Yannis Schumann
| Snapshot Date: 2025-12-05 13:40 -0500 (Fri, 05 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 2e49878 |
| git_last_commit_date: 2025-10-29 11:26:54 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-06 11:35 -0500 (Sat, 06 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 168/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2025-12-05 18:37:40 -0500 (Fri, 05 Dec 2025) |
| EndedAt: 2025-12-05 18:38:18 -0500 (Fri, 05 Dec 2025) |
| EllapsedTime: 37.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.7.0’
* 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 10.181 0.41 7.588
* 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/4.6-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.7.0’ ** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-12-05 18:38:09.177823 INFO::Formatting Data.
2025-12-05 18:38:09.179505 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:09.185016 INFO::Removing potential empty rows and columns
2025-12-05 18:38:09.303422 INFO::Found 0 missing values.
2025-12-05 18:38:09.304683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:09.304904 INFO::Done
2025-12-05 18:38:09.305142 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:09.315087 INFO::Starting hierarchical adjustment
2025-12-05 18:38:09.315542 INFO::Found 3 batches.
2025-12-05 18:38:09.315784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:09.316296 INFO::Using default BPPARAM
2025-12-05 18:38:09.316504 INFO::Processing subtree level 1
2025-12-05 18:38:09.394028 INFO::Adjusting the last 1 batches sequentially
2025-12-05 18:38:09.397033 INFO::Done
2025-12-05 18:38:09.397285 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:09.399021 INFO::ASW Batch was -0.054564751295203 prior to batch effect correction and is now -0.054564751295203 .
2025-12-05 18:38:09.399584 INFO::Total function execution time is 0.222227096557617 s and adjustment time is 0.0816059112548828 s ( 36.72 )
2025-12-05 18:38:09.407547 INFO::Formatting Data.
2025-12-05 18:38:09.407842 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:09.408197 INFO::Removing potential empty rows and columns
2025-12-05 18:38:09.408721 INFO::Found 0 missing values.
2025-12-05 18:38:09.409095 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.
2025-12-05 18:38:09.414518 INFO::Formatting Data.
2025-12-05 18:38:09.414797 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:09.415161 INFO::Removing potential empty rows and columns
2025-12-05 18:38:09.415677 INFO::Found 0 missing values.
2025-12-05 18:38:09.416047 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.
2025-12-05 18:38:09.423256 INFO::Formatting Data.
2025-12-05 18:38:09.423546 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:09.42391 INFO::Removing potential empty rows and columns
2025-12-05 18:38:09.424778 INFO::Found 0 missing values.
2025-12-05 18:38:09.425108 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.
2025-12-05 18:38:09.426686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:09.426896 INFO::Done
2025-12-05 18:38:09.427102 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:09.428028 INFO::Starting hierarchical adjustment
2025-12-05 18:38:09.428298 INFO::Found 2 batches.
2025-12-05 18:38:09.428537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:09.428817 INFO::Using default BPPARAM
2025-12-05 18:38:09.429039 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:09.429404 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 18:38:09.438557 INFO::Done
2025-12-05 18:38:09.438806 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:09.439513 INFO::ASW Batch was -0.0483157398472065 prior to batch effect correction and is now -0.115409944038524 .
2025-12-05 18:38:09.439771 INFO::Total function execution time is 0.0165419578552246 s and adjustment time is 0.0103130340576172 s ( 62.34 )
2025-12-05 18:38:09.440887 INFO::Formatting Data.
2025-12-05 18:38:09.441186 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:09.444464 INFO::Formatting Data.
2025-12-05 18:38:09.444696 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:09.445021 INFO::Removing potential empty rows and columns
2025-12-05 18:38:09.445385 INFO::Found 0 missing values.
2025-12-05 18:38:09.44638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:09.446564 INFO::Done
2025-12-05 18:38:09.446719 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:09.447384 INFO::Starting hierarchical adjustment
2025-12-05 18:38:09.447605 INFO::Found 2 batches.
2025-12-05 18:38:09.447774 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:09.447971 INFO::Using default BPPARAM
2025-12-05 18:38:09.448132 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:09.448402 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 18:38:09.477066 INFO::Done
2025-12-05 18:38:09.477334 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:09.478034 INFO::ASW Batch was 0.0467393531046403 prior to batch effect correction and is now -0.110178836302261 .
2025-12-05 18:38:09.478298 INFO::Total function execution time is 0.0338470935821533 s and adjustment time is 0.0294868946075439 s ( 87.12 )
2025-12-05 18:38:09.478628 INFO::Formatting Data.
2025-12-05 18:38:09.478802 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:09.479084 INFO::Removing potential empty rows and columns
2025-12-05 18:38:09.479405 INFO::Found 0 missing values.
2025-12-05 18:38:09.480297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:09.480487 INFO::Done
2025-12-05 18:38:09.480657 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:09.481277 INFO::Starting hierarchical adjustment
2025-12-05 18:38:09.481517 INFO::Found 2 batches.
2025-12-05 18:38:09.481692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:09.481902 INFO::Using default BPPARAM
2025-12-05 18:38:09.482071 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:09.482354 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 18:38:09.487521 INFO::Done
2025-12-05 18:38:09.487747 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:09.488403 INFO::ASW Batch was 0.0467393531046403 prior to batch effect correction and is now -0.110178836302261 .
2025-12-05 18:38:09.488672 INFO::Total function execution time is 0.0100250244140625 s and adjustment time is 0.00604796409606934 s ( 60.33 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2025-12-05 18:38:10.80976 INFO::Formatting Data.
2025-12-05 18:38:10.81007 INFO::Recognized SummarizedExperiment
2025-12-05 18:38:10.810244 INFO::Typecasting input to dataframe.
2025-12-05 18:38:10.822121 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:10.822582 INFO::Removing potential empty rows and columns
2025-12-05 18:38:10.823837 INFO::Found 0 missing values.
2025-12-05 18:38:10.826157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:10.82636 INFO::Done
2025-12-05 18:38:10.826543 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:10.827864 INFO::Starting hierarchical adjustment
2025-12-05 18:38:10.828138 INFO::Found 2 batches.
2025-12-05 18:38:10.828322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:10.828675 INFO::Using default BPPARAM
2025-12-05 18:38:10.828831 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:10.829153 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 18:38:10.853552 INFO::Done
2025-12-05 18:38:10.853863 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:10.855333 INFO::ASW Batch was -0.0158265362410372 prior to batch effect correction and is now -0.0991085207374507 .
2025-12-05 18:38:10.855648 INFO::Total function execution time is 0.0460028648376465 s and adjustment time is 0.025439977645874 s ( 55.3 )
Warning: stack imbalance in '{', 73 then 75
2025-12-05 18:38:10.862585 INFO::Formatting Data.
2025-12-05 18:38:10.862818 INFO::Recognized SummarizedExperiment
2025-12-05 18:38:10.862977 INFO::Typecasting input to dataframe.
2025-12-05 18:38:10.866074 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:10.866457 INFO::Removing potential empty rows and columns
2025-12-05 18:38:10.867615 INFO::Found 0 missing values.
2025-12-05 18:38:10.869837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:10.870037 INFO::Done
2025-12-05 18:38:10.870205 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:10.871424 INFO::Starting hierarchical adjustment
2025-12-05 18:38:10.87164 INFO::Found 2 batches.
2025-12-05 18:38:10.871795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:10.871979 INFO::Using default BPPARAM
2025-12-05 18:38:10.872141 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:10.872423 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 18:38:10.880237 INFO::Done
2025-12-05 18:38:10.880457 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:10.881613 INFO::ASW Batch was 0.00956408297143086 prior to batch effect correction and is now 0.00956408297143086 .
2025-12-05 18:38:10.881878 INFO::Total function execution time is 0.0192980766296387 s and adjustment time is 0.00863814353942871 s ( 44.76 )
2025-12-05 18:38:10.888506 INFO::Formatting Data.
2025-12-05 18:38:10.888748 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:10.892219 INFO::Removing potential empty rows and columns
2025-12-05 18:38:10.89261 INFO::Found 0 missing values.
2025-12-05 18:38:10.893527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:10.893696 INFO::Done
2025-12-05 18:38:10.893858 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:10.89449 INFO::Starting hierarchical adjustment
2025-12-05 18:38:10.8947 INFO::Found 3 batches.
2025-12-05 18:38:10.894854 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:10.895042 INFO::Using default BPPARAM
2025-12-05 18:38:10.89519 INFO::Processing subtree level 1
2025-12-05 18:38:10.963665 INFO::Adjusting the last 1 batches sequentially
2025-12-05 18:38:10.965069 INFO::Done
2025-12-05 18:38:10.96545 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:10.967457 INFO::ASW Batch was -0.0447949494571271 prior to batch effect correction and is now -0.14742547247826 .
2025-12-05 18:38:10.968049 INFO::Total function execution time is 0.0795040130615234 s and adjustment time is 0.0704038143157959 s ( 88.55 )
2025-12-05 18:38:10.977516 INFO::Skipping initial DF formatting
2025-12-05 18:38:10.977812 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:10.979349 INFO::Starting hierarchical adjustment
2025-12-05 18:38:10.979626 INFO::Found 5 batches.
2025-12-05 18:38:10.979802 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:10.980025 INFO::Using default BPPARAM
2025-12-05 18:38:10.980188 INFO::Processing subtree level 1
2025-12-05 18:38:11.038249 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.040122 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 18:38:11.050054 INFO::Done
2025-12-05 18:38:11.050649 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.052817 INFO::ASW Batch was 0.529657385019748 prior to batch effect correction and is now 0.529657385019748 .
2025-12-05 18:38:11.053463 INFO::ASW Label was 0.36859294087074 prior to batch effect correction and is now 0.36859294087074 .
2025-12-05 18:38:11.054162 INFO::Total function execution time is 0.0766429901123047 s and adjustment time is 0.0704829692840576 s ( 91.96 )
2025-12-05 18:38:11.063104 INFO::Formatting Data.
2025-12-05 18:38:11.063347 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.063669 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.064063 INFO::Found 0 missing values.
2025-12-05 18:38:11.065278 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.065443 INFO::Done
2025-12-05 18:38:11.065608 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.066578 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.066822 INFO::Found 5 batches.
2025-12-05 18:38:11.06704 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.067367 INFO::Using default BPPARAM
2025-12-05 18:38:11.067572 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.
2025-12-05 18:38:11.124726 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.12664 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 18:38:11.135957 INFO::Done
2025-12-05 18:38:11.136367 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.137734 INFO::ASW Batch was 0.416075520183795 prior to batch effect correction and is now -0.0763786716739904 .
2025-12-05 18:38:11.137945 INFO::ASW Label was 0.290116782391618 prior to batch effect correction and is now 0.850327279762021 .
2025-12-05 18:38:11.138266 INFO::Total function execution time is 0.0751590728759766 s and adjustment time is 0.0691699981689453 s ( 92.03 )
2025-12-05 18:38:11.138559 INFO::Formatting Data.
2025-12-05 18:38:11.138749 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.139042 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.139361 INFO::Found 0 missing values.
2025-12-05 18:38:11.140568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.140745 INFO::Done
2025-12-05 18:38:11.140904 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.141809 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.142155 INFO::Found 5 batches.
2025-12-05 18:38:11.142322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.142533 INFO::Using default BPPARAM
2025-12-05 18:38:11.14293 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.
2025-12-05 18:38:11.188897 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.194858 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 18:38:11.205569 INFO::Done
2025-12-05 18:38:11.205981 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.20781 INFO::ASW Batch was 0.416075520183795 prior to batch effect correction and is now -0.0763786716739904 .
2025-12-05 18:38:11.208025 INFO::ASW Label was 0.290116782391618 prior to batch effect correction and is now 0.850327279762021 .
2025-12-05 18:38:11.20845 INFO::Total function execution time is 0.0698549747467041 s and adjustment time is 0.0635390281677246 s ( 90.96 )
2025-12-05 18:38:11.215837 INFO::Formatting Data.
2025-12-05 18:38:11.216112 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.216405 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.216764 INFO::Found 0 missing values.
2025-12-05 18:38:11.218121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.218318 INFO::Done
2025-12-05 18:38:11.218499 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.219501 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.219753 INFO::Found 5 batches.
2025-12-05 18:38:11.219923 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.220153 INFO::Using default BPPARAM
2025-12-05 18:38:11.220362 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.
2025-12-05 18:38:11.274178 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.27673 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 18:38:11.285087 INFO::Done
2025-12-05 18:38:11.285454 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.286789 INFO::ASW Batch was 0.312782299654288 prior to batch effect correction and is now -0.010136928326246 .
2025-12-05 18:38:11.287029 INFO::ASW Label was 0.520557397676509 prior to batch effect correction and is now 0.764499566091164 .
2025-12-05 18:38:11.287371 INFO::Total function execution time is 0.0715279579162598 s and adjustment time is 0.065385103225708 s ( 91.41 )
2025-12-05 18:38:11.287733 INFO::Formatting Data.
2025-12-05 18:38:11.287963 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.28828 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.288672 INFO::Found 0 missing values.
2025-12-05 18:38:11.290477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.290728 INFO::Done
2025-12-05 18:38:11.29094 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.292035 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.292266 INFO::Found 5 batches.
2025-12-05 18:38:11.292613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.292842 INFO::Using default BPPARAM
2025-12-05 18:38:11.293112 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.
2025-12-05 18:38:11.346136 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.350594 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 18:38:11.359385 INFO::Done
2025-12-05 18:38:11.359814 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.361229 INFO::ASW Batch was 0.312782299654288 prior to batch effect correction and is now -0.010136928326246 .
2025-12-05 18:38:11.361441 INFO::ASW Label was 0.520557397676509 prior to batch effect correction and is now 0.764499566091164 .
2025-12-05 18:38:11.361715 INFO::Total function execution time is 0.0739738941192627 s and adjustment time is 0.0671548843383789 s ( 90.78 )
2025-12-05 18:38:11.368274 INFO::Formatting Data.
2025-12-05 18:38:11.368507 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.368802 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.36913 INFO::Found 0 missing values.
2025-12-05 18:38:11.369953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.370116 INFO::Done
2025-12-05 18:38:11.370271 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.371157 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.371583 INFO::Found 2 batches.
2025-12-05 18:38:11.371747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.371956 INFO::Using default BPPARAM
2025-12-05 18:38:11.372105 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.372405 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 18:38:11.377138 INFO::Done
2025-12-05 18:38:11.377395 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.378307 INFO::ASW Batch was 0.178412691357464 prior to batch effect correction and is now 0.0444871834127733 .
2025-12-05 18:38:11.378502 INFO::ASW Label was 0.789939292115487 prior to batch effect correction and is now 0.858669253251291 .
2025-12-05 18:38:11.378731 INFO::Total function execution time is 0.0104870796203613 s and adjustment time is 0.00559806823730469 s ( 53.38 )
2025-12-05 18:38:11.37895 INFO::Formatting Data.
2025-12-05 18:38:11.379118 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.379385 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.379664 INFO::Found 0 missing values.
2025-12-05 18:38:11.380409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.380572 INFO::Done
2025-12-05 18:38:11.380723 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.381592 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.381823 INFO::Found 2 batches.
2025-12-05 18:38:11.381979 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.382157 INFO::Using default BPPARAM
2025-12-05 18:38:11.382306 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.38256 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2025-12-05 18:38:11.387088 INFO::Done
2025-12-05 18:38:11.387294 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.388163 INFO::ASW Batch was 0.178412691357464 prior to batch effect correction and is now 0.0444871834127733 .
2025-12-05 18:38:11.388335 INFO::ASW Label was 0.789939292115487 prior to batch effect correction and is now 0.858669253251291 .
2025-12-05 18:38:11.38874 INFO::Total function execution time is 0.00978493690490723 s and adjustment time is 0.00530481338500977 s ( 54.21 )
2025-12-05 18:38:11.393032 INFO::Formatting Data.
2025-12-05 18:38:11.393394 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.39373 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.394023 INFO::Found 0 missing values.
2025-12-05 18:38:11.394678 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.394843 INFO::Done
2025-12-05 18:38:11.395004 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.39558 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.395788 INFO::Found 2 batches.
2025-12-05 18:38:11.395936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.396129 INFO::Using default BPPARAM
2025-12-05 18:38:11.396281 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.396526 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 18:38:11.409009 INFO::Done
2025-12-05 18:38:11.409326 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.410217 INFO::ASW Batch was 0.183250037239913 prior to batch effect correction and is now -0.150644079518359 .
2025-12-05 18:38:11.41115 INFO::Total function execution time is 0.0181159973144531 s and adjustment time is 0.0132379531860352 s ( 73.07 )
2025-12-05 18:38:11.417059 INFO::Formatting Data.
2025-12-05 18:38:11.417347 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.417659 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.418021 INFO::Found 0 missing values.
2025-12-05 18:38:11.418499 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.
2025-12-05 18:38:11.419906 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.420086 INFO::Done
2025-12-05 18:38:11.420248 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.42121 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.421427 INFO::Found 2 batches.
2025-12-05 18:38:11.421589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.421777 INFO::Using default BPPARAM
2025-12-05 18:38:11.421925 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.422198 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 18:38:11.42853 INFO::Done
2025-12-05 18:38:11.428797 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.429759 INFO::ASW Batch was 0.578395654708321 prior to batch effect correction and is now -0.00509619211055119 .
2025-12-05 18:38:11.429967 INFO::ASW Label was 0.33170882038942 prior to batch effect correction and is now 0.903411931010119 .
2025-12-05 18:38:11.430221 INFO::Total function execution time is 0.0132348537445068 s and adjustment time is 0.00713300704956055 s ( 53.9 )
2025-12-05 18:38:11.430458 INFO::Formatting Data.
2025-12-05 18:38:11.430633 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.430906 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.431205 INFO::Found 0 missing values.
2025-12-05 18:38:11.431483 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.
2025-12-05 18:38:11.432857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.433048 INFO::Done
2025-12-05 18:38:11.433216 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.434219 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.434441 INFO::Found 2 batches.
2025-12-05 18:38:11.434605 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.434793 INFO::Using default BPPARAM
2025-12-05 18:38:11.434947 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:11.435236 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 18:38:11.440732 INFO::Done
2025-12-05 18:38:11.440981 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.441939 INFO::ASW Batch was 0.578395654708321 prior to batch effect correction and is now -0.00509619211055119 .
2025-12-05 18:38:11.442135 INFO::ASW Label was 0.33170882038942 prior to batch effect correction and is now 0.903411931010119 .
2025-12-05 18:38:11.442408 INFO::Total function execution time is 0.0119349956512451 s and adjustment time is 0.00632405281066895 s ( 52.99 )
2025-12-05 18:38:11.514456 INFO::Formatting Data.
2025-12-05 18:38:11.514781 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.515106 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.515451 INFO::Found 0 missing values.
2025-12-05 18:38:11.516376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.516556 INFO::Done
2025-12-05 18:38:11.516718 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.517442 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.51766 INFO::Found 3 batches.
2025-12-05 18:38:11.517812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.518009 INFO::Using default BPPARAM
2025-12-05 18:38:11.518813 INFO::Processing subtree level 1
2025-12-05 18:38:11.558899 INFO::Adjusting the last 1 batches sequentially
2025-12-05 18:38:11.561105 INFO::Done
2025-12-05 18:38:11.561449 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.56337 INFO::ASW Batch was -0.0572073236502988 prior to batch effect correction and is now -0.0572073236502988 .
2025-12-05 18:38:11.563839 INFO::Total function execution time is 0.0494160652160645 s and adjustment time is 0.0434849262237549 s ( 88 )
2025-12-05 18:38:11.564267 INFO::Formatting Data.
2025-12-05 18:38:11.564477 INFO::Typecasting input to dataframe.
2025-12-05 18:38:11.564711 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.565022 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.565437 INFO::Found 0 missing values.
2025-12-05 18:38:11.566386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.566557 INFO::Done
2025-12-05 18:38:11.566724 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.567348 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.567567 INFO::Found 3 batches.
2025-12-05 18:38:11.567734 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.567962 INFO::Using default BPPARAM
2025-12-05 18:38:11.568143 INFO::Processing subtree level 1
2025-12-05 18:38:11.614075 INFO::Adjusting the last 1 batches sequentially
2025-12-05 18:38:11.617905 INFO::Done
2025-12-05 18:38:11.618477 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.621235 INFO::ASW Batch was -0.0572073236502988 prior to batch effect correction and is now -0.0572073236502988 .
2025-12-05 18:38:11.622338 INFO::Total function execution time is 0.0580499172210693 s and adjustment time is 0.0503349304199219 s ( 86.71 )
2025-12-05 18:38:11.629719 INFO::Formatting Data.
2025-12-05 18:38:11.630032 INFO::Typecasting input to dataframe.
2025-12-05 18:38:11.630375 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.630758 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.631234 INFO::Found 0 missing values.
2025-12-05 18:38:11.632384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.632622 INFO::Done
2025-12-05 18:38:11.632837 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.636596 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.636956 INFO::Found 3 batches.
2025-12-05 18:38:11.637159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.637404 INFO::Using default BPPARAM
2025-12-05 18:38:11.637584 INFO::Processing subtree level 1
2025-12-05 18:38:11.688959 INFO::Adjusting the last 1 batches sequentially
2025-12-05 18:38:11.692289 INFO::Done
2025-12-05 18:38:11.692658 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:11.695248 INFO::ASW Batch was -0.103967145588954 prior to batch effect correction and is now -0.103967145588954 .
2025-12-05 18:38:11.696029 INFO::Total function execution time is 0.0663402080535889 s and adjustment time is 0.0553960800170898 s ( 83.5 )
2025-12-05 18:38:11.780408 INFO::Formatting Data.
2025-12-05 18:38:11.780747 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:11.7812 INFO::Removing potential empty rows and columns
2025-12-05 18:38:11.782411 INFO::Found 1000 missing values.
2025-12-05 18:38:11.788317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:11.788581 INFO::Done
2025-12-05 18:38:11.788777 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:11.790958 INFO::Starting hierarchical adjustment
2025-12-05 18:38:11.791487 INFO::Found 10 batches.
2025-12-05 18:38:11.791666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:11.791894 INFO::Using default BPPARAM
2025-12-05 18:38:11.79213 INFO::Processing subtree level 1
2025-12-05 18:38:11.851897 INFO::Processing subtree level 2
2025-12-05 18:38:12.010095 INFO::Adjusting the last 1 batches sequentially
2025-12-05 18:38:12.017732 INFO::Done
2025-12-05 18:38:12.018238 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:12.059792 INFO::ASW Batch was 0.519281103282754 prior to batch effect correction and is now 0.519281103282754 .
2025-12-05 18:38:12.060186 INFO::ASW Label was 0.309494576632328 prior to batch effect correction and is now 0.309494576632328 .
2025-12-05 18:38:12.060648 INFO::Total function execution time is 0.28028416633606 s and adjustment time is 0.22625994682312 s ( 80.73 )
2025-12-05 18:38:12.060996 INFO::Formatting Data.
2025-12-05 18:38:12.061221 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:12.061856 INFO::Removing potential empty rows and columns
2025-12-05 18:38:12.062991 INFO::Found 1000 missing values.
2025-12-05 18:38:12.070504 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:12.070761 INFO::Done
2025-12-05 18:38:12.070939 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:12.073203 INFO::Starting hierarchical adjustment
2025-12-05 18:38:12.073559 INFO::Found 10 batches.
2025-12-05 18:38:12.593099 INFO::Set up parallel execution backend with 2 workers
2025-12-05 18:38:12.593395 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-12-05 18:38:13.362242 INFO::Adjusting the last 2 batches sequentially
2025-12-05 18:38:13.362878 INFO::Adjusting sequential tree level 1 with 2 batches
2025-12-05 18:38:13.369427 INFO::Done
2025-12-05 18:38:13.369626 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:13.371572 INFO::ASW Batch was 0.519281103282754 prior to batch effect correction and is now 0.519281103282754 .
2025-12-05 18:38:13.371748 INFO::ASW Label was 0.309494576632328 prior to batch effect correction and is now 0.309494576632328 .
2025-12-05 18:38:13.371984 INFO::Total function execution time is 1.31099605560303 s and adjustment time is 1.29595303535461 s ( 98.85 )
2025-12-05 18:38:13.436391 INFO::Formatting Data.
2025-12-05 18:38:13.43665 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.436982 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.437405 INFO::Found 0 missing values.
2025-12-05 18:38:13.438726 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.43892 INFO::Done
2025-12-05 18:38:13.439102 INFO::Acquiring quality metrics before batch effect correction.
2025-12-05 18:38:13.440052 INFO::Starting hierarchical adjustment
2025-12-05 18:38:13.440266 INFO::Found 3 batches.
2025-12-05 18:38:13.440426 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-12-05 18:38:13.440632 INFO::Using default BPPARAM
2025-12-05 18:38:13.44079 INFO::Processing subtree level 1
2025-12-05 18:38:13.502273 INFO::Adjusting the last 1 batches sequentially
2025-12-05 18:38:13.504116 INFO::Done
2025-12-05 18:38:13.504381 INFO::Acquiring quality metrics after batch effect correction.
2025-12-05 18:38:13.506923 INFO::ASW Batch was 0.333326214970239 prior to batch effect correction and is now -0.165249113576049 .
2025-12-05 18:38:13.507262 INFO::ASW Label was -0.201488132074291 prior to batch effect correction and is now -0.0861785934574683 .
2025-12-05 18:38:13.507992 INFO::Total function execution time is 0.0715858936309814 s and adjustment time is 0.0638809204101562 s ( 89.24 )
2025-12-05 18:38:13.569682 INFO::Formatting Data.
2025-12-05 18:38:13.570093 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.570479 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.57134 INFO::Found 2 missing values.
2025-12-05 18:38:13.573131 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.57339 INFO::Done
2025-12-05 18:38:13.586047 INFO::Found NA in Reference column
2025-12-05 18:38:13.590156 INFO::Require at least two references per batch.
2025-12-05 18:38:13.598039 INFO::Formatting Data.
2025-12-05 18:38:13.598276 INFO::Recognized SummarizedExperiment
2025-12-05 18:38:13.598447 INFO::Typecasting input to dataframe.
2025-12-05 18:38:13.602041 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.602418 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.603657 INFO::Found 0 missing values.
2025-12-05 18:38:13.605981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.60616 INFO::Done
2025-12-05 18:38:13.611861 INFO::Formatting Data.
2025-12-05 18:38:13.612107 INFO::Recognized SummarizedExperiment
2025-12-05 18:38:13.612287 INFO::Typecasting input to dataframe.
2025-12-05 18:38:13.617972 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.6184 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.619688 INFO::Found 0 missing values.
2025-12-05 18:38:13.623467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.62366 INFO::Done
2025-12-05 18:38:13.630126 INFO::Formatting Data.
2025-12-05 18:38:13.630391 INFO::Recognized SummarizedExperiment
2025-12-05 18:38:13.630596 INFO::Typecasting input to dataframe.
2025-12-05 18:38:13.636563 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.636855 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.637188 INFO::Found 0 missing values.
2025-12-05 18:38:13.637464 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.
2025-12-05 18:38:13.638842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.639006 INFO::Done
2025-12-05 18:38:13.642755 INFO::Formatting Data.
2025-12-05 18:38:13.642984 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.643252 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.643547 INFO::Found 0 missing values.
2025-12-05 18:38:13.644417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.644578 INFO::Done
2025-12-05 18:38:13.648975 INFO::Formatting Data.
2025-12-05 18:38:13.649265 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.649567 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.649875 INFO::Found 0 missing values.
2025-12-05 18:38:13.650808 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.650989 INFO::Done
2025-12-05 18:38:13.663174 INFO::Formatting Data.
2025-12-05 18:38:13.6635 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.663927 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.664415 INFO::Found 1 missing values.
2025-12-05 18:38:13.665374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.665573 INFO::Done
2025-12-05 18:38:13.673568 INFO::Formatting Data.
2025-12-05 18:38:13.673832 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.674125 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.674435 INFO::Found 2 missing values.
2025-12-05 18:38:13.674727 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.
2025-12-05 18:38:13.675542 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.675758 INFO::Done
2025-12-05 18:38:13.680051 INFO::Formatting Data.
2025-12-05 18:38:13.680395 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.68078 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.681083 INFO::Found 2 missing values.
2025-12-05 18:38:13.681609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.681776 INFO::Done
2025-12-05 18:38:13.685734 INFO::Formatting Data.
2025-12-05 18:38:13.685962 INFO::Typecasting input to dataframe.
2025-12-05 18:38:13.686214 INFO::Replacing NaNs with NAs.
2025-12-05 18:38:13.686479 INFO::Removing potential empty rows and columns
2025-12-05 18:38:13.686778 INFO::Found 0 missing values.
2025-12-05 18:38:13.687647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-12-05 18:38:13.687819 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.217 1.796 9.731
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.181 | 0.410 | 7.588 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.001 | 0.005 | |
| generate_data_covariables | 0.005 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |