Yannis Schumann
| Snapshot Date: 2026-03-31 13:40 -0400 (Tue, 31 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-01 13:06 -0400 (Wed, 01 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4816 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4539 |
| 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 170/2374 | 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 | | ||||||||
| See other builds for BERT in R Universe. | ||||||||||||||
|
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: 2026-03-31 18:15:33 -0400 (Tue, 31 Mar 2026) |
| EndedAt: 2026-03-31 18:16:05 -0400 (Tue, 31 Mar 2026) |
| EllapsedTime: 32.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BERT.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-31 22:15:33 UTC
* 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 9.655 0.358 6.831
* 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/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 version 4.6.0 alpha (2026-03-28 r89739)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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")
2026-03-31 18:15:56.995735 INFO::Formatting Data.
2026-03-31 18:15:56.997431 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:57.001937 INFO::Removing potential empty rows and columns
2026-03-31 18:15:57.108472 INFO::Found 0 missing values.
2026-03-31 18:15:57.109751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:57.110075 INFO::Done
2026-03-31 18:15:57.110348 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:57.116238 INFO::Starting hierarchical adjustment
2026-03-31 18:15:57.116653 INFO::Found 3 batches.
2026-03-31 18:15:57.116944 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:57.117445 INFO::Using default BPPARAM
2026-03-31 18:15:57.117714 INFO::Processing subtree level 1
2026-03-31 18:15:57.196082 INFO::Adjusting the last 1 batches sequentially
2026-03-31 18:15:57.197394 INFO::Done
2026-03-31 18:15:57.197773 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:57.199066 INFO::ASW Batch was -0.0646662999639115 prior to batch effect correction and is now -0.0646662999639115 .
2026-03-31 18:15:57.19966 INFO::Total function execution time is 0.204326868057251 s and adjustment time is 0.080786943435669 s ( 39.54 )
2026-03-31 18:15:57.207368 INFO::Formatting Data.
2026-03-31 18:15:57.207854 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:57.208353 INFO::Removing potential empty rows and columns
2026-03-31 18:15:57.208929 INFO::Found 0 missing values.
2026-03-31 18:15:57.209392 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.
2026-03-31 18:15:57.214422 INFO::Formatting Data.
2026-03-31 18:15:57.214855 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:57.215297 INFO::Removing potential empty rows and columns
2026-03-31 18:15:57.215817 INFO::Found 0 missing values.
2026-03-31 18:15:57.216259 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.
2026-03-31 18:15:57.224195 INFO::Formatting Data.
2026-03-31 18:15:57.224716 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:57.225296 INFO::Removing potential empty rows and columns
2026-03-31 18:15:57.225873 INFO::Found 0 missing values.
2026-03-31 18:15:57.226336 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.
2026-03-31 18:15:57.228052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:57.228383 INFO::Done
2026-03-31 18:15:57.228685 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:57.229584 INFO::Starting hierarchical adjustment
2026-03-31 18:15:57.229961 INFO::Found 2 batches.
2026-03-31 18:15:57.230282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:57.230656 INFO::Using default BPPARAM
2026-03-31 18:15:57.23095 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:57.231429 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 18:15:57.24175 INFO::Done
2026-03-31 18:15:57.242216 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:57.243098 INFO::ASW Batch was -0.0230559012633065 prior to batch effect correction and is now -0.125730323722978 .
2026-03-31 18:15:57.243498 INFO::Total function execution time is 0.0193688869476318 s and adjustment time is 0.0118269920349121 s ( 61.06 )
2026-03-31 18:15:57.244819 INFO::Formatting Data.
2026-03-31 18:15:57.245145 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:57.248837 INFO::Formatting Data.
2026-03-31 18:15:57.249278 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:57.249725 INFO::Removing potential empty rows and columns
2026-03-31 18:15:57.250229 INFO::Found 0 missing values.
2026-03-31 18:15:57.25138 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:57.251696 INFO::Done
2026-03-31 18:15:57.25199 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:57.252857 INFO::Starting hierarchical adjustment
2026-03-31 18:15:57.253204 INFO::Found 2 batches.
2026-03-31 18:15:57.25349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:57.253812 INFO::Using default BPPARAM
2026-03-31 18:15:57.254084 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:57.254478 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 18:15:57.260528 INFO::Done
2026-03-31 18:15:57.260921 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:57.261705 INFO::ASW Batch was 0.000204991125111853 prior to batch effect correction and is now -0.126732267120049 .
2026-03-31 18:15:57.262148 INFO::Total function execution time is 0.0133459568023682 s and adjustment time is 0.00736498832702637 s ( 55.19 )
2026-03-31 18:15:57.26269 INFO::Formatting Data.
2026-03-31 18:15:57.26305 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:57.263477 INFO::Removing potential empty rows and columns
2026-03-31 18:15:57.263998 INFO::Found 0 missing values.
2026-03-31 18:15:57.265256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:57.26568 INFO::Done
2026-03-31 18:15:57.266079 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:57.266985 INFO::Starting hierarchical adjustment
2026-03-31 18:15:57.267402 INFO::Found 2 batches.
2026-03-31 18:15:57.267735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:57.268082 INFO::Using default BPPARAM
2026-03-31 18:15:57.2684 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:57.268788 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 18:15:57.273798 INFO::Done
2026-03-31 18:15:57.274217 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:57.275019 INFO::ASW Batch was 0.000204991125111853 prior to batch effect correction and is now -0.126732267120049 .
2026-03-31 18:15:57.275405 INFO::Total function execution time is 0.012721061706543 s and adjustment time is 0.00644803047180176 s ( 50.69 )
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '=', 77 then 79
2026-03-31 18:15:58.544692 INFO::Formatting Data.
2026-03-31 18:15:58.54515 INFO::Recognized SummarizedExperiment
2026-03-31 18:15:58.545437 INFO::Typecasting input to dataframe.
2026-03-31 18:15:58.555521 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:58.556118 INFO::Removing potential empty rows and columns
2026-03-31 18:15:58.557388 INFO::Found 0 missing values.
2026-03-31 18:15:58.55956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:58.559856 INFO::Done
2026-03-31 18:15:58.56011 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:58.561345 INFO::Starting hierarchical adjustment
2026-03-31 18:15:58.561683 INFO::Found 2 batches.
2026-03-31 18:15:58.561926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:58.562324 INFO::Using default BPPARAM
2026-03-31 18:15:58.562598 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:58.56299 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 18:15:58.586762 INFO::Done
2026-03-31 18:15:58.587534 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:58.589239 INFO::ASW Batch was 0.0300276359765236 prior to batch effect correction and is now -0.09464817657916 .
2026-03-31 18:15:58.589844 INFO::Total function execution time is 0.045241117477417 s and adjustment time is 0.0250298976898193 s ( 55.33 )
Warning: stack imbalance in '{', 73 then 75
2026-03-31 18:15:58.596797 INFO::Formatting Data.
2026-03-31 18:15:58.597262 INFO::Recognized SummarizedExperiment
2026-03-31 18:15:58.59756 INFO::Typecasting input to dataframe.
2026-03-31 18:15:58.600875 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:58.60142 INFO::Removing potential empty rows and columns
2026-03-31 18:15:58.602712 INFO::Found 0 missing values.
2026-03-31 18:15:58.605079 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:58.60537 INFO::Done
2026-03-31 18:15:58.605629 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:58.606962 INFO::Starting hierarchical adjustment
2026-03-31 18:15:58.607287 INFO::Found 2 batches.
2026-03-31 18:15:58.607537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:58.607845 INFO::Using default BPPARAM
2026-03-31 18:15:58.608163 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:58.608579 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 18:15:58.616684 INFO::Done
2026-03-31 18:15:58.617039 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:58.618288 INFO::ASW Batch was 0.00366573919569692 prior to batch effect correction and is now 0.00366573919569692 .
2026-03-31 18:15:58.618665 INFO::Total function execution time is 0.0218780040740967 s and adjustment time is 0.00943708419799805 s ( 43.14 )
2026-03-31 18:15:58.625693 INFO::Formatting Data.
2026-03-31 18:15:58.626139 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:58.62657 INFO::Removing potential empty rows and columns
2026-03-31 18:15:58.627074 INFO::Found 0 missing values.
2026-03-31 18:15:58.628118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:58.628406 INFO::Done
2026-03-31 18:15:58.628667 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:58.629453 INFO::Starting hierarchical adjustment
2026-03-31 18:15:58.629769 INFO::Found 3 batches.
2026-03-31 18:15:58.630018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:58.630308 INFO::Using default BPPARAM
2026-03-31 18:15:58.630555 INFO::Processing subtree level 1
2026-03-31 18:15:58.784213 INFO::Adjusting the last 1 batches sequentially
2026-03-31 18:15:58.785677 INFO::Done
2026-03-31 18:15:58.786162 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:58.787821 INFO::ASW Batch was -0.0895783109935875 prior to batch effect correction and is now -0.156239658579056 .
2026-03-31 18:15:58.788475 INFO::Total function execution time is 0.162778854370117 s and adjustment time is 0.15594482421875 s ( 95.8 )
2026-03-31 18:15:58.795849 INFO::Skipping initial DF formatting
2026-03-31 18:15:58.796228 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:58.797743 INFO::Starting hierarchical adjustment
2026-03-31 18:15:58.798222 INFO::Found 5 batches.
2026-03-31 18:15:58.79852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:58.798843 INFO::Using default BPPARAM
2026-03-31 18:15:58.799101 INFO::Processing subtree level 1
2026-03-31 18:15:58.859301 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:58.860372 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 18:15:58.867457 INFO::Done
2026-03-31 18:15:58.86788 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:58.869708 INFO::ASW Batch was 0.533369987079405 prior to batch effect correction and is now 0.533369987079405 .
2026-03-31 18:15:58.870049 INFO::ASW Label was 0.354544351989186 prior to batch effect correction and is now 0.354544351989186 .
2026-03-31 18:15:58.870576 INFO::Total function execution time is 0.0747268199920654 s and adjustment time is 0.0692849159240723 s ( 92.72 )
2026-03-31 18:15:58.878032 INFO::Formatting Data.
2026-03-31 18:15:58.878415 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:58.878877 INFO::Removing potential empty rows and columns
2026-03-31 18:15:58.879359 INFO::Found 0 missing values.
2026-03-31 18:15:58.880699 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:58.881023 INFO::Done
2026-03-31 18:15:58.881342 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:58.882418 INFO::Starting hierarchical adjustment
2026-03-31 18:15:58.882777 INFO::Found 5 batches.
2026-03-31 18:15:58.883068 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:58.883427 INFO::Using default BPPARAM
2026-03-31 18:15:58.883734 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.
2026-03-31 18:15:58.944882 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:58.946454 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 18:15:58.954186 INFO::Done
2026-03-31 18:15:58.954589 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:58.956081 INFO::ASW Batch was 0.232270040241138 prior to batch effect correction and is now -0.053919691678456 .
2026-03-31 18:15:58.956445 INFO::ASW Label was 0.519573122495957 prior to batch effect correction and is now 0.82084537677087 .
2026-03-31 18:15:58.956966 INFO::Total function execution time is 0.0789289474487305 s and adjustment time is 0.0714499950408936 s ( 90.52 )
2026-03-31 18:15:58.957386 INFO::Formatting Data.
2026-03-31 18:15:58.957864 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:58.958335 INFO::Removing potential empty rows and columns
2026-03-31 18:15:58.958826 INFO::Found 0 missing values.
2026-03-31 18:15:58.960407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:58.960721 INFO::Done
2026-03-31 18:15:58.961058 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:58.96218 INFO::Starting hierarchical adjustment
2026-03-31 18:15:58.962602 INFO::Found 5 batches.
2026-03-31 18:15:58.962925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:58.963266 INFO::Using default BPPARAM
2026-03-31 18:15:58.963567 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.
2026-03-31 18:15:59.035425 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:59.037186 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 18:15:59.044814 INFO::Done
2026-03-31 18:15:59.045344 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.0468 INFO::ASW Batch was 0.232270040241138 prior to batch effect correction and is now -0.053919691678456 .
2026-03-31 18:15:59.047136 INFO::ASW Label was 0.519573122495957 prior to batch effect correction and is now 0.82084537677087 .
2026-03-31 18:15:59.047576 INFO::Total function execution time is 0.0901579856872559 s and adjustment time is 0.0822410583496094 s ( 91.22 )
2026-03-31 18:15:59.053707 INFO::Formatting Data.
2026-03-31 18:15:59.054097 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.054554 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.055067 INFO::Found 0 missing values.
2026-03-31 18:15:59.056422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.056747 INFO::Done
2026-03-31 18:15:59.057034 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.05813 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.058503 INFO::Found 5 batches.
2026-03-31 18:15:59.058771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.059097 INFO::Using default BPPARAM
2026-03-31 18:15:59.059372 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.
2026-03-31 18:15:59.129917 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:59.131065 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 18:15:59.137473 INFO::Done
2026-03-31 18:15:59.13787 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.139187 INFO::ASW Batch was 0.416208002414407 prior to batch effect correction and is now -0.0674954153828264 .
2026-03-31 18:15:59.1395 INFO::ASW Label was 0.317515484131918 prior to batch effect correction and is now 0.834054206731164 .
2026-03-31 18:15:59.139912 INFO::Total function execution time is 0.0862181186676025 s and adjustment time is 0.0790250301361084 s ( 91.66 )
2026-03-31 18:15:59.140306 INFO::Formatting Data.
2026-03-31 18:15:59.140609 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.141002 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.141453 INFO::Found 0 missing values.
2026-03-31 18:15:59.142748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.143055 INFO::Done
2026-03-31 18:15:59.143352 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.144332 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.144699 INFO::Found 5 batches.
2026-03-31 18:15:59.14497 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.145298 INFO::Using default BPPARAM
2026-03-31 18:15:59.145567 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.
2026-03-31 18:15:59.213172 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:59.214449 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 18:15:59.222219 INFO::Done
2026-03-31 18:15:59.22274 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.224501 INFO::ASW Batch was 0.416208002414407 prior to batch effect correction and is now -0.0674954153828264 .
2026-03-31 18:15:59.224872 INFO::ASW Label was 0.317515484131918 prior to batch effect correction and is now 0.834054206731164 .
2026-03-31 18:15:59.225343 INFO::Total function execution time is 0.0849809646606445 s and adjustment time is 0.0775549411773682 s ( 91.26 )
2026-03-31 18:15:59.2352 INFO::Formatting Data.
2026-03-31 18:15:59.235663 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.236115 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.236623 INFO::Found 0 missing values.
2026-03-31 18:15:59.237593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.237914 INFO::Done
2026-03-31 18:15:59.238196 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.239241 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.239623 INFO::Found 2 batches.
2026-03-31 18:15:59.239901 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.240244 INFO::Using default BPPARAM
2026-03-31 18:15:59.24052 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:59.241136 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 18:15:59.246252 INFO::Done
2026-03-31 18:15:59.246681 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.247782 INFO::ASW Batch was 0.487927580454803 prior to batch effect correction and is now -0.0378160585410593 .
2026-03-31 18:15:59.248133 INFO::ASW Label was 0.558338128264326 prior to batch effect correction and is now 0.952632906404331 .
2026-03-31 18:15:59.248507 INFO::Total function execution time is 0.0133898258209229 s and adjustment time is 0.00667190551757812 s ( 49.83 )
2026-03-31 18:15:59.248881 INFO::Formatting Data.
2026-03-31 18:15:59.249186 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.249601 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.250017 INFO::Found 0 missing values.
2026-03-31 18:15:59.250927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.251221 INFO::Done
2026-03-31 18:15:59.251498 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.252537 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.252898 INFO::Found 2 batches.
2026-03-31 18:15:59.253169 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.253484 INFO::Using default BPPARAM
2026-03-31 18:15:59.253776 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:59.254153 INFO::Adjusting sequential tree level 1 with 2 batches
design matrix of interest not specified. Assuming a one-group experiment.
2026-03-31 18:15:59.259689 INFO::Done
2026-03-31 18:15:59.260108 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.261201 INFO::ASW Batch was 0.487927580454803 prior to batch effect correction and is now -0.0378160585410593 .
2026-03-31 18:15:59.261504 INFO::ASW Label was 0.558338128264326 prior to batch effect correction and is now 0.952632906404331 .
2026-03-31 18:15:59.261864 INFO::Total function execution time is 0.0129640102386475 s and adjustment time is 0.00681805610656738 s ( 52.59 )
2026-03-31 18:15:59.266239 INFO::Formatting Data.
2026-03-31 18:15:59.266594 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.266963 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.267329 INFO::Found 0 missing values.
2026-03-31 18:15:59.268042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.268339 INFO::Done
2026-03-31 18:15:59.268596 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.269256 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.26958 INFO::Found 2 batches.
2026-03-31 18:15:59.269845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.270124 INFO::Using default BPPARAM
2026-03-31 18:15:59.270376 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:59.270729 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 18:15:59.281212 INFO::Done
2026-03-31 18:15:59.281608 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.282333 INFO::ASW Batch was 0.0437637281177756 prior to batch effect correction and is now -0.13431966339784 .
2026-03-31 18:15:59.282742 INFO::Total function execution time is 0.0165061950683594 s and adjustment time is 0.0116639137268066 s ( 70.66 )
2026-03-31 18:15:59.288348 INFO::Formatting Data.
2026-03-31 18:15:59.28895 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.289926 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.290691 INFO::Found 0 missing values.
2026-03-31 18:15:59.291529 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.
2026-03-31 18:15:59.293885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.294309 INFO::Done
2026-03-31 18:15:59.294634 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.296341 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.296921 INFO::Found 2 batches.
2026-03-31 18:15:59.297266 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.297584 INFO::Using default BPPARAM
2026-03-31 18:15:59.297874 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:59.298294 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 18:15:59.306716 INFO::Done
2026-03-31 18:15:59.307121 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.30851 INFO::ASW Batch was 0.487563695661838 prior to batch effect correction and is now -0.02277090625391 .
2026-03-31 18:15:59.308849 INFO::ASW Label was 0.414677040061258 prior to batch effect correction and is now 0.906348710446301 .
2026-03-31 18:15:59.309504 INFO::Total function execution time is 0.0210890769958496 s and adjustment time is 0.00984406471252441 s ( 46.68 )
2026-03-31 18:15:59.310383 INFO::Formatting Data.
2026-03-31 18:15:59.310712 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.311131 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.311594 INFO::Found 0 missing values.
2026-03-31 18:15:59.312067 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.
2026-03-31 18:15:59.314643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.314996 INFO::Done
2026-03-31 18:15:59.315311 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.316447 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.31682 INFO::Found 2 batches.
2026-03-31 18:15:59.317132 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.31769 INFO::Using default BPPARAM
2026-03-31 18:15:59.3181 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:15:59.318933 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 18:15:59.325672 INFO::Done
2026-03-31 18:15:59.326208 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.327374 INFO::ASW Batch was 0.487563695661838 prior to batch effect correction and is now -0.02277090625391 .
2026-03-31 18:15:59.327714 INFO::ASW Label was 0.414677040061258 prior to batch effect correction and is now 0.906348710446301 .
2026-03-31 18:15:59.32808 INFO::Total function execution time is 0.0177202224731445 s and adjustment time is 0.00887799263000488 s ( 50.1 )
2026-03-31 18:15:59.425755 INFO::Formatting Data.
2026-03-31 18:15:59.426193 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.426626 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.427114 INFO::Found 0 missing values.
2026-03-31 18:15:59.428144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.428508 INFO::Done
2026-03-31 18:15:59.428822 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.429806 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.430406 INFO::Found 3 batches.
2026-03-31 18:15:59.430778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.431223 INFO::Using default BPPARAM
2026-03-31 18:15:59.431683 INFO::Processing subtree level 1
2026-03-31 18:15:59.527624 INFO::Adjusting the last 1 batches sequentially
2026-03-31 18:15:59.529472 INFO::Done
2026-03-31 18:15:59.530061 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.532214 INFO::ASW Batch was -0.118739739841941 prior to batch effect correction and is now -0.118739739841941 .
2026-03-31 18:15:59.533421 INFO::Total function execution time is 0.107502937316895 s and adjustment time is 0.0991108417510986 s ( 92.19 )
2026-03-31 18:15:59.534196 INFO::Formatting Data.
2026-03-31 18:15:59.534731 INFO::Typecasting input to dataframe.
2026-03-31 18:15:59.535288 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.536046 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.537013 INFO::Found 0 missing values.
2026-03-31 18:15:59.539356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.539794 INFO::Done
2026-03-31 18:15:59.540173 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.541294 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.541788 INFO::Found 3 batches.
2026-03-31 18:15:59.542131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.542541 INFO::Using default BPPARAM
2026-03-31 18:15:59.542927 INFO::Processing subtree level 1
2026-03-31 18:15:59.609636 INFO::Adjusting the last 1 batches sequentially
2026-03-31 18:15:59.610823 INFO::Done
2026-03-31 18:15:59.611169 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.61255 INFO::ASW Batch was -0.118739739841941 prior to batch effect correction and is now -0.118739739841941 .
2026-03-31 18:15:59.613193 INFO::Total function execution time is 0.0790212154388428 s and adjustment time is 0.0690958499908447 s ( 87.44 )
2026-03-31 18:15:59.620336 INFO::Formatting Data.
2026-03-31 18:15:59.620788 INFO::Typecasting input to dataframe.
2026-03-31 18:15:59.62122 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.621666 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.622183 INFO::Found 0 missing values.
2026-03-31 18:15:59.623283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.623594 INFO::Done
2026-03-31 18:15:59.62388 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.624677 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.625057 INFO::Found 3 batches.
2026-03-31 18:15:59.625326 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.625678 INFO::Using default BPPARAM
2026-03-31 18:15:59.625978 INFO::Processing subtree level 1
2026-03-31 18:15:59.68915 INFO::Adjusting the last 1 batches sequentially
2026-03-31 18:15:59.690694 INFO::Done
2026-03-31 18:15:59.691256 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.693289 INFO::ASW Batch was -0.0665042105882632 prior to batch effect correction and is now -0.0665042105882632 .
2026-03-31 18:15:59.693923 INFO::Total function execution time is 0.0736031532287598 s and adjustment time is 0.0656599998474121 s ( 89.21 )
2026-03-31 18:15:59.778224 INFO::Formatting Data.
2026-03-31 18:15:59.77872 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.779296 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.78061 INFO::Found 1000 missing values.
2026-03-31 18:15:59.789209 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.789769 INFO::Done
2026-03-31 18:15:59.790116 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:15:59.792368 INFO::Starting hierarchical adjustment
2026-03-31 18:15:59.792813 INFO::Found 10 batches.
2026-03-31 18:15:59.793113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:15:59.793441 INFO::Using default BPPARAM
2026-03-31 18:15:59.793715 INFO::Processing subtree level 1
2026-03-31 18:15:59.899156 INFO::Processing subtree level 2
2026-03-31 18:15:59.981549 INFO::Adjusting the last 1 batches sequentially
2026-03-31 18:15:59.982918 INFO::Done
2026-03-31 18:15:59.983516 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:15:59.986122 INFO::ASW Batch was 0.446516331964287 prior to batch effect correction and is now 0.446516331964287 .
2026-03-31 18:15:59.986564 INFO::ASW Label was 0.36656921703596 prior to batch effect correction and is now 0.36656921703596 .
2026-03-31 18:15:59.987112 INFO::Total function execution time is 0.20890998840332 s and adjustment time is 0.190122127532959 s ( 91.01 )
2026-03-31 18:15:59.987526 INFO::Formatting Data.
2026-03-31 18:15:59.987835 INFO::Replacing NaNs with NAs.
2026-03-31 18:15:59.988403 INFO::Removing potential empty rows and columns
2026-03-31 18:15:59.989604 INFO::Found 1000 missing values.
2026-03-31 18:15:59.99768 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:15:59.998055 INFO::Done
2026-03-31 18:15:59.99837 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:16:00.000513 INFO::Starting hierarchical adjustment
2026-03-31 18:16:00.000939 INFO::Found 10 batches.
2026-03-31 18:16:00.409952 INFO::Set up parallel execution backend with 2 workers
2026-03-31 18:16:00.410541 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2026-03-31 18:16:01.023057 INFO::Adjusting the last 2 batches sequentially
2026-03-31 18:16:01.023948 INFO::Adjusting sequential tree level 1 with 2 batches
2026-03-31 18:16:01.030691 INFO::Done
2026-03-31 18:16:01.031084 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:16:01.033278 INFO::ASW Batch was 0.446516331964287 prior to batch effect correction and is now 0.446516331964287 .
2026-03-31 18:16:01.033613 INFO::ASW Label was 0.36656921703596 prior to batch effect correction and is now 0.36656921703596 .
2026-03-31 18:16:01.034052 INFO::Total function execution time is 1.04652500152588 s and adjustment time is 1.02980613708496 s ( 98.4 )
2026-03-31 18:16:01.199523 INFO::Formatting Data.
2026-03-31 18:16:01.200025 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.20059 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.201309 INFO::Found 0 missing values.
2026-03-31 18:16:01.203185 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.203628 INFO::Done
2026-03-31 18:16:01.203974 INFO::Acquiring quality metrics before batch effect correction.
2026-03-31 18:16:01.205855 INFO::Starting hierarchical adjustment
2026-03-31 18:16:01.206597 INFO::Found 3 batches.
2026-03-31 18:16:01.207014 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2026-03-31 18:16:01.207448 INFO::Using default BPPARAM
2026-03-31 18:16:01.207767 INFO::Processing subtree level 1
2026-03-31 18:16:01.289156 INFO::Adjusting the last 1 batches sequentially
2026-03-31 18:16:01.290474 INFO::Done
2026-03-31 18:16:01.290884 INFO::Acquiring quality metrics after batch effect correction.
2026-03-31 18:16:01.292442 INFO::ASW Batch was 0.166440397956671 prior to batch effect correction and is now -0.156009410102674 .
2026-03-31 18:16:01.292816 INFO::ASW Label was -0.202336131247792 prior to batch effect correction and is now -0.0870021401689897 .
2026-03-31 18:16:01.293326 INFO::Total function execution time is 0.0938680171966553 s and adjustment time is 0.0839841365814209 s ( 89.47 )
2026-03-31 18:16:01.346767 INFO::Formatting Data.
2026-03-31 18:16:01.347263 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.347763 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.348352 INFO::Found 2 missing values.
2026-03-31 18:16:01.349527 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.349878 INFO::Done
2026-03-31 18:16:01.362285 INFO::Found NA in Reference column
2026-03-31 18:16:01.366576 INFO::Require at least two references per batch.
2026-03-31 18:16:01.375212 INFO::Formatting Data.
2026-03-31 18:16:01.37564 INFO::Recognized SummarizedExperiment
2026-03-31 18:16:01.375944 INFO::Typecasting input to dataframe.
2026-03-31 18:16:01.381067 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.381766 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.383418 INFO::Found 0 missing values.
2026-03-31 18:16:01.386427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.40105 INFO::Done
2026-03-31 18:16:01.412818 INFO::Formatting Data.
2026-03-31 18:16:01.413288 INFO::Recognized SummarizedExperiment
2026-03-31 18:16:01.413637 INFO::Typecasting input to dataframe.
2026-03-31 18:16:01.420952 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.421626 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.423064 INFO::Found 0 missing values.
2026-03-31 18:16:01.42702 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.427414 INFO::Done
2026-03-31 18:16:01.43314 INFO::Formatting Data.
2026-03-31 18:16:01.433538 INFO::Recognized SummarizedExperiment
2026-03-31 18:16:01.433832 INFO::Typecasting input to dataframe.
2026-03-31 18:16:01.439466 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.440018 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.440559 INFO::Found 0 missing values.
2026-03-31 18:16:01.441094 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.
2026-03-31 18:16:01.442779 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.443164 INFO::Done
2026-03-31 18:16:01.447942 INFO::Formatting Data.
2026-03-31 18:16:01.448385 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.448867 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.44944 INFO::Found 0 missing values.
2026-03-31 18:16:01.45058 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.450955 INFO::Done
2026-03-31 18:16:01.455787 INFO::Formatting Data.
2026-03-31 18:16:01.456217 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.45664 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.457101 INFO::Found 0 missing values.
2026-03-31 18:16:01.458183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.45851 INFO::Done
2026-03-31 18:16:01.470239 INFO::Formatting Data.
2026-03-31 18:16:01.470692 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.471127 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.471651 INFO::Found 1 missing values.
2026-03-31 18:16:01.472564 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.472847 INFO::Done
2026-03-31 18:16:01.480004 INFO::Formatting Data.
2026-03-31 18:16:01.480392 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.480766 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.481168 INFO::Found 2 missing values.
2026-03-31 18:16:01.481565 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.
2026-03-31 18:16:01.482472 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.482746 INFO::Done
2026-03-31 18:16:01.48693 INFO::Formatting Data.
2026-03-31 18:16:01.487325 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.487749 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.488196 INFO::Found 2 missing values.
2026-03-31 18:16:01.48889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.489175 INFO::Done
2026-03-31 18:16:01.493473 INFO::Formatting Data.
2026-03-31 18:16:01.493863 INFO::Typecasting input to dataframe.
2026-03-31 18:16:01.494281 INFO::Replacing NaNs with NAs.
2026-03-31 18:16:01.494762 INFO::Removing potential empty rows and columns
2026-03-31 18:16:01.495343 INFO::Found 0 missing values.
2026-03-31 18:16:01.496373 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2026-03-31 18:16:01.496653 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
7.067 2.004 9.335
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.655 | 0.358 | 6.831 | |
| compute_asw | 0.009 | 0.001 | 0.010 | |
| count_existing | 0.005 | 0.000 | 0.006 | |
| generate_data_covariables | 0.005 | 0.001 | 0.005 | |
| generate_dataset | 0.004 | 0.000 | 0.005 | |