Yannis Schumann
| Snapshot Date: 2026-01-08 13:40 -0500 (Thu, 08 Jan 2026) |
| 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-09 12:02 -0500 (Fri, 09 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 168/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.7.0 (landing page) Yannis Schumann
| 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: 2026-01-08 18:39:22 -0500 (Thu, 08 Jan 2026) |
| EndedAt: 2026-01-08 18:39:57 -0500 (Thu, 08 Jan 2026) |
| EllapsedTime: 35.5 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 10.228 0.408 7.598
* 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")
2026-01-08 18:39:48.629845 INFO::Formatting Data.
2026-01-08 18:39:48.631536 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:48.636459 INFO::Removing potential empty rows and columns
2026-01-08 18:39:48.748218 INFO::Found 0 missing values.
2026-01-08 18:39:48.749467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:48.749691 INFO::Done
2026-01-08 18:39:48.749896 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:48.757149 INFO::Starting hierarchical adjustment
2026-01-08 18:39:48.75748 INFO::Found 3 batches.
2026-01-08 18:39:48.7577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:48.758258 INFO::Using default BPPARAM
2026-01-08 18:39:48.758418 INFO::Processing subtree level 1
2026-01-08 18:39:48.810756 INFO::Adjusting the last 1 batches sequentially
2026-01-08 18:39:48.811939 INFO::Done
2026-01-08 18:39:48.81216 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:48.813522 INFO::ASW Batch was -0.0321022394443493 prior to batch effect correction and is now -0.0321022394443493 .
2026-01-08 18:39:48.814291 INFO::Total function execution time is 0.184807062149048 s and adjustment time is 0.0545248985290527 s ( 29.5 )
2026-01-08 18:39:48.821364 INFO::Formatting Data.
2026-01-08 18:39:48.821647 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:48.822009 INFO::Removing potential empty rows and columns
2026-01-08 18:39:48.822507 INFO::Found 0 missing values.
2026-01-08 18:39:48.822859 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.
2026-01-08 18:39:48.827514 INFO::Formatting Data.
2026-01-08 18:39:48.827767 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:48.828101 INFO::Removing potential empty rows and columns
2026-01-08 18:39:48.829125 INFO::Found 0 missing values.
2026-01-08 18:39:48.829563 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.
2026-01-08 18:39:48.842942 INFO::Formatting Data.
2026-01-08 18:39:48.843277 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:48.84364 INFO::Removing potential empty rows and columns
2026-01-08 18:39:48.844048 INFO::Found 0 missing values.
2026-01-08 18:39:48.844412 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.
2026-01-08 18:39:48.846191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:48.846426 INFO::Done
2026-01-08 18:39:48.846641 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:48.847588 INFO::Starting hierarchical adjustment
2026-01-08 18:39:48.847884 INFO::Found 2 batches.
2026-01-08 18:39:48.848101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:48.848383 INFO::Using default BPPARAM
2026-01-08 18:39:48.848616 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:48.849254 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-08 18:39:48.858664 INFO::Done
2026-01-08 18:39:48.858937 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:48.859665 INFO::ASW Batch was -0.01128222058941 prior to batch effect correction and is now -0.0942323079034883 .
2026-01-08 18:39:48.859926 INFO::Total function execution time is 0.0170331001281738 s and adjustment time is 0.0108249187469482 s ( 63.55 )
2026-01-08 18:39:48.861126 INFO::Formatting Data.
2026-01-08 18:39:48.86151 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:48.864897 INFO::Formatting Data.
2026-01-08 18:39:48.865126 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:48.865434 INFO::Removing potential empty rows and columns
2026-01-08 18:39:48.86579 INFO::Found 0 missing values.
2026-01-08 18:39:48.866819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:48.867003 INFO::Done
2026-01-08 18:39:48.867171 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:48.86785 INFO::Starting hierarchical adjustment
2026-01-08 18:39:48.868082 INFO::Found 2 batches.
2026-01-08 18:39:48.868247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:48.868449 INFO::Using default BPPARAM
2026-01-08 18:39:48.868614 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:48.868885 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-08 18:39:48.903114 INFO::Done
2026-01-08 18:39:48.903397 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:48.904091 INFO::ASW Batch was -0.00978738240505496 prior to batch effect correction and is now -0.0839322076942212 .
2026-01-08 18:39:48.904345 INFO::Total function execution time is 0.0394389629364014 s and adjustment time is 0.035045862197876 s ( 88.86 )
2026-01-08 18:39:48.904685 INFO::Formatting Data.
2026-01-08 18:39:48.904882 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:48.905169 INFO::Removing potential empty rows and columns
2026-01-08 18:39:48.905515 INFO::Found 0 missing values.
2026-01-08 18:39:48.906453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:48.90665 INFO::Done
2026-01-08 18:39:48.906816 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:48.907435 INFO::Starting hierarchical adjustment
2026-01-08 18:39:48.907684 INFO::Found 2 batches.
2026-01-08 18:39:48.907883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:48.908105 INFO::Using default BPPARAM
2026-01-08 18:39:48.90829 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:48.908594 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-08 18:39:48.913992 INFO::Done
2026-01-08 18:39:48.91424 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:48.914895 INFO::ASW Batch was -0.00978738240505496 prior to batch effect correction and is now -0.0839322076942212 .
2026-01-08 18:39:48.915151 INFO::Total function execution time is 0.0104548931121826 s and adjustment time is 0.0063319206237793 s ( 60.56 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-01-08 18:39:50.270638 INFO::Formatting Data.
2026-01-08 18:39:50.270884 INFO::Recognized SummarizedExperiment
2026-01-08 18:39:50.271042 INFO::Typecasting input to dataframe.
2026-01-08 18:39:50.281125 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.281526 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.282569 INFO::Found 0 missing values.
2026-01-08 18:39:50.284526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.284706 INFO::Done
2026-01-08 18:39:50.284847 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.285973 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.286192 INFO::Found 2 batches.
2026-01-08 18:39:50.286334 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.286646 INFO::Using default BPPARAM
2026-01-08 18:39:50.286795 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.287069 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-08 18:39:50.308323 INFO::Done
2026-01-08 18:39:50.30865 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.310505 INFO::ASW Batch was -0.031991475350928 prior to batch effect correction and is now -0.0892579389267033 .
2026-01-08 18:39:50.310824 INFO::Total function execution time is 0.0402758121490479 s and adjustment time is 0.0221529006958008 s ( 55 )
Warning: stack imbalance in '{', 73 then 75
2026-01-08 18:39:50.317423 INFO::Formatting Data.
2026-01-08 18:39:50.317667 INFO::Recognized SummarizedExperiment
2026-01-08 18:39:50.317829 INFO::Typecasting input to dataframe.
2026-01-08 18:39:50.320851 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.321228 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.322363 INFO::Found 0 missing values.
2026-01-08 18:39:50.324579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.324799 INFO::Done
2026-01-08 18:39:50.324962 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.326363 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.326649 INFO::Found 2 batches.
2026-01-08 18:39:50.326848 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.327083 INFO::Using default BPPARAM
2026-01-08 18:39:50.327265 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.32763 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-08 18:39:50.336697 INFO::Done
2026-01-08 18:39:50.336957 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.338183 INFO::ASW Batch was 0.00948885556964133 prior to batch effect correction and is now 0.00948885556964133 .
2026-01-08 18:39:50.338493 INFO::Total function execution time is 0.0210700035095215 s and adjustment time is 0.0101039409637451 s ( 47.95 )
2026-01-08 18:39:50.346481 INFO::Formatting Data.
2026-01-08 18:39:50.346831 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.347165 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.347548 INFO::Found 0 missing values.
2026-01-08 18:39:50.348527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.348706 INFO::Done
2026-01-08 18:39:50.348874 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.34957 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.349793 INFO::Found 3 batches.
2026-01-08 18:39:50.349945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.350127 INFO::Using default BPPARAM
2026-01-08 18:39:50.350271 INFO::Processing subtree level 1
2026-01-08 18:39:50.427422 INFO::Adjusting the last 1 batches sequentially
2026-01-08 18:39:50.429443 INFO::Done
2026-01-08 18:39:50.429829 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.432148 INFO::ASW Batch was -0.0816707212827668 prior to batch effect correction and is now -0.164453881121651 .
2026-01-08 18:39:50.433088 INFO::Total function execution time is 0.0864200592041016 s and adjustment time is 0.0796949863433838 s ( 92.22 )
2026-01-08 18:39:50.44113 INFO::Skipping initial DF formatting
2026-01-08 18:39:50.441407 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.442897 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.443212 INFO::Found 5 batches.
2026-01-08 18:39:50.443702 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.444094 INFO::Using default BPPARAM
2026-01-08 18:39:50.444359 INFO::Processing subtree level 1
2026-01-08 18:39:50.503553 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.504979 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-08 18:39:50.519888 INFO::Done
2026-01-08 18:39:50.520553 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.524951 INFO::ASW Batch was 0.44904747162716 prior to batch effect correction and is now 0.44904747162716 .
2026-01-08 18:39:50.525249 INFO::ASW Label was 0.423379631335173 prior to batch effect correction and is now 0.423379631335173 .
2026-01-08 18:39:50.526532 INFO::Total function execution time is 0.0851409435272217 s and adjustment time is 0.0767459869384766 s ( 90.14 )
2026-01-08 18:39:50.536211 INFO::Formatting Data.
2026-01-08 18:39:50.5369 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.53743 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.537887 INFO::Found 0 missing values.
2026-01-08 18:39:50.539273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.539463 INFO::Done
2026-01-08 18:39:50.539627 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.540665 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.540907 INFO::Found 5 batches.
2026-01-08 18:39:50.541098 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.541316 INFO::Using default BPPARAM
2026-01-08 18:39:50.541473 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.
2026-01-08 18:39:50.596668 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.598844 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-08 18:39:50.607955 INFO::Done
2026-01-08 18:39:50.608471 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.610039 INFO::ASW Batch was 0.484919208665673 prior to batch effect correction and is now -0.0944178622092263 .
2026-01-08 18:39:50.61029 INFO::ASW Label was 0.18254511927444 prior to batch effect correction and is now 0.857589257286865 .
2026-01-08 18:39:50.610952 INFO::Total function execution time is 0.0746200084686279 s and adjustment time is 0.0670919418334961 s ( 89.91 )
2026-01-08 18:39:50.611281 INFO::Formatting Data.
2026-01-08 18:39:50.611477 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.611776 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.612124 INFO::Found 0 missing values.
2026-01-08 18:39:50.613387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.613573 INFO::Done
2026-01-08 18:39:50.613757 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.614708 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.61498 INFO::Found 5 batches.
2026-01-08 18:39:50.615169 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.615418 INFO::Using default BPPARAM
2026-01-08 18:39:50.615598 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.
2026-01-08 18:39:50.669256 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.671855 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-08 18:39:50.681497 INFO::Done
2026-01-08 18:39:50.682004 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.683667 INFO::ASW Batch was 0.484919208665673 prior to batch effect correction and is now -0.0944178622092263 .
2026-01-08 18:39:50.683884 INFO::ASW Label was 0.18254511927444 prior to batch effect correction and is now 0.857589257286865 .
2026-01-08 18:39:50.684611 INFO::Total function execution time is 0.0731430053710938 s and adjustment time is 0.0665380954742432 s ( 90.97 )
2026-01-08 18:39:50.691729 INFO::Formatting Data.
2026-01-08 18:39:50.691993 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.692298 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.69266 INFO::Found 0 missing values.
2026-01-08 18:39:50.693862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.69403 INFO::Done
2026-01-08 18:39:50.694196 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.695145 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.695374 INFO::Found 5 batches.
2026-01-08 18:39:50.695566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.69584 INFO::Using default BPPARAM
2026-01-08 18:39:50.696001 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.
2026-01-08 18:39:50.751537 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.753903 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-08 18:39:50.770291 INFO::Done
2026-01-08 18:39:50.770766 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.772514 INFO::ASW Batch was 0.233584747649815 prior to batch effect correction and is now -0.0291718929533209 .
2026-01-08 18:39:50.772772 INFO::ASW Label was 0.594105149966591 prior to batch effect correction and is now 0.74808023681642 .
2026-01-08 18:39:50.773437 INFO::Total function execution time is 0.0815651416778564 s and adjustment time is 0.0749349594116211 s ( 91.87 )
2026-01-08 18:39:50.773788 INFO::Formatting Data.
2026-01-08 18:39:50.773982 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.774304 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.774709 INFO::Found 0 missing values.
2026-01-08 18:39:50.776069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.776259 INFO::Done
2026-01-08 18:39:50.776423 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.777483 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.777736 INFO::Found 5 batches.
2026-01-08 18:39:50.777928 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.778176 INFO::Using default BPPARAM
2026-01-08 18:39:50.778496 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.
2026-01-08 18:39:50.832724 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.836156 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-08 18:39:50.846019 INFO::Done
2026-01-08 18:39:50.846282 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.847599 INFO::ASW Batch was 0.233584747649815 prior to batch effect correction and is now -0.0291718929533209 .
2026-01-08 18:39:50.847808 INFO::ASW Label was 0.594105149966591 prior to batch effect correction and is now 0.74808023681642 .
2026-01-08 18:39:50.84867 INFO::Total function execution time is 0.0745358467102051 s and adjustment time is 0.0683228969573975 s ( 91.66 )
2026-01-08 18:39:50.855121 INFO::Formatting Data.
2026-01-08 18:39:50.855385 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.855686 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.856035 INFO::Found 0 missing values.
2026-01-08 18:39:50.856868 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.85704 INFO::Done
2026-01-08 18:39:50.857203 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.858159 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.858488 INFO::Found 2 batches.
2026-01-08 18:39:50.858652 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.858866 INFO::Using default BPPARAM
2026-01-08 18:39:50.859033 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.859449 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-08 18:39:50.865835 INFO::Done
2026-01-08 18:39:50.866069 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.866969 INFO::ASW Batch was 0.748934346419286 prior to batch effect correction and is now -0.0325891133477032 .
2026-01-08 18:39:50.86716 INFO::ASW Label was 0.28713083617162 prior to batch effect correction and is now 0.87317951184547 .
2026-01-08 18:39:50.867405 INFO::Total function execution time is 0.012300968170166 s and adjustment time is 0.0074770450592041 s ( 60.78 )
2026-01-08 18:39:50.867636 INFO::Formatting Data.
2026-01-08 18:39:50.867822 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.868094 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.8684 INFO::Found 0 missing values.
2026-01-08 18:39:50.869218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.869396 INFO::Done
2026-01-08 18:39:50.869563 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.870414 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.87065 INFO::Found 2 batches.
2026-01-08 18:39:50.870812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.871001 INFO::Using default BPPARAM
2026-01-08 18:39:50.871149 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.871407 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-01-08 18:39:50.87627 INFO::Done
2026-01-08 18:39:50.87652 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.877621 INFO::ASW Batch was 0.748934346419286 prior to batch effect correction and is now -0.0325891133477032 .
2026-01-08 18:39:50.877844 INFO::ASW Label was 0.28713083617162 prior to batch effect correction and is now 0.87317951184547 .
2026-01-08 18:39:50.878138 INFO::Total function execution time is 0.010479211807251 s and adjustment time is 0.00565910339355469 s ( 54 )
2026-01-08 18:39:50.883526 INFO::Formatting Data.
2026-01-08 18:39:50.883786 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.884126 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.884469 INFO::Found 0 missing values.
2026-01-08 18:39:50.885219 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.885432 INFO::Done
2026-01-08 18:39:50.885655 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.886322 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.886594 INFO::Found 2 batches.
2026-01-08 18:39:50.886787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.887038 INFO::Using default BPPARAM
2026-01-08 18:39:50.887228 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.887542 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-08 18:39:50.89962 INFO::Done
2026-01-08 18:39:50.899867 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.900508 INFO::ASW Batch was 0.0270756417844415 prior to batch effect correction and is now -0.17077656286877 .
2026-01-08 18:39:50.900772 INFO::Total function execution time is 0.0172600746154785 s and adjustment time is 0.0130720138549805 s ( 75.74 )
2026-01-08 18:39:50.905185 INFO::Formatting Data.
2026-01-08 18:39:50.905419 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.905678 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.905981 INFO::Found 0 missing values.
2026-01-08 18:39:50.906391 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.
2026-01-08 18:39:50.907739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.907912 INFO::Done
2026-01-08 18:39:50.908067 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.908943 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.909149 INFO::Found 2 batches.
2026-01-08 18:39:50.909309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.909492 INFO::Using default BPPARAM
2026-01-08 18:39:50.909639 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.909903 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-08 18:39:50.915356 INFO::Done
2026-01-08 18:39:50.915613 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.91659 INFO::ASW Batch was 0.623393158241871 prior to batch effect correction and is now 0.0614570907299131 .
2026-01-08 18:39:50.916818 INFO::ASW Label was 0.46418692920152 prior to batch effect correction and is now 0.879368654182784 .
2026-01-08 18:39:50.917063 INFO::Total function execution time is 0.0118870735168457 s and adjustment time is 0.00623703002929688 s ( 52.47 )
2026-01-08 18:39:50.917312 INFO::Formatting Data.
2026-01-08 18:39:50.917505 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:50.917821 INFO::Removing potential empty rows and columns
2026-01-08 18:39:50.918142 INFO::Found 0 missing values.
2026-01-08 18:39:50.91841 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.
2026-01-08 18:39:50.919789 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:50.92007 INFO::Done
2026-01-08 18:39:50.920254 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:50.921163 INFO::Starting hierarchical adjustment
2026-01-08 18:39:50.921391 INFO::Found 2 batches.
2026-01-08 18:39:50.921543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:50.921726 INFO::Using default BPPARAM
2026-01-08 18:39:50.92188 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:50.922145 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-08 18:39:50.928218 INFO::Done
2026-01-08 18:39:50.928435 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:50.929379 INFO::ASW Batch was 0.623393158241871 prior to batch effect correction and is now 0.0614570907299131 .
2026-01-08 18:39:50.929557 INFO::ASW Label was 0.46418692920152 prior to batch effect correction and is now 0.879368654182784 .
2026-01-08 18:39:50.929799 INFO::Total function execution time is 0.0124838352203369 s and adjustment time is 0.00686001777648926 s ( 54.95 )
2026-01-08 18:39:51.003179 INFO::Formatting Data.
2026-01-08 18:39:51.003484 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:51.003819 INFO::Removing potential empty rows and columns
2026-01-08 18:39:51.004164 INFO::Found 0 missing values.
2026-01-08 18:39:51.005087 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:51.005278 INFO::Done
2026-01-08 18:39:51.005464 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:51.006159 INFO::Starting hierarchical adjustment
2026-01-08 18:39:51.006401 INFO::Found 3 batches.
2026-01-08 18:39:51.00656 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:51.006761 INFO::Using default BPPARAM
2026-01-08 18:39:51.006911 INFO::Processing subtree level 1
2026-01-08 18:39:51.061916 INFO::Adjusting the last 1 batches sequentially
2026-01-08 18:39:51.063832 INFO::Done
2026-01-08 18:39:51.064172 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:51.066492 INFO::ASW Batch was -0.0914857919187929 prior to batch effect correction and is now -0.0914857919187929 .
2026-01-08 18:39:51.06758 INFO::Total function execution time is 0.0640912055969238 s and adjustment time is 0.0574820041656494 s ( 89.69 )
2026-01-08 18:39:51.06796 INFO::Formatting Data.
2026-01-08 18:39:51.068158 INFO::Typecasting input to dataframe.
2026-01-08 18:39:51.068411 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:51.068735 INFO::Removing potential empty rows and columns
2026-01-08 18:39:51.06913 INFO::Found 0 missing values.
2026-01-08 18:39:51.070143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:51.070346 INFO::Done
2026-01-08 18:39:51.070512 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:51.071181 INFO::Starting hierarchical adjustment
2026-01-08 18:39:51.071415 INFO::Found 3 batches.
2026-01-08 18:39:51.071593 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:51.071838 INFO::Using default BPPARAM
2026-01-08 18:39:51.072224 INFO::Processing subtree level 1
2026-01-08 18:39:51.130299 INFO::Adjusting the last 1 batches sequentially
2026-01-08 18:39:51.145707 INFO::Done
2026-01-08 18:39:51.146053 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:51.148593 INFO::ASW Batch was -0.0914857919187929 prior to batch effect correction and is now -0.0914857919187929 .
2026-01-08 18:39:51.149439 INFO::Total function execution time is 0.0811748504638672 s and adjustment time is 0.0743038654327393 s ( 91.54 )
2026-01-08 18:39:51.170257 INFO::Formatting Data.
2026-01-08 18:39:51.170571 INFO::Typecasting input to dataframe.
2026-01-08 18:39:51.170863 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:51.171197 INFO::Removing potential empty rows and columns
2026-01-08 18:39:51.171597 INFO::Found 0 missing values.
2026-01-08 18:39:51.17254 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:51.172713 INFO::Done
2026-01-08 18:39:51.172896 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:51.17363 INFO::Starting hierarchical adjustment
2026-01-08 18:39:51.173859 INFO::Found 3 batches.
2026-01-08 18:39:51.174019 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:51.174228 INFO::Using default BPPARAM
2026-01-08 18:39:51.174383 INFO::Processing subtree level 1
2026-01-08 18:39:51.219741 INFO::Adjusting the last 1 batches sequentially
2026-01-08 18:39:51.221235 INFO::Done
2026-01-08 18:39:51.22155 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:51.223299 INFO::ASW Batch was -0.0194671380548839 prior to batch effect correction and is now -0.0194671380548839 .
2026-01-08 18:39:51.224196 INFO::Total function execution time is 0.0537581443786621 s and adjustment time is 0.0474028587341309 s ( 88.18 )
2026-01-08 18:39:51.287152 INFO::Formatting Data.
2026-01-08 18:39:51.287461 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:51.287894 INFO::Removing potential empty rows and columns
2026-01-08 18:39:51.288809 INFO::Found 1000 missing values.
2026-01-08 18:39:51.295235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:51.295691 INFO::Done
2026-01-08 18:39:51.295912 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:51.298022 INFO::Starting hierarchical adjustment
2026-01-08 18:39:51.298335 INFO::Found 10 batches.
2026-01-08 18:39:51.298554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:51.298792 INFO::Using default BPPARAM
2026-01-08 18:39:51.299097 INFO::Processing subtree level 1
2026-01-08 18:39:51.36331 INFO::Processing subtree level 2
2026-01-08 18:39:51.5229 INFO::Adjusting the last 1 batches sequentially
2026-01-08 18:39:51.529106 INFO::Done
2026-01-08 18:39:51.530193 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:51.53621 INFO::ASW Batch was 0.512638491960881 prior to batch effect correction and is now 0.512638491960881 .
2026-01-08 18:39:51.5365 INFO::ASW Label was 0.328613263739643 prior to batch effect correction and is now 0.328613263739643 .
2026-01-08 18:39:51.537955 INFO::Total function execution time is 0.250342130661011 s and adjustment time is 0.230787038803101 s ( 92.19 )
2026-01-08 18:39:51.53852 INFO::Formatting Data.
2026-01-08 18:39:51.538745 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:51.579959 INFO::Removing potential empty rows and columns
2026-01-08 18:39:51.581519 INFO::Found 1000 missing values.
2026-01-08 18:39:51.590897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:51.591598 INFO::Done
2026-01-08 18:39:51.59206 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:51.597322 INFO::Starting hierarchical adjustment
2026-01-08 18:39:51.597695 INFO::Found 10 batches.
2026-01-08 18:39:52.077044 INFO::Set up parallel execution backend with 2 workers
2026-01-08 18:39:52.077378 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-01-08 18:39:52.85139 INFO::Adjusting the last 2 batches sequentially
2026-01-08 18:39:52.852087 INFO::Adjusting sequential tree level 1 with 2 batches
2026-01-08 18:39:52.857932 INFO::Done
2026-01-08 18:39:52.858154 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:52.860196 INFO::ASW Batch was 0.512638491960881 prior to batch effect correction and is now 0.512638491960881 .
2026-01-08 18:39:52.860367 INFO::ASW Label was 0.328613263739643 prior to batch effect correction and is now 0.328613263739643 .
2026-01-08 18:39:52.860624 INFO::Total function execution time is 1.32211589813232 s and adjustment time is 1.26030898094177 s ( 95.33 )
2026-01-08 18:39:52.948043 INFO::Formatting Data.
2026-01-08 18:39:52.94848 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:52.948866 INFO::Removing potential empty rows and columns
2026-01-08 18:39:52.949323 INFO::Found 0 missing values.
2026-01-08 18:39:52.950633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:52.950911 INFO::Done
2026-01-08 18:39:52.951112 INFO::Acquiring quality metrics before batch effect correction.
2026-01-08 18:39:52.952117 INFO::Starting hierarchical adjustment
2026-01-08 18:39:52.952379 INFO::Found 3 batches.
2026-01-08 18:39:52.952544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-01-08 18:39:52.952783 INFO::Using default BPPARAM
2026-01-08 18:39:52.952968 INFO::Processing subtree level 1
2026-01-08 18:39:53.021872 INFO::Adjusting the last 1 batches sequentially
2026-01-08 18:39:53.023024 INFO::Done
2026-01-08 18:39:53.023302 INFO::Acquiring quality metrics after batch effect correction.
2026-01-08 18:39:53.025641 INFO::ASW Batch was 0.139212255635953 prior to batch effect correction and is now -0.129127890487525 .
2026-01-08 18:39:53.02609 INFO::ASW Label was -0.188610762293241 prior to batch effect correction and is now -0.14447474961455 .
2026-01-08 18:39:53.026694 INFO::Total function execution time is 0.0785000324249268 s and adjustment time is 0.0706899166107178 s ( 90.05 )
2026-01-08 18:39:53.091784 INFO::Formatting Data.
2026-01-08 18:39:53.092215 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.092659 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.093206 INFO::Found 2 missing values.
2026-01-08 18:39:53.094565 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.094819 INFO::Done
2026-01-08 18:39:53.109979 INFO::Found NA in Reference column
2026-01-08 18:39:53.115363 INFO::Require at least two references per batch.
2026-01-08 18:39:53.125427 INFO::Formatting Data.
2026-01-08 18:39:53.125752 INFO::Recognized SummarizedExperiment
2026-01-08 18:39:53.125979 INFO::Typecasting input to dataframe.
2026-01-08 18:39:53.130507 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.131009 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.132338 INFO::Found 0 missing values.
2026-01-08 18:39:53.135211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.135492 INFO::Done
2026-01-08 18:39:53.14173 INFO::Formatting Data.
2026-01-08 18:39:53.141981 INFO::Recognized SummarizedExperiment
2026-01-08 18:39:53.142174 INFO::Typecasting input to dataframe.
2026-01-08 18:39:53.148042 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.148498 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.149793 INFO::Found 0 missing values.
2026-01-08 18:39:53.153662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.15387 INFO::Done
2026-01-08 18:39:53.159692 INFO::Formatting Data.
2026-01-08 18:39:53.15994 INFO::Recognized SummarizedExperiment
2026-01-08 18:39:53.160173 INFO::Typecasting input to dataframe.
2026-01-08 18:39:53.166153 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.166525 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.16692 INFO::Found 0 missing values.
2026-01-08 18:39:53.167254 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.
2026-01-08 18:39:53.168894 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.169108 INFO::Done
2026-01-08 18:39:53.173773 INFO::Formatting Data.
2026-01-08 18:39:53.17408 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.174392 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.17474 INFO::Found 0 missing values.
2026-01-08 18:39:53.176072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.176318 INFO::Done
2026-01-08 18:39:53.188971 INFO::Formatting Data.
2026-01-08 18:39:53.189375 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.196939 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.197495 INFO::Found 0 missing values.
2026-01-08 18:39:53.199039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.199243 INFO::Done
2026-01-08 18:39:53.213991 INFO::Formatting Data.
2026-01-08 18:39:53.214443 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.214939 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.215418 INFO::Found 1 missing values.
2026-01-08 18:39:53.2165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.216718 INFO::Done
2026-01-08 18:39:53.226132 INFO::Formatting Data.
2026-01-08 18:39:53.226512 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.226847 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.227219 INFO::Found 2 missing values.
2026-01-08 18:39:53.227564 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.
2026-01-08 18:39:53.228397 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.228579 INFO::Done
2026-01-08 18:39:53.234267 INFO::Formatting Data.
2026-01-08 18:39:53.234638 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.235068 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.235426 INFO::Found 2 missing values.
2026-01-08 18:39:53.236011 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.236206 INFO::Done
2026-01-08 18:39:53.240734 INFO::Formatting Data.
2026-01-08 18:39:53.241044 INFO::Typecasting input to dataframe.
2026-01-08 18:39:53.241343 INFO::Replacing NaNs with NAs.
2026-01-08 18:39:53.241714 INFO::Removing potential empty rows and columns
2026-01-08 18:39:53.242116 INFO::Found 0 missing values.
2026-01-08 18:39:53.243226 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-01-08 18:39:53.243452 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.396 1.798 9.903
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 10.228 | 0.408 | 7.598 | |
| compute_asw | 0.012 | 0.000 | 0.013 | |
| count_existing | 0.005 | 0.000 | 0.007 | |
| generate_data_covariables | 0.005 | 0.001 | 0.006 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |