARAM
2025-09-28 19:42:09.624728 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:09.625642 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-28 19:42:09.64221 INFO::Done
2025-09-28 19:42:09.643512 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:09.647136 INFO::ASW Batch was 0.466942347949857 prior to batch effect correction and is now 0.0598674434484136 .
2025-09-28 19:42:09.647788 INFO::ASW Label was 0.619168117433987 prior to batch effect correction and is now 0.878384702531153 .
2025-09-28 19:42:09.648537 INFO::Total function execution time is 0.0397360324859619 s and adjustment time is 0.0195379257202148 s ( 49.17 )
2025-09-28 19:42:09.649295 INFO::Formatting Data.
2025-09-28 19:42:09.650052 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:09.651208 INFO::Removing potential empty rows and columns
2025-09-28 19:42:09.652718 INFO::Found 0 missing values.
2025-09-28 19:42:09.656622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:09.657518 INFO::Done
2025-09-28 19:42:09.658325 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:09.662726 INFO::Starting hierarchical adjustment
2025-09-28 19:42:09.663735 INFO::Found 2 batches.
2025-09-28 19:42:09.664658 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:09.665528 INFO::Using default BPPARAM
2025-09-28 19:42:09.666346 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:09.667744 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-28 19:42:09.685873 INFO::Done
2025-09-28 19:42:09.686712 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:09.690607 INFO::ASW Batch was 0.466942347949857 prior to batch effect correction and is now 0.0598674434484136 .
2025-09-28 19:42:09.691253 INFO::ASW Label was 0.619168117433987 prior to batch effect correction and is now 0.878384702531153 .
2025-09-28 19:42:09.692098 INFO::Total function execution time is 0.0427670478820801 s and adjustment time is 0.0222878456115723 s ( 52.11 )
2025-09-28 19:42:09.708758 INFO::Formatting Data.
2025-09-28 19:42:09.709762 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:09.711078 INFO::Removing potential empty rows and columns
2025-09-28 19:42:09.712365 INFO::Found 0 missing values.
2025-09-28 19:42:09.71575 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:09.716573 INFO::Done
2025-09-28 19:42:09.717312 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:09.719619 INFO::Starting hierarchical adjustment
2025-09-28 19:42:09.720289 INFO::Found 2 batches.
2025-09-28 19:42:09.720781 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:09.721342 INFO::Using default BPPARAM
2025-09-28 19:42:09.722132 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:09.723127 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-28 19:42:09.764967 INFO::Done
2025-09-28 19:42:09.766122 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:09.769237 INFO::ASW Batch was 0.111602039781145 prior to batch effect correction and is now -0.0719725056899043 .
2025-09-28 19:42:09.770398 INFO::Total function execution time is 0.0617828369140625 s and adjustment time is 0.044713020324707 s ( 72.37 )
2025-09-28 19:42:09.790462 INFO::Formatting Data.
2025-09-28 19:42:09.791829 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:09.79331 INFO::Removing potential empty rows and columns
2025-09-28 19:42:09.794871 INFO::Found 0 missing values.
2025-09-28 19:42:09.796605 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.
2025-09-28 19:42:09.803337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:09.804409 INFO::Done
2025-09-28 19:42:09.805287 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:09.809452 INFO::Starting hierarchical adjustment
2025-09-28 19:42:09.810506 INFO::Found 2 batches.
2025-09-28 19:42:09.811276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:09.812242 INFO::Using default BPPARAM
2025-09-28 19:42:09.813078 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:09.814571 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-28 19:42:09.834463 INFO::Done
2025-09-28 19:42:09.835205 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:09.839378 INFO::ASW Batch was 0.722187476676898 prior to batch effect correction and is now 0.176989422763601 .
2025-09-28 19:42:09.840313 INFO::ASW Label was 0.391548479672878 prior to batch effect correction and is now 0.812873907411859 .
2025-09-28 19:42:09.841483 INFO::Total function execution time is 0.0511250495910645 s and adjustment time is 0.024177074432373 s ( 47.29 )
2025-09-28 19:42:09.842638 INFO::Formatting Data.
2025-09-28 19:42:09.843525 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:09.844876 INFO::Removing potential empty rows and columns
2025-09-28 19:42:09.846105 INFO::Found 0 missing values.
2025-09-28 19:42:09.847041 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.
2025-09-28 19:42:09.853792 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:09.854768 INFO::Done
2025-09-28 19:42:09.855599 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:09.858883 INFO::Starting hierarchical adjustment
2025-09-28 19:42:09.859605 INFO::Found 2 batches.
2025-09-28 19:42:09.860112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:09.860673 INFO::Using default BPPARAM
2025-09-28 19:42:09.861369 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:09.862723 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-28 19:42:09.883911 INFO::Done
2025-09-28 19:42:09.884979 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:09.889648 INFO::ASW Batch was 0.722187476676898 prior to batch effect correction and is now 0.176989422763601 .
2025-09-28 19:42:09.890656 INFO::ASW Label was 0.391548479672878 prior to batch effect correction and is now 0.812873907411859 .
2025-09-28 19:42:09.891871 INFO::Total function execution time is 0.0492570400238037 s and adjustment time is 0.0243699550628662 s ( 49.48 )
2025-09-28 19:42:10.176826 INFO::Formatting Data.
2025-09-28 19:42:10.178003 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:10.179374 INFO::Removing potential empty rows and columns
2025-09-28 19:42:10.181034 INFO::Found 0 missing values.
2025-09-28 19:42:10.184892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:10.185883 INFO::Done
2025-09-28 19:42:10.186626 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:10.189441 INFO::Starting hierarchical adjustment
2025-09-28 19:42:10.190414 INFO::Found 3 batches.
2025-09-28 19:42:10.190935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:10.191617 INFO::Using default BPPARAM
2025-09-28 19:42:10.192543 INFO::Processing subtree level 1
2025-09-28 19:42:10.34479 INFO::Adjusting the last 1 batches sequentially
2025-09-28 19:42:10.353807 INFO::Done
2025-09-28 19:42:10.357272 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:10.370354 INFO::ASW Batch was -0.100704593110433 prior to batch effect correction and is now -0.100704593110433 .
2025-09-28 19:42:10.374768 INFO::Total function execution time is 0.196980953216553 s and adjustment time is 0.163495063781738 s ( 83 )
2025-09-28 19:42:10.377052 INFO::Formatting Data.
2025-09-28 19:42:10.378128 INFO::Typecasting input to dataframe.
2025-09-28 19:42:10.380664 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:10.382788 INFO::Removing potential empty rows and columns
2025-09-28 19:42:10.385693 INFO::Found 0 missing values.
2025-09-28 19:42:10.390483 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:10.391728 INFO::Done
2025-09-28 19:42:10.392649 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:10.396037 INFO::Starting hierarchical adjustment
2025-09-28 19:42:10.397573 INFO::Found 3 batches.
2025-09-28 19:42:10.398391 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:10.399418 INFO::Using default BPPARAM
2025-09-28 19:42:10.400913 INFO::Processing subtree level 1
2025-09-28 19:42:10.557955 INFO::Adjusting the last 1 batches sequentially
2025-09-28 19:42:10.566827 INFO::Done
2025-09-28 19:42:10.57011 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:10.579507 INFO::ASW Batch was -0.100704593110433 prior to batch effect correction and is now -0.100704593110433 .
2025-09-28 19:42:10.583185 INFO::Total function execution time is 0.205575942993164 s and adjustment time is 0.169903993606567 s ( 82.65 )
2025-09-28 19:42:10.605864 INFO::Formatting Data.
2025-09-28 19:42:10.607738 INFO::Typecasting input to dataframe.
2025-09-28 19:42:10.609135 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:10.610586 INFO::Removing potential empty rows and columns
2025-09-28 19:42:10.614644 INFO::Found 0 missing values.
2025-09-28 19:42:10.618835 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:10.619698 INFO::Done
2025-09-28 19:42:10.620503 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:10.623309 INFO::Starting hierarchical adjustment
2025-09-28 19:42:10.625236 INFO::Found 3 batches.
2025-09-28 19:42:10.626009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:10.626821 INFO::Using default BPPARAM
2025-09-28 19:42:10.627724 INFO::Processing subtree level 1
2025-09-28 19:42:10.742815 INFO::Adjusting the last 1 batches sequentially
2025-09-28 19:42:10.746631 INFO::Done
2025-09-28 19:42:10.747339 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:10.751298 INFO::ASW Batch was -0.0813330517000066 prior to batch effect correction and is now -0.0813330517000066 .
2025-09-28 19:42:10.752855 INFO::Total function execution time is 0.147029161453247 s and adjustment time is 0.121608018875122 s ( 82.71 )
2025-09-28 19:42:10.953865 INFO::Formatting Data.
2025-09-28 19:42:10.955146 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:10.957016 INFO::Removing potential empty rows and columns
2025-09-28 19:42:10.961253 INFO::Found 1000 missing values.
2025-09-28 19:42:10.984178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:10.98497 INFO::Done
2025-09-28 19:42:10.985985 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:10.995634 INFO::Starting hierarchical adjustment
2025-09-28 19:42:10.997203 INFO::Found 10 batches.
2025-09-28 19:42:10.998164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:10.999264 INFO::Using default BPPARAM
2025-09-28 19:42:11.000421 INFO::Processing subtree level 1
2025-09-28 19:42:11.16098 INFO::Processing subtree level 2
2025-09-28 19:42:11.371266 INFO::Adjusting the last 1 batches sequentially
2025-09-28 19:42:11.378992 INFO::Done
2025-09-28 19:42:11.380381 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:11.390455 INFO::ASW Batch was 0.502215771961481 prior to batch effect correction and is now 0.502215771961481 .
2025-09-28 19:42:11.391759 INFO::ASW Label was 0.326669367631647 prior to batch effect correction and is now 0.326669367631647 .
2025-09-28 19:42:11.39346 INFO::Total function execution time is 0.439629077911377 s and adjustment time is 0.382113933563232 s ( 86.92 )
2025-09-28 19:42:11.394533 INFO::Formatting Data.
2025-09-28 19:42:11.395298 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:11.397545 INFO::Removing potential empty rows and columns
2025-09-28 19:42:11.402425 INFO::Found 1000 missing values.
2025-09-28 19:42:11.426842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:11.427947 INFO::Done
2025-09-28 19:42:11.42866 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:11.43528 INFO::Starting hierarchical adjustment
2025-09-28 19:42:11.436588 INFO::Found 10 batches.
2025-09-28 19:42:13.03697 INFO::Set up parallel execution backend with 2 workers
2025-09-28 19:42:13.037866 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-28 19:42:14.400943 INFO::Adjusting the last 2 batches sequentially
2025-09-28 19:42:14.402267 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-28 19:42:14.415708 INFO::Done
2025-09-28 19:42:14.416367 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:14.422577 INFO::ASW Batch was 0.502215771961481 prior to batch effect correction and is now 0.502215771961481 .
2025-09-28 19:42:14.423541 INFO::ASW Label was 0.326669367631647 prior to batch effect correction and is now 0.326669367631647 .
2025-09-28 19:42:14.424653 INFO::Total function execution time is 3.03012585639954 s and adjustment time is 2.9794750213623 s ( 98.33 )
2025-09-28 19:42:14.666742 INFO::Formatting Data.
2025-09-28 19:42:14.668052 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:14.670049 INFO::Removing potential empty rows and columns
2025-09-28 19:42:14.672417 INFO::Found 0 missing values.
2025-09-28 19:42:14.677647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:14.679506 INFO::Done
2025-09-28 19:42:14.680461 INFO::Acquiring quality metrics before batch effect correction.
2025-09-28 19:42:14.685658 INFO::Starting hierarchical adjustment
2025-09-28 19:42:14.686985 INFO::Found 3 batches.
2025-09-28 19:42:14.68784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-28 19:42:14.688779 INFO::Using default BPPARAM
2025-09-28 19:42:14.689473 INFO::Processing subtree level 1
2025-09-28 19:42:14.841546 INFO::Adjusting the last 1 batches sequentially
2025-09-28 19:42:14.845925 INFO::Done
2025-09-28 19:42:14.847327 INFO::Acquiring quality metrics after batch effect correction.
2025-09-28 19:42:14.854442 INFO::ASW Batch was 0.20198827780441 prior to batch effect correction and is now -0.11818166265586 .
2025-09-28 19:42:14.855798 INFO::ASW Label was -0.201238231797171 prior to batch effect correction and is now -0.00958366355410836 .
2025-09-28 19:42:14.857617 INFO::Total function execution time is 0.190848827362061 s and adjustment time is 0.159127950668335 s ( 83.38 )
2025-09-28 19:42:15.084731 INFO::Formatting Data.
2025-09-28 19:42:15.086174 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.087731 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.089225 INFO::Found 2 missing values.
2025-09-28 19:42:15.093335 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.094098 INFO::Done
2025-09-28 19:42:15.148084 INFO::Found NA in Reference column
2025-09-28 19:42:15.165655 INFO::Require at least two references per batch.
2025-09-28 19:42:15.20587 INFO::Formatting Data.
2025-09-28 19:42:15.206778 INFO::Recognized SummarizedExperiment
2025-09-28 19:42:15.207455 INFO::Typecasting input to dataframe.
2025-09-28 19:42:15.222691 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.224166 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.229103 INFO::Found 0 missing values.
2025-09-28 19:42:15.24216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.243346 INFO::Done
2025-09-28 19:42:15.267449 INFO::Formatting Data.
2025-09-28 19:42:15.268309 INFO::Recognized SummarizedExperiment
2025-09-28 19:42:15.268978 INFO::Typecasting input to dataframe.
2025-09-28 19:42:15.29086 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.292776 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.299123 INFO::Found 0 missing values.
2025-09-28 19:42:15.315726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.316971 INFO::Done
2025-09-28 19:42:15.342149 INFO::Formatting Data.
2025-09-28 19:42:15.343036 INFO::Recognized SummarizedExperiment
2025-09-28 19:42:15.343729 INFO::Typecasting input to dataframe.
2025-09-28 19:42:15.374967 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.37627 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.37786 INFO::Found 0 missing values.
2025-09-28 19:42:15.3794 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.
2025-09-28 19:42:15.385887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.386889 INFO::Done
2025-09-28 19:42:15.405055 INFO::Formatting Data.
2025-09-28 19:42:15.406122 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.40757 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.409124 INFO::Found 0 missing values.
2025-09-28 19:42:15.413894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.415011 INFO::Done
2025-09-28 19:42:15.436851 INFO::Formatting Data.
2025-09-28 19:42:15.438173 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.439496 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.440935 INFO::Found 0 missing values.
2025-09-28 19:42:15.445249 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.446285 INFO::Done
2025-09-28 19:42:15.504442 INFO::Formatting Data.
2025-09-28 19:42:15.505727 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.50769 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.509462 INFO::Found 1 missing values.
2025-09-28 19:42:15.51339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.514531 INFO::Done
2025-09-28 19:42:15.552476 INFO::Formatting Data.
2025-09-28 19:42:15.553731 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.555261 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.556992 INFO::Found 2 missing values.
2025-09-28 19:42:15.558521 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.
2025-09-28 19:42:15.562818 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.564033 INFO::Done
2025-09-28 19:42:15.584224 INFO::Formatting Data.
2025-09-28 19:42:15.585207 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.58635 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.58769 INFO::Found 2 missing values.
2025-09-28 19:42:15.58971 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.590366 INFO::Done
2025-09-28 19:42:15.611811 INFO::Formatting Data.
2025-09-28 19:42:15.613222 INFO::Typecasting input to dataframe.
2025-09-28 19:42:15.614997 INFO::Replacing NaNs with NAs.
2025-09-28 19:42:15.616593 INFO::Removing potential empty rows and columns
2025-09-28 19:42:15.618509 INFO::Found 0 missing values.
2025-09-28 19:42:15.623491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-28 19:42:15.624434 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.625 5.183 26.072
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 29.019 | 1.661 | 20.617 | |
| compute_asw | 0.020 | 0.002 | 0.022 | |
| count_existing | 0.013 | 0.001 | 0.014 | |
| generate_data_covariables | 0.016 | 0.001 | 0.017 | |
| generate_dataset | 0.012 | 0.000 | 0.013 | |