Yannis Schumann
| Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 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 2025-09-04 12:04 -0400 (Thu, 04 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4617 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4564 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 163/2321 | 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: 2025-09-03 19:18:50 -0400 (Wed, 03 Sep 2025) |
| EndedAt: 2025-09-03 19:20:19 -0400 (Wed, 03 Sep 2025) |
| EllapsedTime: 89.2 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 (2025-06-13)
* 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 26.479 1.429 19.05
* 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 (2025-06-13) -- "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")
2025-09-03 19:19:58.532009 INFO::Formatting Data.
2025-09-03 19:19:58.536365 INFO::Replacing NaNs with NAs.
2025-09-03 19:19:58.551661 INFO::Removing potential empty rows and columns
2025-09-03 19:19:58.845733 INFO::Found 0 missing values.
2025-09-03 19:19:58.85054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:19:58.851523 INFO::Done
2025-09-03 19:19:58.852361 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:19:58.870539 INFO::Starting hierarchical adjustment
2025-09-03 19:19:58.87154 INFO::Found 3 batches.
2025-09-03 19:19:58.872167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:19:58.873366 INFO::Using default BPPARAM
2025-09-03 19:19:58.873907 INFO::Processing subtree level 1
2025-09-03 19:19:59.027037 INFO::Adjusting the last 1 batches sequentially
2025-09-03 19:19:59.034279 INFO::Done
2025-09-03 19:19:59.035029 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:19:59.041495 INFO::ASW Batch was -0.089192177089207 prior to batch effect correction and is now -0.089192177089207 .
2025-09-03 19:19:59.043019 INFO::Total function execution time is 0.511712074279785 s and adjustment time is 0.162922143936157 s ( 31.84 )
2025-09-03 19:19:59.068766 INFO::Formatting Data.
2025-09-03 19:19:59.069568 INFO::Replacing NaNs with NAs.
2025-09-03 19:19:59.070481 INFO::Removing potential empty rows and columns
2025-09-03 19:19:59.071695 INFO::Found 0 missing values.
2025-09-03 19:19:59.073134 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.
2025-09-03 19:19:59.087195 INFO::Formatting Data.
2025-09-03 19:19:59.088395 INFO::Replacing NaNs with NAs.
2025-09-03 19:19:59.089507 INFO::Removing potential empty rows and columns
2025-09-03 19:19:59.090963 INFO::Found 0 missing values.
2025-09-03 19:19:59.092128 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.
2025-09-03 19:19:59.113803 INFO::Formatting Data.
2025-09-03 19:19:59.114912 INFO::Replacing NaNs with NAs.
2025-09-03 19:19:59.116409 INFO::Removing potential empty rows and columns
2025-09-03 19:19:59.118185 INFO::Found 0 missing values.
2025-09-03 19:19:59.119508 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.
2025-09-03 19:19:59.125008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:19:59.125622 INFO::Done
2025-09-03 19:19:59.126122 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:19:59.1292 INFO::Starting hierarchical adjustment
2025-09-03 19:19:59.130241 INFO::Found 2 batches.
2025-09-03 19:19:59.130908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:19:59.131673 INFO::Using default BPPARAM
2025-09-03 19:19:59.132318 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:19:59.133538 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-03 19:19:59.163143 INFO::Done
2025-09-03 19:19:59.163851 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:19:59.165962 INFO::ASW Batch was -0.00368074130633369 prior to batch effect correction and is now -0.126348326281392 .
2025-09-03 19:19:59.167136 INFO::Total function execution time is 0.0533461570739746 s and adjustment time is 0.033113956451416 s ( 62.07 )
2025-09-03 19:19:59.171025 INFO::Formatting Data.
2025-09-03 19:19:59.171971 INFO::Replacing NaNs with NAs.
2025-09-03 19:19:59.182888 INFO::Formatting Data.
2025-09-03 19:19:59.183967 INFO::Replacing NaNs with NAs.
2025-09-03 19:19:59.185179 INFO::Removing potential empty rows and columns
2025-09-03 19:19:59.186465 INFO::Found 0 missing values.
2025-09-03 19:19:59.190025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:19:59.190736 INFO::Done
2025-09-03 19:19:59.191383 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:19:59.193914 INFO::Starting hierarchical adjustment
2025-09-03 19:19:59.195077 INFO::Found 2 batches.
2025-09-03 19:19:59.195984 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:19:59.19657 INFO::Using default BPPARAM
2025-09-03 19:19:59.197185 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:19:59.198362 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-03 19:19:59.253687 INFO::Done
2025-09-03 19:19:59.25473 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:19:59.256885 INFO::ASW Batch was -0.0565668627745379 prior to batch effect correction and is now -0.122433910225454 .
2025-09-03 19:19:59.257665 INFO::Total function execution time is 0.0749349594116211 s and adjustment time is 0.0590250492095947 s ( 78.77 )
2025-09-03 19:19:59.258593 INFO::Formatting Data.
2025-09-03 19:19:59.259133 INFO::Replacing NaNs with NAs.
2025-09-03 19:19:59.259919 INFO::Removing potential empty rows and columns
2025-09-03 19:19:59.261187 INFO::Found 0 missing values.
2025-09-03 19:19:59.264383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:19:59.265109 INFO::Done
2025-09-03 19:19:59.265611 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:19:59.267827 INFO::Starting hierarchical adjustment
2025-09-03 19:19:59.268701 INFO::Found 2 batches.
2025-09-03 19:19:59.269292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:19:59.26993 INFO::Using default BPPARAM
2025-09-03 19:19:59.270684 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:19:59.271566 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-03 19:19:59.289774 INFO::Done
2025-09-03 19:19:59.290769 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:19:59.293674 INFO::ASW Batch was -0.0565668627745379 prior to batch effect correction and is now -0.122433910225454 .
2025-09-03 19:19:59.294824 INFO::Total function execution time is 0.0361270904541016 s and adjustment time is 0.0212600231170654 s ( 58.85 )
2025-09-03 19:20:02.577205 INFO::Formatting Data.
2025-09-03 19:20:02.57828 INFO::Recognized SummarizedExperiment
2025-09-03 19:20:02.579094 INFO::Typecasting input to dataframe.
2025-09-03 19:20:02.615692 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:02.61694 INFO::Removing potential empty rows and columns
2025-09-03 19:20:02.620912 INFO::Found 0 missing values.
2025-09-03 19:20:02.630458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:02.631366 INFO::Done
2025-09-03 19:20:02.632083 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:02.637059 INFO::Starting hierarchical adjustment
2025-09-03 19:20:02.638241 INFO::Found 2 batches.
2025-09-03 19:20:02.639052 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:02.640582 INFO::Using default BPPARAM
2025-09-03 19:20:02.641458 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:02.642962 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-03 19:20:02.697079 INFO::Done
2025-09-03 19:20:02.69782 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:02.701976 INFO::ASW Batch was 0.00798686790964709 prior to batch effect correction and is now -0.0900353576621265 .
2025-09-03 19:20:02.702976 INFO::Total function execution time is 0.126117944717407 s and adjustment time is 0.0590729713439941 s ( 46.84 )
2025-09-03 19:20:02.728533 INFO::Formatting Data.
2025-09-03 19:20:02.729689 INFO::Recognized SummarizedExperiment
2025-09-03 19:20:02.730635 INFO::Typecasting input to dataframe.
2025-09-03 19:20:02.745268 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:02.747182 INFO::Removing potential empty rows and columns
2025-09-03 19:20:02.753388 INFO::Found 0 missing values.
2025-09-03 19:20:02.762032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:02.763049 INFO::Done
2025-09-03 19:20:02.764173 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:02.768536 INFO::Starting hierarchical adjustment
2025-09-03 19:20:02.769394 INFO::Found 2 batches.
2025-09-03 19:20:02.769989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:02.770704 INFO::Using default BPPARAM
2025-09-03 19:20:02.771184 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:02.772132 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-03 19:20:02.795889 INFO::Done
2025-09-03 19:20:02.796663 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:02.800862 INFO::ASW Batch was -0.0152801732117767 prior to batch effect correction and is now -0.0152801732117767 .
2025-09-03 19:20:02.802159 INFO::Total function execution time is 0.0736169815063477 s and adjustment time is 0.0266451835632324 s ( 36.19 )
2025-09-03 19:20:02.826905 INFO::Formatting Data.
2025-09-03 19:20:02.827978 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:02.829237 INFO::Removing potential empty rows and columns
2025-09-03 19:20:02.830641 INFO::Found 0 missing values.
2025-09-03 19:20:02.835406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:02.836517 INFO::Done
2025-09-03 19:20:02.837582 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:02.840228 INFO::Starting hierarchical adjustment
2025-09-03 19:20:02.84097 INFO::Found 3 batches.
2025-09-03 19:20:02.841465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:02.842117 INFO::Using default BPPARAM
2025-09-03 19:20:02.842847 INFO::Processing subtree level 1
2025-09-03 19:20:03.06656 INFO::Adjusting the last 1 batches sequentially
2025-09-03 19:20:03.078026 INFO::Done
2025-09-03 19:20:03.080349 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:03.090412 INFO::ASW Batch was -0.0481618875256001 prior to batch effect correction and is now -0.154182718526502 .
2025-09-03 19:20:03.093223 INFO::Total function execution time is 0.266332864761353 s and adjustment time is 0.237126111984253 s ( 89.03 )
2025-09-03 19:20:03.128491 INFO::Skipping initial DF formatting
2025-09-03 19:20:03.129651 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:03.134932 INFO::Starting hierarchical adjustment
2025-09-03 19:20:03.136256 INFO::Found 5 batches.
2025-09-03 19:20:03.137317 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:03.137994 INFO::Using default BPPARAM
2025-09-03 19:20:03.138572 INFO::Processing subtree level 1
2025-09-03 19:20:03.509781 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:03.522567 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-03 19:20:03.576376 INFO::Done
2025-09-03 19:20:03.579366 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:03.589849 INFO::ASW Batch was 0.504907044984234 prior to batch effect correction and is now 0.504907044984234 .
2025-09-03 19:20:03.590831 INFO::ASW Label was 0.358446656153452 prior to batch effect correction and is now 0.358446656153452 .
2025-09-03 19:20:03.593502 INFO::Total function execution time is 0.464318990707397 s and adjustment time is 0.440402030944824 s ( 94.85 )
2025-09-03 19:20:03.694634 INFO::Formatting Data.
2025-09-03 19:20:03.69591 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:03.697349 INFO::Removing potential empty rows and columns
2025-09-03 19:20:03.698902 INFO::Found 0 missing values.
2025-09-03 19:20:03.704798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:03.705679 INFO::Done
2025-09-03 19:20:03.706444 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:03.71076 INFO::Starting hierarchical adjustment
2025-09-03 19:20:03.711852 INFO::Found 5 batches.
2025-09-03 19:20:03.712617 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:03.713485 INFO::Using default BPPARAM
2025-09-03 19:20:03.714308 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.
2025-09-03 19:20:03.943612 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:03.95469 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-03 19:20:03.984086 INFO::Done
2025-09-03 19:20:03.985527 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:03.99113 INFO::ASW Batch was 0.213035993529298 prior to batch effect correction and is now -0.0562510059722603 .
2025-09-03 19:20:03.992125 INFO::ASW Label was 0.527710145865649 prior to batch effect correction and is now 0.803672377509311 .
2025-09-03 19:20:03.993093 INFO::Total function execution time is 0.298632144927979 s and adjustment time is 0.272454977035522 s ( 91.23 )
2025-09-03 19:20:03.994168 INFO::Formatting Data.
2025-09-03 19:20:03.994855 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:03.996319 INFO::Removing potential empty rows and columns
2025-09-03 19:20:03.997723 INFO::Found 0 missing values.
2025-09-03 19:20:04.002921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:04.003643 INFO::Done
2025-09-03 19:20:04.004191 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:04.007481 INFO::Starting hierarchical adjustment
2025-09-03 19:20:04.008263 INFO::Found 5 batches.
2025-09-03 19:20:04.009157 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:04.010147 INFO::Using default BPPARAM
2025-09-03 19:20:04.01114 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.
2025-09-03 19:20:04.191384 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:04.220154 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-03 19:20:04.267141 INFO::Done
2025-09-03 19:20:04.26822 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:04.273201 INFO::ASW Batch was 0.213035993529298 prior to batch effect correction and is now -0.0562510059722603 .
2025-09-03 19:20:04.273995 INFO::ASW Label was 0.527710145865649 prior to batch effect correction and is now 0.803672377509311 .
2025-09-03 19:20:04.276666 INFO::Total function execution time is 0.28190803527832 s and adjustment time is 0.258983135223389 s ( 91.87 )
2025-09-03 19:20:04.299092 INFO::Formatting Data.
2025-09-03 19:20:04.300245 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:04.301616 INFO::Removing potential empty rows and columns
2025-09-03 19:20:04.303097 INFO::Found 0 missing values.
2025-09-03 19:20:04.307635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:04.308269 INFO::Done
2025-09-03 19:20:04.309144 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:04.313613 INFO::Starting hierarchical adjustment
2025-09-03 19:20:04.315062 INFO::Found 5 batches.
2025-09-03 19:20:04.316344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:04.317404 INFO::Using default BPPARAM
2025-09-03 19:20:04.318374 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.
2025-09-03 19:20:04.509763 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:04.523003 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-03 19:20:04.560657 INFO::Done
2025-09-03 19:20:04.562433 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:04.567255 INFO::ASW Batch was 0.374198123345841 prior to batch effect correction and is now -0.0164542537283316 .
2025-09-03 19:20:04.569147 INFO::ASW Label was 0.432537517757507 prior to batch effect correction and is now 0.690755993631018 .
2025-09-03 19:20:04.571304 INFO::Total function execution time is 0.271404981613159 s and adjustment time is 0.245831966400146 s ( 90.58 )
2025-09-03 19:20:04.572683 INFO::Formatting Data.
2025-09-03 19:20:04.573695 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:04.575166 INFO::Removing potential empty rows and columns
2025-09-03 19:20:04.576182 INFO::Found 0 missing values.
2025-09-03 19:20:04.579931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:04.580575 INFO::Done
2025-09-03 19:20:04.581466 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:04.585906 INFO::Starting hierarchical adjustment
2025-09-03 19:20:04.587054 INFO::Found 5 batches.
2025-09-03 19:20:04.58786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:04.588741 INFO::Using default BPPARAM
2025-09-03 19:20:04.589485 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.
2025-09-03 19:20:04.783257 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:04.792508 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-03 19:20:04.826785 INFO::Done
2025-09-03 19:20:04.827924 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:04.833843 INFO::ASW Batch was 0.374198123345841 prior to batch effect correction and is now -0.0164542537283316 .
2025-09-03 19:20:04.835001 INFO::ASW Label was 0.432537517757507 prior to batch effect correction and is now 0.690755993631018 .
2025-09-03 19:20:04.836451 INFO::Total function execution time is 0.263743877410889 s and adjustment time is 0.239914178848267 s ( 90.96 )
2025-09-03 19:20:04.859465 INFO::Formatting Data.
2025-09-03 19:20:04.860482 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:04.861441 INFO::Removing potential empty rows and columns
2025-09-03 19:20:04.86276 INFO::Found 0 missing values.
2025-09-03 19:20:04.865767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:04.866639 INFO::Done
2025-09-03 19:20:04.867341 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:04.870556 INFO::Starting hierarchical adjustment
2025-09-03 19:20:04.871411 INFO::Found 2 batches.
2025-09-03 19:20:04.872549 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:04.873478 INFO::Using default BPPARAM
2025-09-03 19:20:04.874231 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:04.875577 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-03 19:20:04.89813 INFO::Done
2025-09-03 19:20:04.898873 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:04.902664 INFO::ASW Batch was 0.319219788670132 prior to batch effect correction and is now 0.0590687960751386 .
2025-09-03 19:20:04.903689 INFO::ASW Label was 0.701946541134405 prior to batch effect correction and is now 0.874769596120893 .
2025-09-03 19:20:04.904912 INFO::Total function execution time is 0.0455389022827148 s and adjustment time is 0.0268769264221191 s ( 59.02 )
2025-09-03 19:20:04.906049 INFO::Formatting Data.
2025-09-03 19:20:04.906965 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:04.908276 INFO::Removing potential empty rows and columns
2025-09-03 19:20:04.910088 INFO::Found 0 missing values.
2025-09-03 19:20:04.914129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:04.915112 INFO::Done
2025-09-03 19:20:04.915985 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:04.920381 INFO::Starting hierarchical adjustment
2025-09-03 19:20:04.921256 INFO::Found 2 batches.
2025-09-03 19:20:04.92183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:04.922414 INFO::Using default BPPARAM
2025-09-03 19:20:04.922925 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:04.923853 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-09-03 19:20:04.940902 INFO::Done
2025-09-03 19:20:04.941998 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:04.946558 INFO::ASW Batch was 0.319219788670132 prior to batch effect correction and is now 0.0590687960751386 .
2025-09-03 19:20:04.947511 INFO::ASW Label was 0.701946541134405 prior to batch effect correction and is now 0.874769596120893 .
2025-09-03 19:20:04.948678 INFO::Total function execution time is 0.0426681041717529 s and adjustment time is 0.0197510719299316 s ( 46.29 )
2025-09-03 19:20:04.96836 INFO::Formatting Data.
2025-09-03 19:20:04.969637 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:04.971251 INFO::Removing potential empty rows and columns
2025-09-03 19:20:04.972282 INFO::Found 0 missing values.
2025-09-03 19:20:04.974926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:04.976833 INFO::Done
2025-09-03 19:20:04.977421 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:04.980022 INFO::Starting hierarchical adjustment
2025-09-03 19:20:04.981146 INFO::Found 2 batches.
2025-09-03 19:20:04.982016 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:04.982976 INFO::Using default BPPARAM
2025-09-03 19:20:04.983809 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:04.985206 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-03 19:20:05.029859 INFO::Done
2025-09-03 19:20:05.031033 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:05.034301 INFO::ASW Batch was -0.113809201817657 prior to batch effect correction and is now -0.15051234351825 .
2025-09-03 19:20:05.035654 INFO::Total function execution time is 0.067406177520752 s and adjustment time is 0.0489671230316162 s ( 72.64 )
2025-09-03 19:20:05.055872 INFO::Formatting Data.
2025-09-03 19:20:05.057133 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:05.058639 INFO::Removing potential empty rows and columns
2025-09-03 19:20:05.06019 INFO::Found 0 missing values.
2025-09-03 19:20:05.062083 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.
2025-09-03 19:20:05.066801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:05.06745 INFO::Done
2025-09-03 19:20:05.068101 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:05.072565 INFO::Starting hierarchical adjustment
2025-09-03 19:20:05.073752 INFO::Found 2 batches.
2025-09-03 19:20:05.074584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:05.075505 INFO::Using default BPPARAM
2025-09-03 19:20:05.076275 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:05.077702 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-03 19:20:05.098871 INFO::Done
2025-09-03 19:20:05.100097 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:05.104189 INFO::ASW Batch was 0.619563748874474 prior to batch effect correction and is now -0.017554492788522 .
2025-09-03 19:20:05.10519 INFO::ASW Label was 0.360785042196503 prior to batch effect correction and is now 0.908015013950223 .
2025-09-03 19:20:05.106371 INFO::Total function execution time is 0.0506458282470703 s and adjustment time is 0.025327205657959 s ( 50.01 )
2025-09-03 19:20:05.107551 INFO::Formatting Data.
2025-09-03 19:20:05.108461 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:05.109796 INFO::Removing potential empty rows and columns
2025-09-03 19:20:05.111257 INFO::Found 0 missing values.
2025-09-03 19:20:05.112212 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.
2025-09-03 19:20:05.118385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:05.118999 INFO::Done
2025-09-03 19:20:05.119511 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:05.122621 INFO::Starting hierarchical adjustment
2025-09-03 19:20:05.12332 INFO::Found 2 batches.
2025-09-03 19:20:05.12401 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:05.124895 INFO::Using default BPPARAM
2025-09-03 19:20:05.125416 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:05.126312 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-03 19:20:05.142763 INFO::Done
2025-09-03 19:20:05.143808 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:05.147091 INFO::ASW Batch was 0.619563748874474 prior to batch effect correction and is now -0.017554492788522 .
2025-09-03 19:20:05.147751 INFO::ASW Label was 0.360785042196503 prior to batch effect correction and is now 0.908015013950223 .
2025-09-03 19:20:05.148507 INFO::Total function execution time is 0.0410621166229248 s and adjustment time is 0.0195071697235107 s ( 47.51 )
2025-09-03 19:20:05.415674 INFO::Formatting Data.
2025-09-03 19:20:05.416843 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:05.418354 INFO::Removing potential empty rows and columns
2025-09-03 19:20:05.419943 INFO::Found 0 missing values.
2025-09-03 19:20:05.424816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:05.42575 INFO::Done
2025-09-03 19:20:05.426521 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:05.42901 INFO::Starting hierarchical adjustment
2025-09-03 19:20:05.429739 INFO::Found 3 batches.
2025-09-03 19:20:05.430432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:05.431235 INFO::Using default BPPARAM
2025-09-03 19:20:05.431753 INFO::Processing subtree level 1
2025-09-03 19:20:05.562545 INFO::Adjusting the last 1 batches sequentially
2025-09-03 19:20:05.581453 INFO::Done
2025-09-03 19:20:05.582771 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:05.596893 INFO::ASW Batch was 0.0140752591872686 prior to batch effect correction and is now 0.0140752591872686 .
2025-09-03 19:20:05.60042 INFO::Total function execution time is 0.184787034988403 s and adjustment time is 0.150603055953979 s ( 81.5 )
2025-09-03 19:20:05.60352 INFO::Formatting Data.
2025-09-03 19:20:05.604953 INFO::Typecasting input to dataframe.
2025-09-03 19:20:05.606339 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:05.608491 INFO::Removing potential empty rows and columns
2025-09-03 19:20:05.610639 INFO::Found 0 missing values.
2025-09-03 19:20:05.616123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:05.616788 INFO::Done
2025-09-03 19:20:05.617326 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:05.619193 INFO::Starting hierarchical adjustment
2025-09-03 19:20:05.619927 INFO::Found 3 batches.
2025-09-03 19:20:05.620611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:05.621608 INFO::Using default BPPARAM
2025-09-03 19:20:05.623655 INFO::Processing subtree level 1
2025-09-03 19:20:05.766125 INFO::Adjusting the last 1 batches sequentially
2025-09-03 19:20:05.780595 INFO::Done
2025-09-03 19:20:05.7835 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:05.793866 INFO::ASW Batch was 0.0140752591872686 prior to batch effect correction and is now 0.0140752591872686 .
2025-09-03 19:20:05.797247 INFO::Total function execution time is 0.194020986557007 s and adjustment time is 0.160782098770142 s ( 82.87 )
2025-09-03 19:20:05.818647 INFO::Formatting Data.
2025-09-03 19:20:05.819424 INFO::Typecasting input to dataframe.
2025-09-03 19:20:05.820718 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:05.821702 INFO::Removing potential empty rows and columns
2025-09-03 19:20:05.826481 INFO::Found 0 missing values.
2025-09-03 19:20:05.831123 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:05.832009 INFO::Done
2025-09-03 19:20:05.832873 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:05.835283 INFO::Starting hierarchical adjustment
2025-09-03 19:20:05.836242 INFO::Found 3 batches.
2025-09-03 19:20:05.837018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:05.837873 INFO::Using default BPPARAM
2025-09-03 19:20:05.838581 INFO::Processing subtree level 1
2025-09-03 19:20:05.982578 INFO::Adjusting the last 1 batches sequentially
2025-09-03 19:20:05.995754 INFO::Done
2025-09-03 19:20:05.996585 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:06.008597 INFO::ASW Batch was -0.0917118264563167 prior to batch effect correction and is now -0.0917118264563167 .
2025-09-03 19:20:06.011387 INFO::Total function execution time is 0.192647933959961 s and adjustment time is 0.1596999168396 s ( 82.9 )
2025-09-03 19:20:06.252471 INFO::Formatting Data.
2025-09-03 19:20:06.253474 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:06.255518 INFO::Removing potential empty rows and columns
2025-09-03 19:20:06.259163 INFO::Found 1000 missing values.
2025-09-03 19:20:06.28378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:06.284638 INFO::Done
2025-09-03 19:20:06.285486 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:06.293142 INFO::Starting hierarchical adjustment
2025-09-03 19:20:06.294351 INFO::Found 10 batches.
2025-09-03 19:20:06.295831 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:06.29679 INFO::Using default BPPARAM
2025-09-03 19:20:06.297579 INFO::Processing subtree level 1
2025-09-03 19:20:06.488724 INFO::Processing subtree level 2
2025-09-03 19:20:06.702151 INFO::Adjusting the last 1 batches sequentially
2025-09-03 19:20:06.713155 INFO::Done
2025-09-03 19:20:06.715075 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:06.729917 INFO::ASW Batch was 0.515174557911427 prior to batch effect correction and is now 0.515174557911427 .
2025-09-03 19:20:06.732313 INFO::ASW Label was 0.329462203325431 prior to batch effect correction and is now 0.329462203325431 .
2025-09-03 19:20:06.735169 INFO::Total function execution time is 0.48282790184021 s and adjustment time is 0.419020891189575 s ( 86.78 )
2025-09-03 19:20:06.736906 INFO::Formatting Data.
2025-09-03 19:20:06.738569 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:06.739747 INFO::Removing potential empty rows and columns
2025-09-03 19:20:06.746284 INFO::Found 1000 missing values.
2025-09-03 19:20:06.771996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:06.772759 INFO::Done
2025-09-03 19:20:06.773341 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:06.780085 INFO::Starting hierarchical adjustment
2025-09-03 19:20:06.781954 INFO::Found 10 batches.
2025-09-03 19:20:07.837283 INFO::Set up parallel execution backend with 2 workers
2025-09-03 19:20:07.838304 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-09-03 19:20:09.106933 INFO::Adjusting the last 2 batches sequentially
2025-09-03 19:20:09.108005 INFO::Adjusting sequential tree level 1 with 2 batches
2025-09-03 19:20:09.127032 INFO::Done
2025-09-03 19:20:09.127878 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:09.13283 INFO::ASW Batch was 0.515174557911427 prior to batch effect correction and is now 0.515174557911427 .
2025-09-03 19:20:09.133844 INFO::ASW Label was 0.329462203325431 prior to batch effect correction and is now 0.329462203325431 .
2025-09-03 19:20:09.134596 INFO::Total function execution time is 2.39784502983093 s and adjustment time is 2.34532594680786 s ( 97.81 )
2025-09-03 19:20:09.358424 INFO::Formatting Data.
2025-09-03 19:20:09.359218 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:09.360112 INFO::Removing potential empty rows and columns
2025-09-03 19:20:09.361097 INFO::Found 0 missing values.
2025-09-03 19:20:09.365143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:09.365674 INFO::Done
2025-09-03 19:20:09.366271 INFO::Acquiring quality metrics before batch effect correction.
2025-09-03 19:20:09.369652 INFO::Starting hierarchical adjustment
2025-09-03 19:20:09.37066 INFO::Found 3 batches.
2025-09-03 19:20:09.371391 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-09-03 19:20:09.372937 INFO::Using default BPPARAM
2025-09-03 19:20:09.373656 INFO::Processing subtree level 1
2025-09-03 19:20:09.541093 INFO::Adjusting the last 1 batches sequentially
2025-09-03 19:20:09.551093 INFO::Done
2025-09-03 19:20:09.552601 INFO::Acquiring quality metrics after batch effect correction.
2025-09-03 19:20:09.564171 INFO::ASW Batch was 0.177013571980582 prior to batch effect correction and is now -0.141390688314429 .
2025-09-03 19:20:09.565165 INFO::ASW Label was -0.225004243671297 prior to batch effect correction and is now 0.01635553552471 .
2025-09-03 19:20:09.568413 INFO::Total function execution time is 0.20978307723999 s and adjustment time is 0.180609941482544 s ( 86.09 )
2025-09-03 19:20:09.749598 INFO::Formatting Data.
2025-09-03 19:20:09.750725 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:09.752021 INFO::Removing potential empty rows and columns
2025-09-03 19:20:09.753578 INFO::Found 2 missing values.
2025-09-03 19:20:09.757862 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:09.758717 INFO::Done
2025-09-03 19:20:09.802499 INFO::Found NA in Reference column
2025-09-03 19:20:09.816427 INFO::Require at least two references per batch.
2025-09-03 19:20:09.845084 INFO::Formatting Data.
2025-09-03 19:20:09.84609 INFO::Recognized SummarizedExperiment
2025-09-03 19:20:09.846886 INFO::Typecasting input to dataframe.
2025-09-03 19:20:09.858911 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:09.860376 INFO::Removing potential empty rows and columns
2025-09-03 19:20:09.865168 INFO::Found 0 missing values.
2025-09-03 19:20:09.874528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:09.875206 INFO::Done
2025-09-03 19:20:09.89472 INFO::Formatting Data.
2025-09-03 19:20:09.895439 INFO::Recognized SummarizedExperiment
2025-09-03 19:20:09.895967 INFO::Typecasting input to dataframe.
2025-09-03 19:20:09.911813 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:09.912997 INFO::Removing potential empty rows and columns
2025-09-03 19:20:09.916094 INFO::Found 0 missing values.
2025-09-03 19:20:09.925251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:09.926146 INFO::Done
2025-09-03 19:20:09.944817 INFO::Formatting Data.
2025-09-03 19:20:09.945858 INFO::Recognized SummarizedExperiment
2025-09-03 19:20:09.946602 INFO::Typecasting input to dataframe.
2025-09-03 19:20:09.962158 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:09.963196 INFO::Removing potential empty rows and columns
2025-09-03 19:20:09.964186 INFO::Found 0 missing values.
2025-09-03 19:20:09.96505 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.
2025-09-03 19:20:09.969308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:09.969851 INFO::Done
2025-09-03 19:20:09.98448 INFO::Formatting Data.
2025-09-03 19:20:09.985343 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:09.986192 INFO::Removing potential empty rows and columns
2025-09-03 19:20:09.987177 INFO::Found 0 missing values.
2025-09-03 19:20:09.990571 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:09.991368 INFO::Done
2025-09-03 19:20:10.008241 INFO::Formatting Data.
2025-09-03 19:20:10.008993 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:10.009812 INFO::Removing potential empty rows and columns
2025-09-03 19:20:10.011211 INFO::Found 0 missing values.
2025-09-03 19:20:10.015362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:10.016127 INFO::Done
2025-09-03 19:20:10.063795 INFO::Formatting Data.
2025-09-03 19:20:10.065066 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:10.06652 INFO::Removing potential empty rows and columns
2025-09-03 19:20:10.06807 INFO::Found 1 missing values.
2025-09-03 19:20:10.07154 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:10.072146 INFO::Done
2025-09-03 19:20:10.101832 INFO::Formatting Data.
2025-09-03 19:20:10.102627 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:10.103465 INFO::Removing potential empty rows and columns
2025-09-03 19:20:10.104653 INFO::Found 2 missing values.
2025-09-03 19:20:10.105731 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.
2025-09-03 19:20:10.108719 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:10.109494 INFO::Done
2025-09-03 19:20:10.126936 INFO::Formatting Data.
2025-09-03 19:20:10.127764 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:10.128858 INFO::Removing potential empty rows and columns
2025-09-03 19:20:10.130229 INFO::Found 2 missing values.
2025-09-03 19:20:10.132493 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:10.133225 INFO::Done
2025-09-03 19:20:10.14958 INFO::Formatting Data.
2025-09-03 19:20:10.150711 INFO::Typecasting input to dataframe.
2025-09-03 19:20:10.151536 INFO::Replacing NaNs with NAs.
2025-09-03 19:20:10.152371 INFO::Removing potential empty rows and columns
2025-09-03 19:20:10.153279 INFO::Found 0 missing values.
2025-09-03 19:20:10.155753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-09-03 19:20:10.156433 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.352 4.282 24.862
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.479 | 1.429 | 19.050 | |
| compute_asw | 0.026 | 0.002 | 0.028 | |
| count_existing | 0.015 | 0.001 | 0.016 | |
| generate_data_covariables | 0.013 | 0.000 | 0.014 | |
| generate_dataset | 0.012 | 0.001 | 0.014 | |